diff --git a/R/Xmod-SIS.R b/R/Xmod-SIS.R index 4630831..6f69747 100644 --- a/R/Xmod-SIS.R +++ b/R/Xmod-SIS.R @@ -3,34 +3,46 @@ #' @inheritParams split_stratum_by_biting #' #' @return pars a list -#' @param i the stratum to split +#' @param i the host species index +#' @param j the stratum to split #' @param p the fraction that gets multiplied by `fac` #' @param fac a factor #' @return a [list] #' @export -split_stratum_by_biting.SIS = function(pars, i, p, fac){ - stopifnot(i <= pars$nStrata) - pars$nStrata = pars$nStrata + 1 +split_stratum_by_biting.SIS = function(pars, i, j, p, fac){ + stopifnot(i <= pars$Hpar[[i]]$nStrata) + nj_ix = pars$Hpar[[i]]$nStrata + 1 + pars$Hpar[[i]]$nStrata = nj_ix + Xpar = pars$Xpar[[1]] - Xpar$b <- c(Xpar$b, Xpar$b[i]) - Xpar$r <- c(Xpar$r, Xpar$r[i]) - Xpar$c <- c(Xpar$c, Xpar$c[i]) - - Xinits = pars$inits[[1]] - Xinits$X0 <- c(Xinits$X0, Xinits$X0[i]) - Xinits$X0[i] <- Xinits$X0[i]*p - Xinits$X0[pars$nStrata] <- Xinits$X0[i]*(1-p) - - pars$Hpar$residence = c(pars$Hpar$residence, pars$Hpar$residence[i]) - pars$Hpar$wts_f = c(pars$Hpar$wts_f, pars$Hpar$wts_f[i]) - pars$Hpar$wts_f[pars$nStrata] = pars$Hpar$wts_f[i]*fac - pars$Hpar$wts_f[i] = pars$Hpar$wts_f[i]/fac - pars$Hpar$rbr = with(pars$Hpar, wts_f*sum(H)/sum(wts_f*H)) - pars$Hpar$H = c(pars$Hpar$H, pars$Hpar$H[i]) - pars$Hpar$H[pars$nStrata] = pars$Hpar$H[i]*p - pars$Hpar$H[i] = pars$Hpar$H[i]*(1-p) - pars$Hpar$TaR = cbind(pars$Hpar$TaR, pars$Hpar$TaR[,i]) + Xpar$b <- c(Xpar$b, Xpar$b[j]) + Xpar$r <- c(Xpar$r, Xpar$r[j]) + Xpar$c <- c(Xpar$c, Xpar$c[j]) + pars$Xpar[[1]] = Xpar + + Xinits = pars$Xinits[[1]] + Xinits$S <- c(Xinits$S, p*Xinits$S[j]) + Xinits$S[j] <- Xinits$S[j]*(1-p) + Xinits$I <- c(Xinits$I, p*Xinits$I[j]) + Xinits$I[j] <- Xinits$I[j]*(1-p) + pars$Xinits[[1]] = Xinits + + residence = pars$BFpar$residence[[i]] + pars$BFpar$residence[[i]] = c(residence, residence[j]) + for(s in 1:pars$nVectors){ + wts_f = pars$BFpar$searchWts[[i]][[s]] + pars$BFpar$searchWts[[i]][[s]] = c(wts_f, fac*wts_f[j]) + } + + H = pars$Hpar[[i]]$H + pars$Hpar[[i]]$H = c(H, p*H[j]) + pars$Hpar[[i]]$H[j] = H[j]*(1-p) + + TimeSpent = pars$BFpar$TimeSpent[[i]] + TimeSpent = cbind(TimeSpent, TimeSpent[,j]) + + for(s in 1:pars$nVectors) pars = make_TaR(0, pars, i, 1) pars <- exDE::make_indices(pars) diff --git a/R/plot-terms.R b/R/plot-terms.R index 8a74c13..f6b1931 100644 --- a/R/plot-terms.R +++ b/R/plot-terms.R @@ -2,44 +2,47 @@ #' Plot EIR(t) *vs.* the PR(t) #' #' @param pars a [list] that defines an `exDE` model (*e.g.*, generated by `exDE::xde_setup()`) +#' @param i the host species index #' @param clrs a [character] vector of colors #' @param llty an [integer] that specifies `lty` for plotting #' @param stable a [logical] set to FALSE for `orbits` and TRUE for `stable_orbits` #' @param add_axes a [logical] to plot add_axes only if FALSE #' #' @export -plot_eirVpr <- function(pars, clrs="black", llty=1, stable=FALSE, add_axes=TRUE){ +plot_eirVpr <- function(pars, i=1, clrs="black", llty=1, stable=FALSE, add_axes=TRUE){ vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits}) - if(add_axes==TRUE) - with(vars$terms,{ - aeir = 365*eir - plot(aeir, pr, type = "l", xaxt="n", lty = llty, + pr = vars$terms$pr[[i]] + eir = vars$terms$eir[[i]] + aeir = 365*eir + if(add_axes==TRUE){ + plot(aeir, pr, type = "n", xaxt="n", lty = llty, xlab = "aEIR", ylab = "PR", xlim = range(0, aeir), ylim = c(0,1), col = clrs) axis(1, 10^c(-1:3), c(".1", "1", "10", "100","1000")) - }) - lines_eirVpr(vars$terms, pars, clrs, llty) + } + lines_eirVpr(eir, pr, pars$Hpar[[i]]$nStrata, clrs, llty) } #' Add lines for the EIR(t) *vs.* the PR(t) #' -#' @param terms a [list] with the outputs of `exDE::parse_deout()` -#' @param pars a [list] that defines an `exDE` model (*e.g.*, generated by `exDE::xde_setup()`) +#' @param eir the daily EIR +#' @param pr the parasite rate +#' @param nStrata the number of population strata #' @param clrs a [character] vector of colors #' @param llty an [integer] (or integers) that specifies `lty` for plotting #' #' @export -lines_eirVpr <- function(terms, pars, clrs= "black", llty = 1){ - with(terms,{ +lines_eirVpr <- function(eir, pr, nStrata, clrs= "black", llty = 1){ aeir = 365*eir - if(pars$nStrata==1) lines(aeir, pr, col=clrs[1], lty = llty[1]) - if(pars$nStrata>1){ - if(length(clrs)==1) clrs=rep(clrs, pars$nStrata) - if(length(llty)==1) llty=rep(llty, pars$nStrata) - for(i in 1:pars$nStrata) + if(nStrata==1) + lines(aeir, pr, col=clrs[1], lty = llty[1]) + if(nStrata>1){ + if(length(clrs)==1) clrs=rep(clrs, nStrata) + if(length(llty)==1) llty=rep(llty, nStrata) + for(i in 1:nStrata) lines(aeir[,i], pr[,i], col=clrs[i], lty = llty[i]) - }}) + } } #' Plot the eir-pr scaling relationship diff --git a/R/scaling.R b/R/scaling.R index e89061e..6b397bf 100644 --- a/R/scaling.R +++ b/R/scaling.R @@ -8,38 +8,32 @@ xde_scaling_eir = function(model, N=25){ stopifnot(model$nPatches == 1) stopifnot(class(model$xde) == "cohort") - # make sure that eir & ni are output - model <- exDE::make_indices(model) + scale_base = model$EIRpar$scale # Get the - F_eir_base = model$F_eir - wts_f = as.vector(model$BFpar$searchWts[[1]][[1]]) - H = F_H(0, get_inits(model), model, 1) - scl_a = sum(wts_f*H)/sum(H) - scl_b = stats::integrate(F_eir_base, 0, 365, pars=model)$value - model$scl = 1/scl_a/scl_b - model$F_eir = function(t, model){with(model,aeir*scl*F_eir_base(t, model))} + scl = with(model$EIRpar, stats::integrate(model$F_eir, 0, 365, scale=scale)$value) eir = 10^seq(-1,3, length.out=N) pr = 0*eir ni = 0*eir scaling = list() - for(i in 1:N){ - model$aeir = eir[i] + model$EIRpar$scale = eir[i]/scl xde_tmp <- exDE::xde_stable_orbit(model) tmp <- xde_tmp$outputs$stable_orbit H = tmp$XH[[1]]$H - ni = tmp$terms$ni - tot_pr <- rowSums(as.matrix(tmp$terms$pr[[1]]*H))/rowSums(as.matrix(H)) - mean_ni <- rowSums(as.matrix(ni*wts_f*H))/rowSums(as.matrix(wts_f*H)) + wts_f = as.vector(model$BFpar$searchWts[[1]][[1]]) + pr_t = tmp$terms$pr + ni_t = tmp$terms$ni + tot_pr <- rowSums(as.matrix(pr_t*H))/rowSums(as.matrix(H)) + mean_ni <- rowSums(as.matrix(ni_t*wts_f*H))/rowSums(as.matrix(wts_f*H)) scaling[[i]] = with(tmp$terms, list(aeir=365*eir, eir=eir, pr=tot_pr, ni=mean_ni, pr_t = pr, ni_t = ni)) pr[i] = mean(tot_pr) ni[i] = mean(mean_ni) } model$outputs$eirpr <- list(aeir=eir, eir=eir/365, pr=pr, ni=ni, scaling=scaling) - model$F_eir = F_eir_base + model$EIRPar$scale = scale_base return(model) } diff --git a/R/stratify.R b/R/stratify.R index 7d81eab..92cf8bb 100644 --- a/R/stratify.R +++ b/R/stratify.R @@ -2,14 +2,15 @@ #' Split a stratum into two strata, assigning #' #' @param pars a [list] defining a model -#' @param i the stratum to split +#' @param i the host species index +#' @param j the stratum to split #' @param p the fraction in the higher exposure stratum #' @param fac the factor increase #' #' @return pars a list #' @export -split_stratum_by_biting = function(pars, i, p, fac){ - UseMethod("split_stratum_by_biting", pars$Xpar) +split_stratum_by_biting = function(pars, i, j, p, fac){ + UseMethod("split_stratum_by_biting", pars$Xpar[[i]]) } diff --git a/docs/articles/X-How_To_Add_Model.html b/docs/articles/X-How_To_Add_Model.html index ea6a72f..5ae34c3 100644 --- a/docs/articles/X-How_To_Add_Model.html +++ b/docs/articles/X-How_To_Add_Model.html @@ -71,7 +71,7 @@

How to add a new model to the library: Human Infection

-

December 19, 2023

+

January 18, 2024

Source: vignettes/X-How_To_Add_Model.Rmd
X-How_To_Add_Model.Rmd
@@ -164,6 +164,33 @@

}

+

+F_X +

+

The function F_X returns the effective density of +infectious humans for each stratum. The following is a template for a +model:

+
+#' @title Size of effective infectious human population
+#' @description Implements [F_H] for the NEW model.
+#' @inheritParams exDE::F_H
+#' @return a [numeric] vector of length `nStrata`
+#' @export
+F_H.NEW <- function(t, y, pars) {
+  ########################
+  # extract: 
+  # VAR <- y[pars$ix$X$...] 
+  ########################
+  with(pars$Xpar, 
+       ########################
+       # compute: 
+       # X <- ... F(VAR) 
+       ########################
+    )
+  return(H)
+}
+
+

F_b

@@ -175,7 +202,7 @@

include the combined effects of inefficient transmission, pre-erytrocytic immunity, and perhaps some effects of blood stage immunity. In a model with no effect, the return value would be \(1\).

-
+
 #' @title Infection blocking pre-erythrocytic immunity
 #' @description Implements [F_b] for the SIS model.
 #' @inheritParams exDE::F_b
@@ -196,7 +223,7 @@ 

 }

 
Once again, we provide the SIS model from
 exDE as our example:

-
+
 #' @title Infection blocking pre-erythrocytic immunity
 #' @description Implements [F_b] for the SIS model.
 #' @inheritParams F_b
@@ -224,7 +251,7 @@ 
DynamicsdHdt.

-
+
 #' @title Derivatives for human population
 #' @description Implements [dXdt] for the NEW model, no demography.
 #' @inheritParams exDE::dXdt
@@ -258,7 +285,7 @@ 

 

 
In exDE, we write two versions of the derivatives
 function, to make it easy for the average user to scale up.

-
+
 dXdt.SISdx <- function(t, y, pars, FoI) {
   with(pars$Xpar, {
     X <- y[X_ix]
@@ -279,7 +306,7 @@ 

 population density, H. Any disease induced mortality should
 be included in the derivative describing changes in human population
 density, dH.

-
+
 dXdt.SISdH <- function(t, y, pars, FoI) {
   with(pars$Xpar, {
 
@@ -304,7 +331,7 @@ 

 
This function must set up Xpar and it must also set up
 the initial values. By convention, the functions that get called are not
 S3 class functions.

-
+
 #' @title Setup Xpar.NEW
 #' @description Implements [setup_X] for the NEW model
 #' @inheritParams exDE::setup_X
@@ -318,7 +345,7 @@ 

 
   return(pars)
 }

-
+
 setup_X.SIS = function(pars, Xname, Xopts=list()){
   pars$Xname = "SIS"
   pars = make_Xpar_SIS(pars, Xopts)
@@ -331,7 +358,7 @@ 

 

 make_Xpar_...
 

-
+
 #' @title Make parameters for NEW human model, with defaults
 #' @param pars a [list]
 #' @param Xopts a [list] that could overwrite defaults
@@ -354,7 +381,7 @@ 

     return(pars)
   })}

 
The function that makes parameters should assign

-
+
 make_Xpar_SIS = function(pars, Xopts=list(),
                          b=0.55, r=1/180, c=0.15){
   with(Xopts,{
@@ -373,7 +400,7 @@ 

 

 make_Xinits_...
 

-
+
 #' @title Make initial values for the NEW human model, with defaults
 #' @param pars a [list]
 #' @param Xopts a [list] to overwrite defaults
@@ -390,7 +417,7 @@ 

   pars$Xinits = inits
   return(pars)
 })}

-
+
 make_Xinits_SIS = function(pars, Xopts = list(), X0=1){with(Xopts,{
   inits = list()
   inits$X0 = checkIt(X0, pars$nStrata)
@@ -402,7 +429,7 @@ 

 

 make_indices_X
 

-
+
 #' @title Add indices for human population to parameter list
 #' @description Implements [make_indices_X] for the NEW model.
 #' @inheritParams exDE::make_indices_X
@@ -422,7 +449,7 @@ 

   
   return(pars)
 }

-
+
 #' @title Add indices for human population to parameter list
 #' @description Implements [make_indices_X] for the SIS model.
 #' @inheritParams make_indices_X
@@ -443,7 +470,7 @@ 
Initial Values
 update_inits_X
 

-
+
 #' @title Update inits for the SIS human model from a vector of states
 #' @inheritParams exDE::update_inits_X 
 #' @return none
@@ -456,7 +483,7 @@ 

     pars = make_Xinits_SIS(pars, list(), X10, X20, X30)
     return(pars)
 })}

-
+
 update_inits_X.SIS <- function(pars, y0) {
   X0 = y0[pars$ix$X$X_ix]
   make_Xinits_SIS(pars, list(), X0)
@@ -467,7 +494,7 @@ 

 

 get_inits_X
 

-
+
 #' @title Return initial values as a vector
 #' @description This method dispatches on the type of `pars$Xpar`.
 #' @param pars a [list]
@@ -478,7 +505,7 @@ 

     return(c(X1, X2, X3)) 
   })
 }

-
+
 #' @title Return initial values as a vector
 #' @description This method dispatches on the type of `pars$Xpar`.
 #' @param pars a [list]
@@ -496,7 +523,7 @@ 
Outputs
 parse_deout_X
 

-
+
 #' @title Parse the output of deSolve and return variables for the NEW model
 #' @description Implements [parse_deout_X] for the NEW model
 #' @inheritParams exDE::parse_deout_X
@@ -511,7 +538,7 @@ 

     X3= deout[,pars$ix$X$X3_ix+1]
     return(list(time=time, X1=X1, X2=X2, X3=X3, H=H))
 })}

-
+
 #' @title Parse the output of deSolve and return variables for the SIS model
 #' @description Implements [parse_deout_X] for the SIS model
 #' @inheritParams parse_deout_X
@@ -533,7 +560,7 @@ 

 prevalence using the variable names. It is passed the
 varslist that is created by parse_deout (see
 above).

-
+
 #' @title Compute the "true" prevalence of infection / parasite rate
 #' @description Implements [F_pr] for the NEW model.
 #' @inheritParams exDE::F_pr
@@ -548,7 +575,7 @@ 

 

 HTC
 

-
+
 #' @title Compute the HTC for the NEW model
 #' @description Implements [HTC] for the NEW model with demography.
 #' @inheritParams exDE::HTC
@@ -568,7 +595,7 @@ 
Plotting
 xde_plot_X
 

-
+
 #' Plot the density of infected individuals for the NEW model
 #'
 #' @inheritParams xde_plot_X
@@ -588,7 +615,7 @@ 

 

 xde_lines_X
 

-
+
 #' Add lines for the density of infected individuals for the NEW model
 #'
 #' @inheritParams xde_lines_X
diff --git a/docs/articles/Xmod-SIS.html b/docs/articles/Xmod-SIS.html
index fb3714f..8a0e13d 100644
--- a/docs/articles/Xmod-SIS.html
+++ b/docs/articles/Xmod-SIS.html
@@ -71,7 +71,7 @@
   

       
The `SIS` model for malaria

             
-            
December 19, 2023

+            
January 18, 2024

       
       Source: vignettes/Xmod-SIS.Rmd
       
Xmod-SIS.Rmd

@@ -88,7 +88,7 @@ 

 
Variables
 

 

 

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 2bf2166..0291208 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   X-How_To_Add_Model: X-How_To_Add_Model.html
   Xmod-SIS: Xmod-SIS.html
-last_built: 2024-01-05T21:59Z
+last_built: 2024-01-19T05:20Z
 urls:
   reference: https://dd-harp.github.io/mobwork/reference
   article: https://dd-harp.github.io/mobwork/articles
diff --git a/docs/search.json b/docs/search.json
index 45c3878..2baea53 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"required-functions","dir":"Articles","previous_headings":"","what":"Required Functions","title":"How to add a new model to the library: Human Infection","text":"package motrap extends package exDE, implements modular, flexible, extensible framework building ordinary delay differential equations models malaria mosquito-transmitted pathogens. underlying mathematics explained Spatial Dynamics Malaria Transmission 1 One important functions motrap host model families model libraries main dynamical components. vignette discusses add new model family describing human infection dynamics immunity. Adding new model dynamical component class \\(\\cal X\\) – human infection dynamics, including immunity – follows standard template. S3 class functions defined human-interface.R, several examples posted exDE github repository, including SIS model human-SIS.R. code can serve template new model. Simply execute following command, start editing Xmod-NEW.R","code":"knitr::purl(\"X-How_To_Add_Model.Rmd\", output = \"Xmod-NEW.R\", documentation = 0, quiet=TRUE)"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_x","dir":"Articles","previous_headings":"Required Functions > Terms, etcetera","what":"F_X","title":"How to add a new model to the library: Human Infection","text":"function F_X returns effective density infectious humans stratum. following template model: commented code relevant code must changed commented . preferred style extract relevant variables name, compute effective infectious density,individuals stratum, return value. manuscript\\(^1\\), quantity called X. Example example, include \\(SIS\\) model exDE. SIS model, returned value \\(cX\\) prevalence \\(X/H\\). constant \\(c\\) probability mosquito become infected blood feeding infected human. Two things note: First, exDE holds indices component pars$ix, pars$ix$X holds index names variable names. Putting X helps avoid conflicts , example, another dynamical component happened use variable name. declaration inheritParams SIS model exDE works naturally. namespace exDE needed, NEW function () exDE::F_X","code":"#' @title Size of effective infectious human population #' @description Implements [F_X] for the NEW model. #' @inheritParams exDE::F_X #' @return a [numeric] vector of length `nStrata` #' @export F_X.NEW <- function(t, y, pars) {   ########################   # extract:    # VAR <- y[pars$ix$X$...]    ########################   with(pars$Xpar,         ########################        # compute:         # X <- ... F(VAR)         ########################   )   return(X) } #' @title Size of effective infectious human population #' @description Implements [F_X] for the SIS model. #' @inheritParams F_X #' @return a [numeric] vector of length `nStrata` #' @export F_X.SIS <- function(t, y, pars) {   X = y[pars$ix$X$X_ix]   with(pars$Xpar, c*X) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_b","dir":"Articles","previous_headings":"Required Functions > Terms, etcetera","what":"F_b","title":"How to add a new model to the library: Human Infection","text":"exDE, recognize problem translating local EIR FoI. local EIR computed one core model terms one model strata. function F_b returns model-defined probability infective bite mosquito cause infection. include combined effects inefficient transmission, pre-erytrocytic immunity, perhaps effects blood stage immunity. model effect, return value \\(1\\). , provide SIS model exDE example:","code":"#' @title Infection blocking pre-erythrocytic immunity #' @description Implements [F_b] for the SIS model. #' @inheritParams exDE::F_b #' @return a [numeric] vector of length `nStrata` #' @export F_b.NEW <- function(t, y, pars) {   with(pars$Xpar,         ########################        # retrieve it:         # ...          ########################   )      #######################   # return it:    # return(...)   ######################## } #' @title Infection blocking pre-erythrocytic immunity #' @description Implements [F_b] for the SIS model. #' @inheritParams F_b #' @return a [numeric] vector of length `nStrata` #' @export F_b.SIS <- function(y, pars) {   with(pars$Xpar, b) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"dynamics","dir":"Articles","previous_headings":"Required Functions","what":"Dynamics","title":"How to add a new model to the library: Human Infection","text":"style guidelines : Extract variables name using indices attached Xpar Use (pars$Xpar, attach parameter values name Compute derivatives using human readable formulas. Return derivatives concatenated vector straightforward, ’s one important wrinkle. want able use exDE capabilities cohort dynamics vital dynamics, dynamics must extended carefully call demographic matrix function dHdt.","code":"#' @title Derivatives for human population #' @description Implements [dXdt] for the NEW model, no demography. #' @inheritParams exDE::dXdt #' @return a [numeric] vector #' @export dXdt.NEW <- function(t, y, pars, FoI) {    ###############################   # get variables by name from y    # ...     ###############################    with(pars$Xpar, {     ###############################     # Compute the derivatives      #      # dX <- FoI*(H - X) - r*X + dHdt(t, X, pars)     # dH <- Births(t, H, pars) + dHdt(t, H, pars)      ###############################          ###############################     # Return the derivatives      # ...       ###############################     return(c(dX1, dX2, dX3, dH))   }) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"dxdt","dir":"Articles","previous_headings":"Required Functions > Dynamics","what":"dXdt","title":"How to add a new model to the library: Human Infection","text":"exDE, write two versions derivatives function, make easy average user scale .","code":"dXdt.SISdx <- function(t, y, pars, FoI) {   with(pars$Xpar, {     X <- y[X_ix]     H <- F_H(t, y, pars)      dX <- FoI*(H - X) - r*X      return(c(dX))   }) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"dxhdt","dir":"Articles","previous_headings":"Required Functions > Dynamics","what":"dXHdt","title":"How to add a new model to the library: Human Infection","text":"model human demography, variable’s derivative must transformed matrix human population density, H. disease induced mortality included derivative describing changes human population density, dH.","code":"dXdt.SISdH <- function(t, y, pars, FoI) {   with(pars$Xpar, {      H <- F_H(t, y, pars)     X <- y[X_ix]      dX <- FoI*(H - X) - r*X + dHdt(t, X, pars)     dH <- Births(t, H, pars) + dHdt(t, H, pars)      return(c(dX, dH))   }) }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"setup_x","dir":"Articles","previous_headings":"Required Functions > Setup","what":"setup_X","title":"How to add a new model to the library: Human Infection","text":"function must set Xpar must also set initial values. convention, functions get called S3 class functions.","code":"#' @title Setup Xpar.NEW #' @description Implements [setup_X] for the NEW model #' @inheritParams exDE::setup_X #' @return a [list] vector #' @export setup_X.NEW = function(pars, Xname, Xopts=list()){    pars$Xname = \"NEW\"   pars = make_Xpar_NEW(pars, Xopts)   pars = make_Xinits_NEW(pars, Xopts)    return(pars) } setup_X.SIS = function(pars, Xname, Xopts=list()){   pars$Xname = \"SIS\"   pars = make_Xpar_SIS(pars, Xopts)   pars = make_Xinits_SIS(pars, Xopts)    return(pars) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"make_xpar_---","dir":"Articles","previous_headings":"Required Functions > Setup","what":"make_Xpar_...","title":"How to add a new model to the library: Human Infection","text":"function makes parameters assign","code":"#' @title Make parameters for NEW human model, with defaults #' @param pars a [list] #' @param Xopts a [list] that could overwrite defaults #' @param p1 the first parameter  #' @param p2 the second parameter  #' @param p3 the third parameter  #' @return a [list] #' @export make_Xpar_NEW = function(pars, Xopts=list(),                          p1=1, p2=2, p3=3){   with(Xopts,{     Xpar = list()     class(Xpar) <- c(\"NEW\")      Xpar$p1 = checkIt(p1, pars$nStrata)     Xpar$p2 = checkIt(p2, pars$nStrata)     Xpar$p3 = checkIt(p3, pars$nStrata)      pars$Xpar = Xpar     return(pars)   })} make_Xpar_SIS = function(pars, Xopts=list(),                          b=0.55, r=1/180, c=0.15){   with(Xopts,{     Xpar = list()     class(Xpar) <- c(\"SISdX\", \"SISdXdH\")      Xpar$b = checkIt(b, pars$nStrata)     Xpar$c = checkIt(c, pars$nStrata)     Xpar$r = checkIt(r, pars$nStrata)      pars$Xpar = Xpar     return(pars) })}"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"make_xinits_---","dir":"Articles","previous_headings":"Required Functions > Setup","what":"make_Xinits_...","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Make initial values for the NEW human model, with defaults #' @param pars a [list] #' @param Xopts a [list] to overwrite defaults #' @param X10 the initial values of the parameter X1 #' @param X20 the initial values of the parameter X2 #' @param X30 the initial values of the parameter X3 #' @return a [list] #' @export make_Xinits_NEW = function(pars, Xopts = list(), X10=1, X20=2, X30=3){with(Xopts,{   inits = list()   inits$X10 = checkIt(X10, pars$nStrata)   inits$X20 = checkIt(X20, pars$nStrata)   inits$X30 = checkIt(X30, pars$nStrata)   pars$Xinits = inits   return(pars) })} make_Xinits_SIS = function(pars, Xopts = list(), X0=1){with(Xopts,{   inits = list()   inits$X0 = checkIt(X0, pars$nStrata)   pars$Xinits = inits   return(pars) })}"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"make_indices_x","dir":"Articles","previous_headings":"Required Functions > Setup","what":"make_indices_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Add indices for human population to parameter list #' @description Implements [make_indices_X] for the NEW model. #' @inheritParams exDE::make_indices_X #' @return none #' @importFrom utils tail #' @export make_indices_X.NEW <- function(pars) {      pars$Xpar$X1_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X1_ix, 1)      pars$Xpar$X2_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X2_ix, 1)      pars$Xpar$X3_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X3_ix, 1)      return(pars) } #' @title Add indices for human population to parameter list #' @description Implements [make_indices_X] for the SIS model. #' @inheritParams make_indices_X #' @return none #' @importFrom utils tail #' @export make_indices_X.SIS <- function(pars) {   pars$Xpar$X_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X_ix, 1)   return(pars) }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"update_inits_x","dir":"Articles","previous_headings":"Required Functions > Initial Values","what":"update_inits_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Update inits for the SIS human model from a vector of states #' @inheritParams exDE::update_inits_X  #' @return none #' @export update_inits_X.NEW <- function(pars, y0) {   with(pars$ix$X,{     X10 = y0[X1_ix]     X20 = y0[X2_ix]     X30 = y0[X3_ix]     pars = make_Xinits_SIS(pars, list(), X10, X20, X30)     return(pars) })} update_inits_X.SIS <- function(pars, y0) {   X0 = y0[pars$ix$X$X_ix]   make_Xinits_SIS(pars, list(), X0)   return(pars) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"get_inits_x","dir":"Articles","previous_headings":"Required Functions > Initial Values","what":"get_inits_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Return initial values as a vector #' @description This method dispatches on the type of `pars$Xpar`. #' @param pars a [list] #' @return none #' @export get_inits_X.NEW <- function(pars){   with(pars$Xinits,{     return(c(X1, X2, X3))    }) } #' @title Return initial values as a vector #' @description This method dispatches on the type of `pars$Xpar`. #' @param pars a [list] #' @return none #' @export get_inits_X.SIS <- function(pars){   pars$Xinits$X0 }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"parse_deout_x","dir":"Articles","previous_headings":"Required Functions > Outputs","what":"parse_deout_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Parse the output of deSolve and return variables for the NEW model #' @description Implements [parse_deout_X] for the NEW model #' @inheritParams exDE::parse_deout_X #' @return none #' @export parse_deout_X.NEW <- function(deout, pars) {   time = deout[,1]   Hlist <- parse_deout_H(deout, pars)   with(Hlist,{     X1= deout[,pars$ix$X$X1_ix+1]     X2= deout[,pars$ix$X$X1_ix+1]     X3= deout[,pars$ix$X$X3_ix+1]     return(list(time=time, X1=X1, X2=X2, X3=X3, H=H)) })} #' @title Parse the output of deSolve and return variables for the SIS model #' @description Implements [parse_deout_X] for the SIS model #' @inheritParams parse_deout_X #' @return none #' @export parse_deout_X.SIS <- function(deout, pars) {   time = deout[,1]   Hlist <- parse_deout_H(deout, pars)   with(Hlist,{     X = deout[,pars$ix$X$X_ix+1]     return(list(time=time, X=X, H=H)) })}"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_pr","dir":"Articles","previous_headings":"Required Functions > Outputs","what":"F_pr","title":"How to add a new model to the library: Human Infection","text":"function F_pr computes models true prevalence using variable names. passed varslist created parse_deout (see ).","code":"#' @title Compute the \"true\" prevalence of infection / parasite rate #' @description Implements [F_pr] for the NEW model. #' @inheritParams exDE::F_pr #' @return a [numeric] vector of length `nStrata` #' @export F_pr.NEW<- function(varslist, pars) {   pr = with(varslist$XH, X1/H)   return(pr) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"htc","dir":"Articles","previous_headings":"Required Functions > Outputs","what":"HTC","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Compute the HTC for the NEW model #' @description Implements [HTC] for the NEW model with demography. #' @inheritParams exDE::HTC #' @return a [numeric] vector #' @export HTC.NEW <- function(pars) {   with(pars$Xpar,     return(c/r)   ) }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"xde_plot_x","dir":"Articles","previous_headings":"Required Functions > Plotting","what":"xde_plot_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' Plot the density of infected individuals for the NEW model #' #' @inheritParams xde_plot_X #' @export xde_plot_X.NEW = function(pars, clrs=\"black\", llty=1, stable=FALSE, add_axes=TRUE){   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})    if(add_axes==TRUE)     with(vars$XH,          plot(time, 0*time, type = \"n\", ylim = c(0, max(H)),               ylab = \"# Infected\", xlab = \"Time\"))    xde_lines_X(vars$XH, pars, clrs, llty) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"xde_lines_x","dir":"Articles","previous_headings":"Required Functions > Plotting","what":"xde_lines_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' Add lines for the density of infected individuals for the NEW model #' #' @inheritParams xde_lines_X #' #' @export xde_lines_X.NEW = function(XH, pars, clrs=\"black\", llty=1){   with(XH,{     if(pars$nStrata==1) lines(time, X1, col=clrs[1], lty = llty[1])     if(pars$nStrata>1){       if (length(clrs)==1) clrs=rep(clrs, pars$nStrata)       if (length(llty)==1) llty=rep(llty, pars$nStrata)       for(i in 1:pars$nStrata){         lines(time, X1[,i], col=clrs[i], lty = llty[i])       }     }   })}"},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"section","dir":"Articles","previous_headings":"","what":"The `SIS` model for malaria","title":"The `SIS` model for malaria","text":"SIS model, now called, simple compartmental model, first introduced Ross. included exDE base model.","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"variables","dir":"Articles","previous_headings":"","what":"Variables","title":"The `SIS` model for malaria","text":"\\(X\\) density infected humans \\(H\\) density humans","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"parameters","dir":"Articles","previous_headings":"","what":"Parameters","title":"The `SIS` model for malaria","text":"\\(r\\) rate infections clear \\(b\\) fraction bites infective mosquitoes transmit parasites cause infection. \\(c\\) fraction bites infectious human infect mosquito.","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"dynamics","dir":"Articles","previous_headings":"","what":"Dynamics","title":"The `SIS` model for malaria","text":"model defined herein defined two parts. model exposure infection (.e. conversion eir foi), assume fraction infective bites cause infection \\(b\\). dynamics given : \\[ \\frac{dX}{dt} = h (H-X)-rX \\]","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"terms","dir":"Articles","previous_headings":"","what":"Terms","title":"The `SIS` model for malaria","text":"Net Infectiousness True prevalence : \\[x = \\frac{X}{H}.\\] implementation, net infectiousness (NI) linearly proportional prevalence: \\[c x.\\] Human Transmitting Capacity exposure, human remain infected \\(1/r\\) days, transmitting probability \\(c\\) : \\[c/r\\] Exposure Infection model family, immunity. model assumes constant fraction infectious bites, \\(b\\), cause infection.","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"The `SIS` model for malaria","text":"Ross R. Report Prevention Malaria Mauritius. London: Waterlow; 1908. Ross R. Prevention Malaria. 2nd ed. London: John Murray; 1911. Smith DL, Battle KE, Hay SI, Barker CM, Scott TW, McKenzie FE. Ross, Macdonald, theory dynamics control mosquito-transmitted pathogens. PLoS Pathog. 2012;8: e1002588. doi:10.1371/journal.ppat.1002588","code":""},{"path":"https://dd-harp.github.io/mobwork/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"David L Smith. Maintainer.","code":""},{"path":"https://dd-harp.github.io/mobwork/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Smith DL (2023). mobwork: Enhanced functionality exDE. R package version 0.1.0, https://dd-harp.github.io/mobwork/.","code":"@Manual{,   title = {mobwork: Enhanced functionality for exDE},   author = {David L Smith},   year = {2023},   note = {R package version 0.1.0},   url = {https://dd-harp.github.io/mobwork/}, }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/index.html","id":"what-is-mobwork","dir":"","previous_headings":"","what":"What is mobwork?","title":"Enhanced functionality for exDE ","text":"mobwork developed supplement exDE.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.SEIR","title":"Size of effective infectious human population — F_X.SEIR","text":"Implements F_X SEIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.SEIR","text":"","code":"# S3 method for SEIR F_X(t, y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.SEIR","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.SEIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.SIR","title":"Size of effective infectious human population — F_X.SIR","text":"Implements F_X SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.SIR","text":"","code":"# S3 method for SIR F_X(t, y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.SIR","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.SIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.garki","title":"Size of effective infectious human population — F_X.garki","text":"Implements F_X Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.garki","text":"","code":"# S3 method for garki F_X(t, y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.garki","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.garki","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.SEIR","title":"Infection blocking pre-erythrocytic immunity — F_b.SEIR","text":"Implements F_b SEIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.SEIR","text":"","code":"# S3 method for SEIR F_b(y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.SEIR","text":"y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.SEIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.SIR","title":"Infection blocking pre-erythrocytic immunity — F_b.SIR","text":"Implements F_b SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.SIR","text":"","code":"# S3 method for SIR F_b(y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.SIR","text":"y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.SIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.garki","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"Implements F_b Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"","code":"# S3 method for garki F_b(y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"Implements F_eggs RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"","code":"# S3 method for RMG F_eggs(t, y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"Implements F_fqZ RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"","code":"# S3 method for RMG F_fqZ(t, y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the ","title":"Compute the ","text":"Implements F_pr SEIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the ","text":"","code":"# S3 method for SEIR F_pr(varslist, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the ","text":"varslist list variables attached name pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the ","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the ","title":"Compute the ","text":"Implements F_pr SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the ","text":"","code":"# S3 method for SIR F_pr(varslist, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the ","text":"varslist list variables attached name pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the ","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the ","title":"Compute the ","text":"Implements F_pr Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the ","text":"","code":"# S3 method for garki F_pr(varslist, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the ","text":"varslist list variables attached name pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_pr.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the ","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the SEIR model — HTC.SEIR","title":"Compute the HTC for the SEIR model — HTC.SEIR","text":"Implements HTC SEIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the SEIR model — HTC.SEIR","text":"","code":"# S3 method for SEIR HTC(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the SEIR model — HTC.SEIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the SEIR model — HTC.SEIR","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the SIR model — HTC.SIR","title":"Compute the HTC for the SIR model — HTC.SIR","text":"Implements HTC SIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the SIR model — HTC.SIR","text":"","code":"# S3 method for SIR HTC(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the SIR model — HTC.SIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the SIR model — HTC.SIR","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the garki model — HTC.garki","title":"Compute the HTC for the garki model — HTC.garki","text":"Implements HTC garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the garki model — HTC.garki","text":"","code":"# S3 method for garki HTC(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the garki model — HTC.garki","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the garki model — HTC.garki","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"Implements MBionomics RMG model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"","code":"# S3 method for RMG MBionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"named list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.RMG","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"Implements dMYZdt RMG ODE model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"","code":"# S3 method for RMG dMYZdt(t, y, pars, Lambda, kappa)"},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"t current simulation time y state vector pars list Lambda emergence rate adult mosquitoes kappa net infectiousness human population","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SEIRdX","title":"Derivatives for human population — dXdt.SEIRdX","text":"Implements dXdt SEIR model, demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SEIRdX","text":"","code":"# S3 method for SEIRdX dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SEIRdX","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SEIRdX","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SEIRdXdH","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"Implements dXdt SEIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"","code":"# S3 method for SEIRdXdH dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIRdX","title":"Derivatives for human population — dXdt.SIRdX","text":"Implements dXdt SIR model, demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIRdX","text":"","code":"# S3 method for SIRdX dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIRdX","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIRdX","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIRdXdH","title":"Derivatives for human population — dXdt.SIRdXdH","text":"Implements dXdt SIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIRdXdH","text":"","code":"# S3 method for SIRdXdH dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIRdXdH","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIRdXdH","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.garki","title":"Derivatives for human population — dXdt.garki","text":"Implements dXdt Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.garki","text":"","code":"# S3 method for garki dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.garki","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.garki","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.RMG","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"Implements get_inits_MYZ RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"","code":"# S3 method for RMG get_inits_MYZ(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SEIR","title":"Return initial values as a vector — get_inits_X.SEIR","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SEIR","text":"","code":"# S3 method for SEIR get_inits_X(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SEIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SIR","title":"Return initial values as a vector — get_inits_X.SIR","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SIR","text":"","code":"# S3 method for SIR get_inits_X(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector for the Garki model — get_inits_X.garki","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"","code":"# S3 method for garki get_inits_X(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"pars named list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"named list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the EIR vs. time — lines_EIR","title":"Add lines for the EIR vs. time — lines_EIR","text":"Add lines EIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the EIR vs. time — lines_EIR","text":"","code":"lines_EIR(terms, model, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the EIR vs. time — lines_EIR","text":"terms list outputs exDE::parse_deout() model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","text":"","code":"# S3 method for RM lines_M(MYZ, model, clrs = \"darkblue\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","text":"MYZ list outputs exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","text":"","code":"# S3 method for RMG lines_M(MYZ, model, clrs = \"darkblue\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","text":"MYZ list outputs exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: add to a plot for mosquito population density — lines_M","title":"Basic plotting: add to a plot for mosquito population density — lines_M","text":"Basic plotting: add plot mosquito population density","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: add to a plot for mosquito population density — lines_M","text":"","code":"lines_M(MYZ, model, clrs)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: add to a plot for mosquito population density — lines_M","text":"MYZ list outputs exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","text":"","code":"lines_PR(terms, model, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","text":"terms list outputs exDE::parse_deout() model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) specifies lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","text":"","code":"# S3 method for SIS lines_X(XH, model, clrs = \"black\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","text":"XH list exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","title":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","text":"Basic plotting: add outputs plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","text":"","code":"lines_X(XH, model, clrs = \"black\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","text":"XH list exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","text":"","code":"# S3 method for RM lines_YZ(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","text":"","code":"# S3 method for RMG lines_YZ(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","title":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","text":"Basic plotting: add lines density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","text":"","code":"lines_YZ(MYZ, model, Yclrs, Zclrs)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction infected and infective for the ","title":"Add lines for the fraction infected and infective for the ","text":"Add lines fraction infected infective \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction infected and infective for the ","text":"","code":"# S3 method for RM lines_YZ_fracs(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction infected and infective for the ","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction infected and infective for the ","title":"Add lines for the fraction infected and infective for the ","text":"Add lines fraction infected infective \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction infected and infective for the ","text":"","code":"# S3 method for RMG lines_YZ_fracs(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction infected and infective for the ","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","title":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","text":"Add lines fraction mosquitoes infected infective","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","text":"","code":"lines_YZ_fracs(MYZ, model, Yclrs, Zclrs)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the aEIR vs. time — lines_aEIR","title":"Add lines for the aEIR vs. time — lines_aEIR","text":"Add lines aEIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the aEIR vs. time — lines_aEIR","text":"","code":"lines_aEIR(terms, model, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the aEIR vs. time — lines_aEIR","text":"terms list outputs exDE::parse_deout() model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirVpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","title":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","text":"Add lines EIR(t) vs. PR(t)","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirVpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","text":"","code":"lines_eirVpr(terms, pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirVpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","text":"terms list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs character vector colors llty integer (integers) specifies lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for an eir-pr scaling relationship — lines_eirpr","title":"Add lines for an eir-pr scaling relationship — lines_eirpr","text":"Add lines eir-pr scaling relationship","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for an eir-pr scaling relationship — lines_eirpr","text":"","code":"lines_eirpr(pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for an eir-pr scaling relationship — lines_eirpr","text":"pars list e.g.,  generated exDE::xde_setup() defines model exDE clrs character vector colors llty list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"Make inits RMG adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"","code":"make_MYZinits_RMG(   pars,   MYZopts = list(),   U0 = 5,   Gu0 = 1,   Y0 = 1,   Gy0 = 1,   Z0 = 1,   Gz0 = 1 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"pars list MYZopts list values overwrites defaults U0 total uninfected, gravid mosquito density patch Gu0 total uninfected, gravid mosquito density patch Y0 infected, gravid mosquito density patch Gy0 infected, gravid mosquito density patch Z0 infectious, gravid mosquito density patch Gz0 infectious, gravid mosquito density patch","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RMG ODE adult mosquito model — make_MYZpar_RMG","title":"Make parameters for RMG ODE adult mosquito model — make_MYZpar_RMG","text":"Make parameters RMG ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RMG ODE adult mosquito model — make_MYZpar_RMG","text":"","code":"make_MYZpar_RMG(   pars,   MYZopts = list(),   calK,   solve_as = \"dde\",   g = 1/12,   sigma = 1/8,   f = 0.5,   q = 0.95,   eip = 11,   nu = 1,   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RMG ODE adult mosquito model — make_MYZpar_RMG","text":"pars list MYZopts list values overwrites defaults calK mosquito dispersal matrix dimensions nPatches nPatches solve_as either ode solve ode dde solve dde g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction eip length extrinsic incubation period nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RMG ODE adult mosquito model — make_MYZpar_RMG","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"Make initial values SEIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"","code":"make_Xinits_SEIR(pars, Xopts = list(), E0 = 1, I0 = 0, R0 = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"pars list Xopts list overwrite defaults E0 initial values parameter E I0 initial values parameter R0 initial values parameter R","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"Make initial values SIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"","code":"make_Xinits_SIR(pars, Xopts = list(), I0 = 1, R0 = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"pars list Xopts list overwrite defaults I0 initial values parameter R0 initial values parameter R","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"Make inits Garki human model. Note variables sum H, initial value x1 set. values passed order presented original paper.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"","code":"make_Xinits_garki(   pars,   Xopts = list(),   x1 = NULL,   x2 = 0,   y1 = 0,   y2 = 0,   y3 = 0,   x3 = 0,   x4 = 0 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"pars environment Xopts list values override default values x1 numeric initial value variable x1 x2 numeric initial value variable x2 y1 numeric initial value variable y1 y2 numeric initial value variable y2 y3 numeric initial value variable y3 x3 numeric initial value variable x3 x4 numeric initial value variable x4","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"Make parameters SEIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"","code":"make_Xpar_SEIR(pars, Xopts = list(), b = 0.55, r = 1/180, c = 0.15, tau = 1/5)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"pars list Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito tau latent period 1/tau","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"Make parameters SIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"","code":"make_Xpar_SIR(pars, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"pars list Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Garki human model — make_Xpar_garki","title":"Make parameters for Garki human model — make_Xpar_garki","text":"Make parameters Garki human model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Garki human model — make_Xpar_garki","text":"","code":"make_Xpar_garki(   pars,   Xopts = list(),   b = 0.55,   r1 = 0.0023,   r2 = 0.023,   nu = 1/15,   alpha1 = 0.002,   alpha2 = 0.00019,   q1 = 0.7,   q2 = 0.5,   q3 = 0.3,   mu = 1/65/365 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Garki human model — make_Xpar_garki","text":"pars list Xopts list b transmission probability (efficiency) mosquito human r1 numeric recovery rate non-immunes r2 numericrecovery rate partially immmunes nu numericincubation period alpha1 numeric rate losing infectivity alpha2 numeric rate acquiring immunity q1 numeric detection y1 q2 numeric detection y2 q3 numeric detection y3 mu numeric death rate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Garki human model — make_Xpar_garki","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"Implements make_indices_MYZ RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"","code":"# S3 method for RMG make_indices_MYZ(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SEIR","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"Implements make_indices_X SEIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"","code":"# S3 method for SEIR make_indices_X(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SIR","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"Implements make_indices_X SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"","code":"# S3 method for SIR make_indices_X(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.garki","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"Implements make_indices_X Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"","code":"# S3 method for garki make_indices_X(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"Make inits RMG adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"","code":"make_inits_MYZ_RMG(pars, U0, Gu0, Y0, Gy0, Z0, Gz0)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"pars list U0 total mosquito density patch Gu0 total gravid uninfected mosquito density patch Y0 infected mosquito density patch Gy0 total gravid infected mosquito density patch Z0 infectious mosquito density patch Gz0 total gravid infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"Make parameters RMG ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"","code":"make_parameters_MYZ_RMG(pars, g, sigma, f, q, nu, eggsPerBatch, eip, calK)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"pars list g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition eip length extrinsic incubation period calK mosquito dispersal matrix dimensions nPatches nPatches","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/mobwork-package.html","id":null,"dir":"Reference","previous_headings":"","what":"mobwork: Enhanced functionality for exDE — mobwork-package","title":"mobwork: Enhanced functionality for exDE — mobwork-package","text":"(maybe one line) Use four spaces indenting paragraphs within Description.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"Implements parse_deout_MYZ RMG model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"","code":"# S3 method for RMG parse_deout_MYZ(deout, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"deout matrix outputs deSolve pars list defines model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"Implements parse_deout_X SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"","code":"# S3 method for SEIR parse_deout_X(deout, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"deout matrix outputs deSolve pars list defines model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"Implements parse_deout_X SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"","code":"# S3 method for SIR parse_deout_X(deout, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"deout matrix outputs deSolve pars list defines model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"Implements parse_deout_X Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"","code":"# S3 method for garki parse_deout_X(deout, pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"deout matrix outputs deSolve pars list defines model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the EIR vs. time — plot_EIR","title":"Plot the EIR vs. time — plot_EIR","text":"Plot EIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the EIR vs. time — plot_EIR","text":"","code":"plot_EIR(model, clrs = \"black\", llty = 1, stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the EIR vs. time — plot_EIR","text":"model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add logical plot axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RM plot_M(model, clrs = \"darkblue\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RMG plot_M(model, clrs = \"darkblue\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density — plot_M","title":"Basic plotting: plot mosquito population density — plot_M","text":"Basic plotting: plot mosquito population density","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density — plot_M","text":"","code":"plot_M(model, clrs, stable, add)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density — plot_M","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the true PR. — plot_PR","title":"Basic plotting: plot the true PR. — plot_PR","text":"Basic plotting: plot true PR.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the true PR. — plot_PR","text":"","code":"plot_PR(model, clrs = \"black\", llty = 1, stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the true PR. — plot_PR","text":"model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) specifies lty plotting stable logical set FALSE orbits TRUE stable_orbits add logical plot axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","title":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","text":"Basic plotting: plot density infected humans SIS model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","text":"","code":"# S3 method for SIS plot_X(model, clrs = \"black\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: default plot for models of human infection and immunity — plot_X","title":"Basic plotting: default plot for models of human infection and immunity — plot_X","text":"Basic plotting: default plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: default plot for models of human infection and immunity — plot_X","text":"","code":"plot_X(model, clrs = \"black\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: default plot for models of human infection and immunity — plot_X","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RM plot_YZ(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RMG plot_YZ(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","title":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","text":"Basic plotting: plot density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","text":"","code":"plot_YZ(model, Yclrs, Zclrs, stable, add)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the fraction infected and infective for the ","title":"Basic plotting: plot the fraction infected and infective for the ","text":"Basic plotting: plot fraction infected infective \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the fraction infected and infective for the ","text":"","code":"# S3 method for RM plot_YZ_fracs(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the fraction infected and infective for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the fraction infected and infective for the ","title":"Basic plotting: plot the fraction infected and infective for the ","text":"Basic plotting: plot fraction infected infective \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the fraction infected and infective for the ","text":"","code":"# S3 method for RMG plot_YZ_fracs(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the fraction infected and infective for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","title":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","text":"Basic plotting: plot proportion mosquitoes infected infective.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","text":"","code":"plot_YZ_fracs(model, Yclrs, Zclrs, stable, add)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"PLot the aEIR vs. time — plot_aEIR","title":"PLot the aEIR vs. time — plot_aEIR","text":"PLot aEIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PLot the aEIR vs. time — plot_aEIR","text":"","code":"plot_aEIR(model, clrs = \"black\", llty = 1, stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PLot the aEIR vs. time — plot_aEIR","text":"model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add logical plot axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirVpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","title":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","text":"Plot EIR(t) vs. PR(t)","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirVpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","text":"","code":"plot_eirVpr(pars, clrs = \"black\", llty = 1, stable = FALSE, add_axes = TRUE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirVpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","text":"pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs character vector colors llty integer specifies lty plotting stable logical set FALSE orbits TRUE stable_orbits add_axes logical plot add_axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the eir-pr scaling relationship — plot_eirpr","title":"Plot the eir-pr scaling relationship — plot_eirpr","text":"Plot eir-pr scaling relationship","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the eir-pr scaling relationship — plot_eirpr","text":"","code":"plot_eirpr(pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the eir-pr scaling relationship — plot_eirpr","text":"pars list e.g.,  generated exDE::xde_setup() defines model exDE clrs character vector colors llty list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/pr2Lambda.html","id":null,"dir":"Reference","previous_headings":"","what":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","title":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","text":"takes model uses XH component define eirpr relationship using xde_scaling_eir calls xde_scaling_lambda","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/pr2Lambda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","text":"","code":"pr2Lambda(pr, model, constrain = TRUE)"},{"path":"https://dd-harp.github.io/mobwork/reference/pr2Lambda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","text":"pr numeric vector model list constrain logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the RMG model — setup_MYZ.RMG","title":"Setup the RMG model — setup_MYZ.RMG","text":"Implements setup_MYZ RMG model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the RMG model — setup_MYZ.RMG","text":"","code":"# S3 method for RMG setup_MYZ(pars, MYZname, nPatches = 1, MYZopts = list(), calK = diag(1))"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the RMG model — setup_MYZ.RMG","text":"pars list MYZname character string nPatches numeric value (integer), number patches MYZopts list calK matrix","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the RMG model — setup_MYZ.RMG","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SEIR — setup_X.SEIR","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"Implements setup_X SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"","code":"# S3 method for SEIR setup_X(pars, Xname, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"pars list Xname character string Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIR — setup_X.SIR","title":"Setup Xpar.SIR — setup_X.SIR","text":"Implements setup_X SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIR — setup_X.SIR","text":"","code":"# S3 method for SIR setup_X(pars, Xname, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIR — setup_X.SIR","text":"pars list Xname character string Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIR — setup_X.SIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.Garki — setup_X.garki","title":"Setup Xpar.Garki — setup_X.garki","text":"Implements setup_X Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.Garki — setup_X.garki","text":"","code":"# S3 method for garki setup_X(pars, Xname, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.Garki — setup_X.garki","text":"pars list Xname character string Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.Garki — setup_X.garki","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"Split stratum two strata, assigning fraction p new biting weight multiplied factor fac compared old one. biting weight remaining 1-p gets new factor 1/fac","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"","code":"# S3 method for SIS split_stratum_by_biting(pars, i, p, fac)"},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"pars list defining model stratum split p fraction higher exposure stratum fac factor increase","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"pars list integer -- stratum split p numeric -- fraction gets multiplied fac fac numeric -- factor","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a stratum into two strata, assigning — split_stratum_by_biting","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"Split stratum two strata, assigning","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"","code":"split_stratum_by_biting(pars, i, p, fac)"},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"pars list defining model stratum split p fraction higher exposure stratum fac factor increase","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/ssMYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","title":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","text":"function computes several quantities require","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/ssMYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","text":"","code":"ssMYZ(model)"},{"path":"https://dd-harp.github.io/mobwork/reference/ssMYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","text":"model list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"Make inits RMG adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"","code":"# S3 method for RMG update_inits_MYZ(pars, y0)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"pars list y0 vector initial values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"Update inits SEIR human model vector states","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"","code":"# S3 method for SEIR update_inits_X(pars, y0)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"pars list y0 vector initial values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"Update inits SIR human model vector states","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"","code":"# S3 method for SIR update_inits_X(pars, y0)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"pars list y0 vector initial values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Xinits for the Garki model — update_inits_X.garki","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"Update Xinits Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"","code":"# S3 method for garki update_inits_X(pars, y0)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"pars list y0 vector initial values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2ni.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert eir to ni — xde_eir2ni","title":"Convert eir to ni — xde_eir2ni","text":"Use outputs$eirpr table interpolate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2ni.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert eir to ni — xde_eir2ni","text":"","code":"xde_eir2ni(eir, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2ni.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert eir to ni — xde_eir2ni","text":"eir vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2pr.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert eir to pr — xde_eir2pr","title":"Convert eir to pr — xde_eir2pr","text":"Use outputs$eirpr table interpolate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2pr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert eir to pr — xde_eir2pr","text":"","code":"xde_eir2pr(eir, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2pr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert eir to pr — xde_eir2pr","text":"eir vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","text":"Add lines density infected individuals SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","text":"","code":"# S3 method for SEIR xde_lines_X(XH, pars, clrs = c(\"darkgreen\", \"darkred\", \"darkblue\"), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","text":"XH list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","text":"Add lines density infected individuals SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","text":"","code":"# S3 method for SIR xde_lines_X(XH, pars, clrs = c(\"darkred\", \"darkblue\"), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","text":"XH list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","text":"Add lines density infected individuals Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","text":"","code":"# S3 method for garki xde_lines_X(XH, pars, clrs = viridisLite::turbo(7), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","text":"XH list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","title":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","text":"Plot density infected individuals SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","text":"","code":"# S3 method for SEIR xde_plot_X(   pars,   clrs = c(\"darkgreen\", \"darkred\", \"darkblue\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","text":"pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add_axes logical plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","title":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","text":"Plot density infected individuals SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","text":"","code":"# S3 method for SIR xde_plot_X(   pars,   clrs = c(\"darkred\", \"darkblue\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","text":"pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add_axes logical plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","title":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","text":"Plot density infected individuals Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","text":"","code":"# S3 method for garki xde_plot_X(   pars,   clrs = viridisLite::turbo(7),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","text":"pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add_axes logical plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2eir.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to eir — xde_pr2eir","title":"Convert pr to eir — xde_pr2eir","text":"Use outputs$eirpr table convert set pr values eir values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to eir — xde_pr2eir","text":"","code":"xde_pr2eir(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to eir — xde_pr2eir","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2lambda.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to lambda — xde_pr2lambda","title":"Convert pr to lambda — xde_pr2lambda","text":"Use outputs$lambdapr table convert set pr values lambda values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2lambda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to lambda — xde_pr2lambda","text":"","code":"xde_pr2lambda(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2lambda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to lambda — xde_pr2lambda","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2m.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to mosquito density — xde_pr2m","title":"Convert pr to mosquito density — xde_pr2m","text":"Use outputs$eirpr table convert set pr values scaled mosquito density values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2m.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to mosquito density — xde_pr2m","text":"","code":"xde_pr2m(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2m.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to mosquito density — xde_pr2m","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2ni.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to ni — xde_pr2ni","title":"Convert pr to ni — xde_pr2ni","text":"Use outputs$eirpr table interpolate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2ni.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to ni — xde_pr2ni","text":"","code":"xde_pr2ni(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2ni.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to ni — xde_pr2ni","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct an eirpr object for an arbitary model — xde_scaling","title":"Construct an eirpr object for an arbitary model — xde_scaling","text":"takes model uses XH component define eirpr relationship using xde_scaling_eir calls xde_scaling_lambda","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct an eirpr object for an arbitary model — xde_scaling","text":"","code":"xde_scaling(model, N = 25, F_eir = NULL)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct an eirpr object for an arbitary model — xde_scaling","text":"model list N integer, size mesh aEIR F_eir function, size mesh aEIR","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_Z.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eir-pr scaling relationships — xde_scaling_Z","title":"Compute eir-pr scaling relationships — xde_scaling_Z","text":"function computes average annual values eir, pr, interesting terms returns table. computed model class \"human\"","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_Z.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eir-pr scaling relationships — xde_scaling_Z","text":"","code":"xde_scaling_Z(model, N = 25)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_Z.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eir-pr scaling relationships — xde_scaling_Z","text":"model list N integer, size mesh aEIR","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_eir.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eir-pr scaling relationships — xde_scaling_eir","title":"Compute eir-pr scaling relationships — xde_scaling_eir","text":"function computes average annual values eir, pr, interesting terms returns table. computed model class \"cohort\"","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eir-pr scaling relationships — xde_scaling_eir","text":"","code":"xde_scaling_eir(model, N = 25)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eir-pr scaling relationships — xde_scaling_eir","text":"model list N integer","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_lambda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","title":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","text":"function computes m lambda output one xde_scaling_eir xde_scaling_Z.  outputs attached eirpr","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_lambda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","text":"","code":"xde_scaling_lambda(model)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_lambda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","text":"model list","code":""}]
+[{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"required-functions","dir":"Articles","previous_headings":"","what":"Required Functions","title":"How to add a new model to the library: Human Infection","text":"package motrap extends package exDE, implements modular, flexible, extensible framework building ordinary delay differential equations models malaria mosquito-transmitted pathogens. underlying mathematics explained Spatial Dynamics Malaria Transmission 1 One important functions motrap host model families model libraries main dynamical components. vignette discusses add new model family describing human infection dynamics immunity. Adding new model dynamical component class \\(\\cal X\\) – human infection dynamics, including immunity – follows standard template. S3 class functions defined human-interface.R, several examples posted exDE github repository, including SIS model human-SIS.R. code can serve template new model. Simply execute following command, start editing Xmod-NEW.R","code":"knitr::purl(\"X-How_To_Add_Model.Rmd\", output = \"Xmod-NEW.R\", documentation = 0, quiet=TRUE)"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_x","dir":"Articles","previous_headings":"Required Functions > Terms, etcetera","what":"F_X","title":"How to add a new model to the library: Human Infection","text":"function F_X returns effective density infectious humans stratum. following template model: commented code relevant code must changed commented . preferred style extract relevant variables name, compute effective infectious density,individuals stratum, return value. manuscript\\(^1\\), quantity called X. Example example, include \\(SIS\\) model exDE. SIS model, returned value \\(cX\\) prevalence \\(X/H\\). constant \\(c\\) probability mosquito become infected blood feeding infected human. Two things note: First, exDE holds indices component pars$ix, pars$ix$X holds index names variable names. Putting X helps avoid conflicts , example, another dynamical component happened use variable name. declaration inheritParams SIS model exDE works naturally. namespace exDE needed, NEW function () exDE::F_X","code":"#' @title Size of effective infectious human population #' @description Implements [F_X] for the NEW model. #' @inheritParams exDE::F_X #' @return a [numeric] vector of length `nStrata` #' @export F_X.NEW <- function(t, y, pars) {   ########################   # extract:    # VAR <- y[pars$ix$X$...]    ########################   with(pars$Xpar,         ########################        # compute:         # X <- ... F(VAR)         ########################   )   return(X) } #' @title Size of effective infectious human population #' @description Implements [F_X] for the SIS model. #' @inheritParams F_X #' @return a [numeric] vector of length `nStrata` #' @export F_X.SIS <- function(t, y, pars) {   X = y[pars$ix$X$X_ix]   with(pars$Xpar, c*X) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_x-1","dir":"Articles","previous_headings":"Required Functions > Terms, etcetera","what":"F_X","title":"How to add a new model to the library: Human Infection","text":"function F_X returns effective density infectious humans stratum. following template model:","code":"#' @title Size of effective infectious human population #' @description Implements [F_H] for the NEW model. #' @inheritParams exDE::F_H #' @return a [numeric] vector of length `nStrata` #' @export F_H.NEW <- function(t, y, pars) {   ########################   # extract:    # VAR <- y[pars$ix$X$...]    ########################   with(pars$Xpar,         ########################        # compute:         # X <- ... F(VAR)         ########################     )   return(H) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_b","dir":"Articles","previous_headings":"Required Functions > Terms, etcetera","what":"F_b","title":"How to add a new model to the library: Human Infection","text":"exDE, recognize problem translating local EIR FoI. local EIR computed one core model terms one model strata. function F_b returns model-defined probability infective bite mosquito cause infection. include combined effects inefficient transmission, pre-erytrocytic immunity, perhaps effects blood stage immunity. model effect, return value \\(1\\). , provide SIS model exDE example:","code":"#' @title Infection blocking pre-erythrocytic immunity #' @description Implements [F_b] for the SIS model. #' @inheritParams exDE::F_b #' @return a [numeric] vector of length `nStrata` #' @export F_b.NEW <- function(t, y, pars) {   with(pars$Xpar,         ########################        # retrieve it:         # ...          ########################   )      #######################   # return it:    # return(...)   ######################## } #' @title Infection blocking pre-erythrocytic immunity #' @description Implements [F_b] for the SIS model. #' @inheritParams F_b #' @return a [numeric] vector of length `nStrata` #' @export F_b.SIS <- function(y, pars) {   with(pars$Xpar, b) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"dynamics","dir":"Articles","previous_headings":"Required Functions","what":"Dynamics","title":"How to add a new model to the library: Human Infection","text":"style guidelines : Extract variables name using indices attached Xpar Use (pars$Xpar, attach parameter values name Compute derivatives using human readable formulas. Return derivatives concatenated vector straightforward, ’s one important wrinkle. want able use exDE capabilities cohort dynamics vital dynamics, dynamics must extended carefully call demographic matrix function dHdt.","code":"#' @title Derivatives for human population #' @description Implements [dXdt] for the NEW model, no demography. #' @inheritParams exDE::dXdt #' @return a [numeric] vector #' @export dXdt.NEW <- function(t, y, pars, FoI) {    ###############################   # get variables by name from y    # ...     ###############################    with(pars$Xpar, {     ###############################     # Compute the derivatives      #      # dX <- FoI*(H - X) - r*X + dHdt(t, X, pars)     # dH <- Births(t, H, pars) + dHdt(t, H, pars)      ###############################          ###############################     # Return the derivatives      # ...       ###############################     return(c(dX1, dX2, dX3, dH))   }) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"dxdt","dir":"Articles","previous_headings":"Required Functions > Dynamics","what":"dXdt","title":"How to add a new model to the library: Human Infection","text":"exDE, write two versions derivatives function, make easy average user scale .","code":"dXdt.SISdx <- function(t, y, pars, FoI) {   with(pars$Xpar, {     X <- y[X_ix]     H <- F_H(t, y, pars)      dX <- FoI*(H - X) - r*X      return(c(dX))   }) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"dxhdt","dir":"Articles","previous_headings":"Required Functions > Dynamics","what":"dXHdt","title":"How to add a new model to the library: Human Infection","text":"model human demography, variable’s derivative must transformed matrix human population density, H. disease induced mortality included derivative describing changes human population density, dH.","code":"dXdt.SISdH <- function(t, y, pars, FoI) {   with(pars$Xpar, {      H <- F_H(t, y, pars)     X <- y[X_ix]      dX <- FoI*(H - X) - r*X + dHdt(t, X, pars)     dH <- Births(t, H, pars) + dHdt(t, H, pars)      return(c(dX, dH))   }) }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"setup_x","dir":"Articles","previous_headings":"Required Functions > Setup","what":"setup_X","title":"How to add a new model to the library: Human Infection","text":"function must set Xpar must also set initial values. convention, functions get called S3 class functions.","code":"#' @title Setup Xpar.NEW #' @description Implements [setup_X] for the NEW model #' @inheritParams exDE::setup_X #' @return a [list] vector #' @export setup_X.NEW = function(pars, Xname, Xopts=list()){    pars$Xname = \"NEW\"   pars = make_Xpar_NEW(pars, Xopts)   pars = make_Xinits_NEW(pars, Xopts)    return(pars) } setup_X.SIS = function(pars, Xname, Xopts=list()){   pars$Xname = \"SIS\"   pars = make_Xpar_SIS(pars, Xopts)   pars = make_Xinits_SIS(pars, Xopts)    return(pars) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"make_xpar_---","dir":"Articles","previous_headings":"Required Functions > Setup","what":"make_Xpar_...","title":"How to add a new model to the library: Human Infection","text":"function makes parameters assign","code":"#' @title Make parameters for NEW human model, with defaults #' @param pars a [list] #' @param Xopts a [list] that could overwrite defaults #' @param p1 the first parameter  #' @param p2 the second parameter  #' @param p3 the third parameter  #' @return a [list] #' @export make_Xpar_NEW = function(pars, Xopts=list(),                          p1=1, p2=2, p3=3){   with(Xopts,{     Xpar = list()     class(Xpar) <- c(\"NEW\")      Xpar$p1 = checkIt(p1, pars$nStrata)     Xpar$p2 = checkIt(p2, pars$nStrata)     Xpar$p3 = checkIt(p3, pars$nStrata)      pars$Xpar = Xpar     return(pars)   })} make_Xpar_SIS = function(pars, Xopts=list(),                          b=0.55, r=1/180, c=0.15){   with(Xopts,{     Xpar = list()     class(Xpar) <- c(\"SISdX\", \"SISdXdH\")      Xpar$b = checkIt(b, pars$nStrata)     Xpar$c = checkIt(c, pars$nStrata)     Xpar$r = checkIt(r, pars$nStrata)      pars$Xpar = Xpar     return(pars) })}"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"make_xinits_---","dir":"Articles","previous_headings":"Required Functions > Setup","what":"make_Xinits_...","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Make initial values for the NEW human model, with defaults #' @param pars a [list] #' @param Xopts a [list] to overwrite defaults #' @param X10 the initial values of the parameter X1 #' @param X20 the initial values of the parameter X2 #' @param X30 the initial values of the parameter X3 #' @return a [list] #' @export make_Xinits_NEW = function(pars, Xopts = list(), X10=1, X20=2, X30=3){with(Xopts,{   inits = list()   inits$X10 = checkIt(X10, pars$nStrata)   inits$X20 = checkIt(X20, pars$nStrata)   inits$X30 = checkIt(X30, pars$nStrata)   pars$Xinits = inits   return(pars) })} make_Xinits_SIS = function(pars, Xopts = list(), X0=1){with(Xopts,{   inits = list()   inits$X0 = checkIt(X0, pars$nStrata)   pars$Xinits = inits   return(pars) })}"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"make_indices_x","dir":"Articles","previous_headings":"Required Functions > Setup","what":"make_indices_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Add indices for human population to parameter list #' @description Implements [make_indices_X] for the NEW model. #' @inheritParams exDE::make_indices_X #' @return none #' @importFrom utils tail #' @export make_indices_X.NEW <- function(pars) {      pars$Xpar$X1_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X1_ix, 1)      pars$Xpar$X2_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X2_ix, 1)      pars$Xpar$X3_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X3_ix, 1)      return(pars) } #' @title Add indices for human population to parameter list #' @description Implements [make_indices_X] for the SIS model. #' @inheritParams make_indices_X #' @return none #' @importFrom utils tail #' @export make_indices_X.SIS <- function(pars) {   pars$Xpar$X_ix <- seq(from = pars$max_ix+1, length.out = pars$nStrata)   pars$max_ix <- tail(pars$Xpar$X_ix, 1)   return(pars) }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"update_inits_x","dir":"Articles","previous_headings":"Required Functions > Initial Values","what":"update_inits_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Update inits for the SIS human model from a vector of states #' @inheritParams exDE::update_inits_X  #' @return none #' @export update_inits_X.NEW <- function(pars, y0) {   with(pars$ix$X,{     X10 = y0[X1_ix]     X20 = y0[X2_ix]     X30 = y0[X3_ix]     pars = make_Xinits_SIS(pars, list(), X10, X20, X30)     return(pars) })} update_inits_X.SIS <- function(pars, y0) {   X0 = y0[pars$ix$X$X_ix]   make_Xinits_SIS(pars, list(), X0)   return(pars) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"get_inits_x","dir":"Articles","previous_headings":"Required Functions > Initial Values","what":"get_inits_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Return initial values as a vector #' @description This method dispatches on the type of `pars$Xpar`. #' @param pars a [list] #' @return none #' @export get_inits_X.NEW <- function(pars){   with(pars$Xinits,{     return(c(X1, X2, X3))    }) } #' @title Return initial values as a vector #' @description This method dispatches on the type of `pars$Xpar`. #' @param pars a [list] #' @return none #' @export get_inits_X.SIS <- function(pars){   pars$Xinits$X0 }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"parse_deout_x","dir":"Articles","previous_headings":"Required Functions > Outputs","what":"parse_deout_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Parse the output of deSolve and return variables for the NEW model #' @description Implements [parse_deout_X] for the NEW model #' @inheritParams exDE::parse_deout_X #' @return none #' @export parse_deout_X.NEW <- function(deout, pars) {   time = deout[,1]   Hlist <- parse_deout_H(deout, pars)   with(Hlist,{     X1= deout[,pars$ix$X$X1_ix+1]     X2= deout[,pars$ix$X$X1_ix+1]     X3= deout[,pars$ix$X$X3_ix+1]     return(list(time=time, X1=X1, X2=X2, X3=X3, H=H)) })} #' @title Parse the output of deSolve and return variables for the SIS model #' @description Implements [parse_deout_X] for the SIS model #' @inheritParams parse_deout_X #' @return none #' @export parse_deout_X.SIS <- function(deout, pars) {   time = deout[,1]   Hlist <- parse_deout_H(deout, pars)   with(Hlist,{     X = deout[,pars$ix$X$X_ix+1]     return(list(time=time, X=X, H=H)) })}"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"f_pr","dir":"Articles","previous_headings":"Required Functions > Outputs","what":"F_pr","title":"How to add a new model to the library: Human Infection","text":"function F_pr computes models true prevalence using variable names. passed varslist created parse_deout (see ).","code":"#' @title Compute the \"true\" prevalence of infection / parasite rate #' @description Implements [F_pr] for the NEW model. #' @inheritParams exDE::F_pr #' @return a [numeric] vector of length `nStrata` #' @export F_pr.NEW<- function(varslist, pars) {   pr = with(varslist$XH, X1/H)   return(pr) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"htc","dir":"Articles","previous_headings":"Required Functions > Outputs","what":"HTC","title":"How to add a new model to the library: Human Infection","text":"","code":"#' @title Compute the HTC for the NEW model #' @description Implements [HTC] for the NEW model with demography. #' @inheritParams exDE::HTC #' @return a [numeric] vector #' @export HTC.NEW <- function(pars) {   with(pars$Xpar,     return(c/r)   ) }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"xde_plot_x","dir":"Articles","previous_headings":"Required Functions > Plotting","what":"xde_plot_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' Plot the density of infected individuals for the NEW model #' #' @inheritParams xde_plot_X #' @export xde_plot_X.NEW = function(pars, clrs=\"black\", llty=1, stable=FALSE, add_axes=TRUE){   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})    if(add_axes==TRUE)     with(vars$XH,          plot(time, 0*time, type = \"n\", ylim = c(0, max(H)),               ylab = \"# Infected\", xlab = \"Time\"))    xde_lines_X(vars$XH, pars, clrs, llty) }"},{"path":"https://dd-harp.github.io/mobwork/articles/X-How_To_Add_Model.html","id":"xde_lines_x","dir":"Articles","previous_headings":"Required Functions > Plotting","what":"xde_lines_X","title":"How to add a new model to the library: Human Infection","text":"","code":"#' Add lines for the density of infected individuals for the NEW model #' #' @inheritParams xde_lines_X #' #' @export xde_lines_X.NEW = function(XH, pars, clrs=\"black\", llty=1){   with(XH,{     if(pars$nStrata==1) lines(time, X1, col=clrs[1], lty = llty[1])     if(pars$nStrata>1){       if (length(clrs)==1) clrs=rep(clrs, pars$nStrata)       if (length(llty)==1) llty=rep(llty, pars$nStrata)       for(i in 1:pars$nStrata){         lines(time, X1[,i], col=clrs[i], lty = llty[i])       }     }   })}"},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"section","dir":"Articles","previous_headings":"","what":"The `SIS` model for malaria","title":"The `SIS` model for malaria","text":"SIS model, now called, simple compartmental model, first introduced Ross. included exDE base model.","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"variables","dir":"Articles","previous_headings":"","what":"Variables","title":"The `SIS` model for malaria","text":"\\(\\) density infected humans \\(H\\) density humans","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"parameters","dir":"Articles","previous_headings":"","what":"Parameters","title":"The `SIS` model for malaria","text":"\\(r\\) rate infections clear \\(b\\) fraction bites infective mosquitoes transmit parasites cause infection. \\(c\\) fraction bites infectious human infect mosquito.","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"dynamics","dir":"Articles","previous_headings":"","what":"Dynamics","title":"The `SIS` model for malaria","text":"model defined herein defined two parts. model exposure infection (.e. conversion eir foi), assume fraction infective bites cause infection \\(b\\). dynamics given : \\[ \\frac{dI}{dt} = h (H-)-rI \\]","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"terms","dir":"Articles","previous_headings":"","what":"Terms","title":"The `SIS` model for malaria","text":"Net Infectiousness True prevalence : \\[x = \\frac{X}{H}.\\] implementation, net infectiousness (NI) linearly proportional prevalence: \\[c x.\\] Human Transmitting Capacity exposure, human remain infected \\(1/r\\) days, transmitting probability \\(c\\) : \\[c/r\\] Exposure Infection model family, immunity. model assumes constant fraction infectious bites, \\(b\\), cause infection.","code":""},{"path":"https://dd-harp.github.io/mobwork/articles/Xmod-SIS.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"The `SIS` model for malaria","text":"Ross R. Report Prevention Malaria Mauritius. London: Waterlow; 1908. Ross R. Prevention Malaria. 2nd ed. London: John Murray; 1911. Smith DL, Battle KE, Hay SI, Barker CM, Scott TW, McKenzie FE. Ross, Macdonald, theory dynamics control mosquito-transmitted pathogens. PLoS Pathog. 2012;8: e1002588. doi:10.1371/journal.ppat.1002588","code":""},{"path":"https://dd-harp.github.io/mobwork/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"David L Smith. Maintainer.","code":""},{"path":"https://dd-harp.github.io/mobwork/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Smith DL (2024). mobwork: Enhanced functionality exDE. R package version 0.1.0, https://dd-harp.github.io/mobwork/.","code":"@Manual{,   title = {mobwork: Enhanced functionality for exDE},   author = {David L Smith},   year = {2024},   note = {R package version 0.1.0},   url = {https://dd-harp.github.io/mobwork/}, }"},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/index.html","id":"what-is-mobwork","dir":"","previous_headings":"","what":"What is mobwork?","title":"Enhanced functionality for exDE ","text":"mobwork developed supplement exDE.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of human population — F_H.SEIR","title":"Size of human population — F_H.SEIR","text":"Implements F_H SEIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of human population — F_H.SEIR","text":"","code":"# S3 method for SEIR F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of human population — F_H.SEIR","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of human population — F_H.SEIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of human population — F_H.SIR","title":"Size of human population — F_H.SIR","text":"Implements F_H SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of human population — F_H.SIR","text":"","code":"# S3 method for SIR F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of human population — F_H.SIR","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of human population — F_H.SIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_H.garki","title":"Size of effective infectious human population — F_H.garki","text":"Implements F_H SIS model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_H.garki","text":"","code":"# S3 method for garki F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_H.garki","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_H.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_H.garki","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.SEIR","title":"Size of effective infectious human population — F_X.SEIR","text":"Implements F_X SEIR 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human population — F_X.SIR","title":"Size of effective infectious human population — F_X.SIR","text":"Implements F_X SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.SIR","text":"","code":"# S3 method for SIR F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.SIR","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.SIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.garki","title":"Size of effective infectious human population — F_X.garki","text":"Implements F_X Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.garki","text":"","code":"# S3 method for garki F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.garki","text":"t current simulation time y state vector pars list host species 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i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.SIR","text":"y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.SIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.garki","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"Implements F_b Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"","code":"# S3 method for garki F_b(y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_b.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.garki","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"Implements F_eggs RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"","code":"# S3 method for RMG F_eggs(t, y, pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of eggs laid by adult mosquitoes — F_eggs.RMG","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqM.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Blood feeding rate of the infective mosquito population — F_fqM.RMG","title":"Blood feeding rate of the infective mosquito population — F_fqM.RMG","text":"Implements F_fqM RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqM.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blood feeding rate of the infective mosquito population — F_fqM.RMG","text":"","code":"# S3 method for RMG F_fqM(t, y, pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqM.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blood feeding rate of the infective mosquito population — F_fqM.RMG","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqM.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blood feeding rate of the infective mosquito population — F_fqM.RMG","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"Implements F_fqZ RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"","code":"# S3 method for RMG F_fqZ(t, y, pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blood feeding rate of the infective mosquito population — F_fqZ.RMG","text":"t current simulation time y state vector pars list s species 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list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the SEIR model — HTC.SEIR","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the SIR model — HTC.SIR","title":"Compute the HTC for the SIR model — HTC.SIR","text":"Implements HTC SIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the SIR model — HTC.SIR","text":"","code":"# S3 method for SIR HTC(pars)"},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the SIR model — HTC.SIR","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the SIR model — HTC.SIR","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the garki model — HTC.garki","title":"Compute the HTC for the garki model — HTC.garki","text":"Implements HTC garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the garki model — HTC.garki","text":"","code":"# S3 method for garki HTC(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the garki model — HTC.garki","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/HTC.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the garki model — HTC.garki","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"Implements MBionomics RMG model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"","code":"# S3 method for RMG MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/MBionomics.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RMG","text":"named list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.RMG","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"Implements dMYZdt RMG ODE model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"","code":"# S3 method for RMG dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.RMG","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SEIR","title":"Derivatives for human population — dXdt.SEIR","text":"Implements dXdt SEIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SEIR","text":"","code":"# S3 method for SEIR dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SEIR","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SEIR","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SEIRdX","title":"Derivatives for human population — dXdt.SEIRdX","text":"Implements dXdt SEIR model, demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SEIRdX","text":"","code":"# S3 method for SEIRdX dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SEIRdX","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SEIRdX","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SEIRdXdH","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"Implements dXdt SEIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"","code":"# S3 method for SEIRdXdH dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SEIRdXdH","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIR","title":"Derivatives for human population — dXdt.SIR","text":"Implements dXdt SIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIR","text":"","code":"# S3 method for SIR dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIR","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIR","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIRdX","title":"Derivatives for human population — dXdt.SIRdX","text":"Implements dXdt SIR model, demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIRdX","text":"","code":"# S3 method for SIRdX dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIRdX","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIRdX","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIRdXdH","title":"Derivatives for human population — dXdt.SIRdXdH","text":"Implements dXdt SIR model demography.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIRdXdH","text":"","code":"# S3 method for SIRdXdH dXdt(t, y, pars, FoI)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIRdXdH","text":"t current simulation time y state vector pars list FoI vector giving per-capita force infection strata","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.SIRdXdH.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIRdXdH","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.garki","title":"Derivatives for human population — dXdt.garki","text":"Implements dXdt Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.garki","text":"","code":"# S3 method for garki dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.garki","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/dXdt.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.garki","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.RMG","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"Implements get_inits_MYZ RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"","code":"# S3 method for RMG get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SEIR","title":"Return initial values as a vector — get_inits_X.SEIR","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SEIR","text":"","code":"# S3 method for SEIR get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SEIR","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SIR","title":"Return initial values as a vector — get_inits_X.SIR","text":"method dispatches type pars$Xpar","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SIR","text":"","code":"# S3 method for SIR get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SIR","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector for the Garki model — get_inits_X.garki","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"","code":"# S3 method for garki get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/get_inits_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector for the Garki model — get_inits_X.garki","text":"named list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the EIR vs. time — lines_EIR","title":"Add lines for the EIR vs. time — lines_EIR","text":"Add lines EIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the EIR vs. time — lines_EIR","text":"","code":"lines_EIR(terms, model, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the EIR vs. time — lines_EIR","text":"terms list outputs exDE::parse_deout() model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","text":"","code":"# S3 method for RM lines_M(MYZ, model, clrs = \"darkblue\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RM","text":"MYZ list outputs exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","text":"","code":"# S3 method for RMG lines_M(MYZ, model, clrs = \"darkblue\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_M.RMG","text":"MYZ list outputs exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: add to a plot for mosquito population density — lines_M","title":"Basic plotting: add to a plot for mosquito population density — lines_M","text":"Basic plotting: add plot mosquito population density","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: add to a plot for mosquito population density — lines_M","text":"","code":"lines_M(MYZ, model, clrs)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: add to a plot for mosquito population density — lines_M","text":"MYZ list outputs exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","text":"","code":"lines_PR(terms, model, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_PR","text":"terms list outputs exDE::parse_deout() model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) specifies lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","text":"","code":"# S3 method for SIS lines_X(XH, model, clrs = \"black\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_X.SIS","text":"XH list exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","title":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","text":"Basic plotting: add outputs plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","text":"","code":"lines_X(XH, model, clrs = \"black\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: add outputs to a plot for models of human infection and immunity — lines_X","text":"XH list exDE::parse_deout model list specifying model clrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","text":"","code":"# S3 method for RM lines_YZ(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RM","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","text":"Add orbits SIS model plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","text":"","code":"# S3 method for RMG lines_YZ(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add the orbits for the SIS model to a plot for models of human infection and immunity — lines_YZ.RMG","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","title":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","text":"Basic plotting: add lines density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","text":"","code":"lines_YZ(MYZ, model, Yclrs, Zclrs)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: add lines for the density of infected and infective mosquitoes — lines_YZ","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction infected and infective for the ","title":"Add lines for the fraction infected and infective for the ","text":"Add lines fraction infected infective \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction infected and infective for the ","text":"","code":"# S3 method for RM lines_YZ_fracs(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction infected and infective for the ","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction infected and infective for the ","title":"Add lines for the fraction infected and infective for the ","text":"Add lines fraction infected infective \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction infected and infective for the ","text":"","code":"# S3 method for RMG lines_YZ_fracs(MYZ, model, Yclrs = \"purple\", Zclrs = \"darkred\")"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction infected and infective for the ","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","title":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","text":"Add lines fraction mosquitoes infected infective","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","text":"","code":"lines_YZ_fracs(MYZ, model, Yclrs, Zclrs)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction of mosquitoes infected and infective — lines_YZ_fracs","text":"MYZ list output exDE::parse_deout model list specifying model Yclrs list colors Zclrs list colors","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the aEIR vs. time — lines_aEIR","title":"Add lines for the aEIR vs. time — lines_aEIR","text":"Add lines aEIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the aEIR vs. time — lines_aEIR","text":"","code":"lines_aEIR(terms, model, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the aEIR vs. time — lines_aEIR","text":"terms list outputs exDE::parse_deout() model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirVpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","title":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","text":"Add lines EIR(t) vs. PR(t)","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirVpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","text":"","code":"lines_eirVpr(terms, pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirVpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the EIR(t) vs. the PR(t) — lines_eirVpr","text":"terms list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs character vector colors llty integer (integers) specifies lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for an eir-pr scaling relationship — lines_eirpr","title":"Add lines for an eir-pr scaling relationship — lines_eirpr","text":"Add lines eir-pr scaling relationship","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for an eir-pr scaling relationship — lines_eirpr","text":"","code":"lines_eirpr(pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/lines_eirpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for an eir-pr scaling relationship — lines_eirpr","text":"pars list e.g.,  generated exDE::xde_setup() defines model exDE clrs character vector colors llty list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"Make inits RMG adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"","code":"make_MYZinits_RMG(   nPatches,   MYZopts = list(),   U0 = 5,   Gu0 = 1,   Y0 = 1,   Gy0 = 1,   Z0 = 1,   Gz0 = 1 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"nPatches number patches model MYZopts list values overwrites defaults U0 total uninfected, gravid mosquito density patch Gu0 total uninfected, gravid mosquito density patch Y0 infected, gravid mosquito density patch Gy0 infected, gravid mosquito density patch Z0 infectious, gravid mosquito density patch Gz0 infectious, gravid mosquito density patch","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZinits_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RMG adult mosquito model — make_MYZinits_RMG","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RMG","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RMG","text":"Make parameters RM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RMG","text":"","code":"make_MYZpar_RMG(   nPatches,   MYZopts = list(),   EIPmod,   calK,   g = 1/12,   sigma = 1/8,   f = 0.3,   q = 0.95,   nu = 1,   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RMG","text":"nPatches number patches, integer MYZopts list values overwrites defaults EIPmod list defines EIP model calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_MYZpar_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RMG","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"Make initial values SEIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"","code":"make_Xinits_SEIR(   nStrata,   Xopts = list(),   H0 = NULL,   S0 = NULL,   E0 = 0,   I0 = 1,   R0 = 0 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"nStrata number strata model Xopts list overwrite defaults H0 initial human population density S0 initial values parameter S E0 initial values parameter E I0 initial values parameter R0 initial values parameter R","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SEIR human model, with defaults — make_Xinits_SEIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"Make initial values SIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"","code":"make_Xinits_SIR(nStrata, Xopts = list(), H0 = NULL, S0 = NULL, I0 = 1, R0 = 0)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"nStrata number strata model Xopts list overwrite defaults H0 initial human population density S0 initial values parameter S I0 initial values parameter R0 initial values parameter R","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SIR human model, with defaults — make_Xinits_SIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"Make inits Garki human model. Note variables sum H, initial value x1 set. values passed order presented original paper.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"","code":"make_Xinits_garki(   nStrata,   Xopts = list(),   H0 = NULL,   x1 = NULL,   x2 = 0,   y1 = 0,   y2 = 0,   y3 = 0,   x3 = 0,   x4 = 0 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"nStrata number population strata Xopts list values override default values H0 numeric initial value total human population density x1 numeric initial value variable x1 x2 numeric initial value variable x2 y1 numeric initial value variable y1 y2 numeric initial value variable y2 y3 numeric initial value variable y3 x3 numeric initial value variable x3 x4 numeric initial value variable x4","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xinits_garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for Garki human model. Note that the variables should sum up to H, so the initial value of x1 is not set. The values are passed in the same order as they are presented in the original paper. — make_Xinits_garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"Make parameters SEIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"","code":"make_Xpar_SEIR(nStrata, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"nStrata number population strata Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SEIR human model, with defaults — make_Xpar_SEIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"Make parameters SIR human model, defaults","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"","code":"make_Xpar_SIR(nStrata, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"nStrata number population strata Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIR human model, with defaults — make_Xpar_SIR","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Garki human model — make_Xpar_garki","title":"Make parameters for Garki human model — make_Xpar_garki","text":"Make parameters Garki human model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Garki human model — make_Xpar_garki","text":"","code":"make_Xpar_garki(   nStrata,   Xopts = list(),   b = 0.55,   r1 = 0.0023,   r2 = 0.023,   nu = 1/15,   alpha1 = 0.002,   alpha2 = 0.00019,   q1 = 0.7,   q2 = 0.5,   q3 = 0.3,   mu = 1/65/365 )"},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Garki human model — make_Xpar_garki","text":"nStrata number population strata Xopts list b transmission probability (efficiency) mosquito human r1 numeric recovery rate non-immunes r2 numericrecovery rate partially immmunes nu numericincubation period alpha1 numeric rate losing infectivity alpha2 numeric rate acquiring immunity q1 numeric detection y1 q2 numeric detection y2 q3 numeric detection y3 mu numeric death rate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_Xpar_garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Garki human model — make_Xpar_garki","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"Implements make_indices_MYZ RMG model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"","code":"# S3 method for RMG make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SEIR","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"Implements make_indices_X SEIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"","code":"# S3 method for SEIR make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SIR","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"Implements make_indices_X SIR model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"","code":"# S3 method for SIR make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.garki","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"Implements make_indices_X Garki model.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"","code":"# S3 method for garki make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_indices_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"Make inits RMG adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"","code":"make_inits_MYZ_RMG(pars, U0, Gu0, Y0, Gy0, Z0, Gz0)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"pars list U0 total mosquito density patch Gu0 total gravid uninfected mosquito density patch Y0 infected mosquito density patch Gy0 total gravid infected mosquito density patch Z0 infectious mosquito density patch Gz0 total gravid infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_inits_MYZ_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RMG adult mosquito model — make_inits_MYZ_RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"Make parameters RMG ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"","code":"make_parameters_MYZ_RMG(pars, g, sigma, f, q, nu, eggsPerBatch, eip, calK)"},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"pars list g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition eip length extrinsic incubation period calK mosquito dispersal matrix dimensions nPatches nPatches","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/make_parameters_MYZ_RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RMG ODE adult mosquito model — make_parameters_MYZ_RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/mobwork-package.html","id":null,"dir":"Reference","previous_headings":"","what":"mobwork: Enhanced functionality for exDE — mobwork-package","title":"mobwork: Enhanced functionality for exDE — mobwork-package","text":"(maybe one line) Use four spaces indenting paragraphs within Description.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"Implements parse_deout_MYZ RMG model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"","code":"# S3 method for RMG parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the RMG model — parse_deout_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"Implements parse_deout_X SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"","code":"# S3 method for SEIR parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SEIR model — parse_deout_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"Implements parse_deout_X SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"","code":"# S3 method for SIR parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SIR model — parse_deout_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"Implements parse_deout_X Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"","code":"# S3 method for garki parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/parse_deout_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the Garki model — parse_deout_X.garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the EIR vs. time — plot_EIR","title":"Plot the EIR vs. time — plot_EIR","text":"Plot EIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the EIR vs. time — plot_EIR","text":"","code":"plot_EIR(model, clrs = \"black\", llty = 1, stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the EIR vs. time — plot_EIR","text":"model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add logical plot axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RM plot_M(model, clrs = \"darkblue\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RMG plot_M(model, clrs = \"darkblue\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density — plot_M","title":"Basic plotting: plot mosquito population density — plot_M","text":"Basic plotting: plot mosquito population density","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density — plot_M","text":"","code":"plot_M(model, clrs, stable, add)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density — plot_M","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the true PR. — plot_PR","title":"Basic plotting: plot the true PR. — plot_PR","text":"Basic plotting: plot true PR.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the true PR. — plot_PR","text":"","code":"plot_PR(model, clrs = \"black\", llty = 1, stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the true PR. — plot_PR","text":"model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) specifies lty plotting stable logical set FALSE orbits TRUE stable_orbits add logical plot axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","title":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","text":"Basic plotting: plot density infected humans SIS model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","text":"","code":"# S3 method for SIS plot_X(model, clrs = \"black\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the density of infected humans for an SIS model — plot_X.SIS","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: default plot for models of human infection and immunity — plot_X","title":"Basic plotting: default plot for models of human infection and immunity — plot_X","text":"Basic plotting: default plot models human infection immunity","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: default plot for models of human infection and immunity — plot_X","text":"","code":"plot_X(model, clrs = \"black\", stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: default plot for models of human infection and immunity — plot_X","text":"model list specifying model clrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RM plot_YZ(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot mosquito population density for the ","title":"Basic plotting: plot mosquito population density for the ","text":"Basic plotting: plot mosquito population density \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot mosquito population density for the ","text":"","code":"# S3 method for RMG plot_YZ(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot mosquito population density for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","title":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","text":"Basic plotting: plot density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","text":"","code":"plot_YZ(model, Yclrs, Zclrs, stable, add)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the density of infected and infective mosquitoes — plot_YZ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the fraction infected and infective for the ","title":"Basic plotting: plot the fraction infected and infective for the ","text":"Basic plotting: plot fraction infected infective \"RM\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the fraction infected and infective for the ","text":"","code":"# S3 method for RM plot_YZ_fracs(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the fraction infected and infective for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the fraction infected and infective for the ","title":"Basic plotting: plot the fraction infected and infective for the ","text":"Basic plotting: plot fraction infected infective \"RMG\" model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the fraction infected and infective for the ","text":"","code":"# S3 method for RMG plot_YZ_fracs(   model,   Yclrs = \"purple\",   Zclrs = \"darkred\",   stable = FALSE,   add = FALSE )"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the fraction infected and infective for the ","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","title":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","text":"Basic plotting: plot proportion mosquitoes infected infective.","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","text":"","code":"plot_YZ_fracs(model, Yclrs, Zclrs, stable, add)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting: plot the proportion of mosquitoes that are infected and infective. — plot_YZ_fracs","text":"model list specifying model Yclrs list colors Zclrs list colors stable logical add logical","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"PLot the aEIR vs. time — plot_aEIR","title":"PLot the aEIR vs. time — plot_aEIR","text":"PLot aEIR vs. time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PLot the aEIR vs. time — plot_aEIR","text":"","code":"plot_aEIR(model, clrs = \"black\", llty = 1, stable = FALSE, add = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PLot the aEIR vs. time — plot_aEIR","text":"model list e.g.,  generated exDE::xde_setup() defines model exDE clrs list colors plotting llty integer (integers) set lty plotting stable logical set FALSE orbits TRUE stable_orbits add logical plot axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirVpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","title":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","text":"Plot EIR(t) vs. PR(t)","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirVpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","text":"","code":"plot_eirVpr(pars, clrs = \"black\", llty = 1, stable = FALSE, add_axes = TRUE)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirVpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot EIR(t) vs. the PR(t) — plot_eirVpr","text":"pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs character vector colors llty integer specifies lty plotting stable logical set FALSE orbits TRUE stable_orbits add_axes logical plot add_axes FALSE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirpr.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the eir-pr scaling relationship — plot_eirpr","title":"Plot the eir-pr scaling relationship — plot_eirpr","text":"Plot eir-pr scaling relationship","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirpr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the eir-pr scaling relationship — plot_eirpr","text":"","code":"plot_eirpr(pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/plot_eirpr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the eir-pr scaling relationship — plot_eirpr","text":"pars list e.g.,  generated exDE::xde_setup() defines model exDE clrs character vector colors llty list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/pr2Lambda.html","id":null,"dir":"Reference","previous_headings":"","what":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","title":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","text":"takes model uses XH component define eirpr relationship using xde_scaling_eir calls xde_scaling_lambda","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/pr2Lambda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","text":"","code":"pr2Lambda(pr, model, constrain = TRUE)"},{"path":"https://dd-harp.github.io/mobwork/reference/pr2Lambda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Using the eirpr matrix and a RM model, convert pr to Lambda — pr2Lambda","text":"pr vector model list defines exDE model (e.g.,  generated xde_setup()) constrain logical, TRUE set negative values zero","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the RMG model — setup_MYZ.RMG","title":"Setup the RMG model — setup_MYZ.RMG","text":"Implements setup_MYZ RMG model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the RMG model — setup_MYZ.RMG","text":"","code":"# S3 method for RMG setup_MYZ(pars, MYZname, nPatches = 1, MYZopts = list(), calK = diag(1))"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the RMG model — setup_MYZ.RMG","text":"pars list MYZname character string nPatches numeric value (integer), number patches MYZopts list calK matrix","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the RMG model — setup_MYZ.RMG","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZinits.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup initial values for the RMG model — setup_MYZinits.RMG","title":"Setup initial values for the RMG model — setup_MYZinits.RMG","text":"Implements setup_MYZinits RM model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZinits.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup initial values for the RMG model — setup_MYZinits.RMG","text":"","code":"# S3 method for RMG setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZinits.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup initial values for the RMG model — setup_MYZinits.RMG","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZinits.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup initial values for the RMG model — setup_MYZinits.RMG","text":"list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZpar.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the RMG model — setup_MYZpar.RMG","title":"Setup MYZpar for the RMG model — setup_MYZpar.RMG","text":"Implements setup_MYZpar RM model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZpar.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the RMG model — setup_MYZpar.RMG","text":"","code":"# S3 method for RMG setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod, calK)"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZpar.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the RMG model — setup_MYZpar.RMG","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_MYZpar.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the RMG model — setup_MYZpar.RMG","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SEIR — setup_X.SEIR","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"Implements setup_X SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"","code":"# S3 method for SEIR setup_X(pars, Xname, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"pars list Xname character string Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SEIR — setup_X.SEIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIR — setup_X.SIR","title":"Setup Xpar.SIR — setup_X.SIR","text":"Implements setup_X SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIR — setup_X.SIR","text":"","code":"# S3 method for SIR setup_X(pars, Xname, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIR — setup_X.SIR","text":"pars list Xname character string Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIR — setup_X.SIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.Garki — setup_X.garki","title":"Setup Xpar.Garki — setup_X.garki","text":"Implements setup_X Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.Garki — setup_X.garki","text":"","code":"# S3 method for garki setup_X(pars, Xname, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.Garki — setup_X.garki","text":"pars list Xname character string Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.Garki — setup_X.garki","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.SEIR — setup_Xinits.SEIR","title":"Setup Xinits.SEIR — setup_Xinits.SEIR","text":"Implements setup_Xinits SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.SEIR — setup_Xinits.SEIR","text":"","code":"# S3 method for SEIR setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.SEIR — setup_Xinits.SEIR","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.SEIR — setup_Xinits.SEIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.SIR — setup_Xinits.SIR","title":"Setup Xinits.SIR — setup_Xinits.SIR","text":"Implements setup_Xinits SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.SIR — setup_Xinits.SIR","text":"","code":"# S3 method for SIR setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.SIR — setup_Xinits.SIR","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.SIR — setup_Xinits.SIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.garki — setup_Xinits.garki","title":"Setup Xinits.garki — setup_Xinits.garki","text":"Implements setup_Xinits garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.garki — setup_Xinits.garki","text":"","code":"# S3 method for garki setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.garki — setup_Xinits.garki","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xinits.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.garki — setup_Xinits.garki","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SEIR — setup_Xpar.SEIR","title":"Setup Xpar.SEIR — setup_Xpar.SEIR","text":"Implements setup_Xpar SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SEIR — setup_Xpar.SEIR","text":"","code":"# S3 method for SEIR setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SEIR — setup_Xpar.SEIR","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SEIR — setup_Xpar.SEIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIR — setup_Xpar.SIR","title":"Setup Xpar.SIR — setup_Xpar.SIR","text":"Implements setup_Xpar SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIR — setup_Xpar.SIR","text":"","code":"# S3 method for SIR setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIR — setup_Xpar.SIR","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIR — setup_Xpar.SIR","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.garki — setup_Xpar.garki","title":"Setup Xpar.garki — setup_Xpar.garki","text":"Implements setup_Xpar garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.garki — setup_Xpar.garki","text":"","code":"# S3 method for garki setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.garki — setup_Xpar.garki","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/setup_Xpar.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.garki — setup_Xpar.garki","text":"list vector","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"Split stratum two strata, assigning fraction p new biting weight multiplied factor fac compared old one. biting weight remaining 1-p gets new factor 1/fac","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"","code":"# S3 method for SIS split_stratum_by_biting(pars, i, p, fac)"},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"pars list defining model stratum split p fraction gets multiplied fac fac factor","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a stratum into two strata, assigning a fraction p a new biting weight that is multiplied by a factor fac compared with the old one. The biting weight for the remaining 1-p gets a new factor 1/fac — split_stratum_by_biting.SIS","text":"pars list list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a stratum into two strata, assigning — split_stratum_by_biting","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"Split stratum two strata, assigning","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"","code":"split_stratum_by_biting(pars, i, p, fac)"},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"pars list defining model stratum split p fraction higher exposure stratum fac factor increase","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a stratum into two strata, assigning — split_stratum_by_biting","text":"pars list","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/ssMYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","title":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","text":"function computes several quantities require","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/ssMYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","text":"","code":"ssMYZ(model)"},{"path":"https://dd-harp.github.io/mobwork/reference/ssMYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the MYZss object for xde_scaling_lambda — ssMYZ","text":"model list defines exDE model (e.g.,  generated xde_setup())","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"Make inits RMG adult mosquito model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"","code":"# S3 method for RMG update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_MYZ.RMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RMG adult mosquito model — update_inits_MYZ.RMG","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"Update inits SEIR human model vector states","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"","code":"# S3 method for SEIR update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SEIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SEIR human model from a vector of states — update_inits_X.SEIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"Update inits SIR human model vector states","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"","code":"# S3 method for SIR update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.SIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SIR human model from a vector of states — update_inits_X.SIR","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Xinits for the Garki model — update_inits_X.garki","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"Update Xinits Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"","code":"# S3 method for garki update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/update_inits_X.garki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Xinits for the Garki model — update_inits_X.garki","text":"none","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2ni.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert eir to ni — xde_eir2ni","title":"Convert eir to ni — xde_eir2ni","text":"Use outputs$eirpr table interpolate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2ni.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert eir to ni — xde_eir2ni","text":"","code":"xde_eir2ni(eir, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2ni.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert eir to ni — xde_eir2ni","text":"eir vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2pr.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert eir to pr — xde_eir2pr","title":"Convert eir to pr — xde_eir2pr","text":"Use outputs$eirpr table interpolate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2pr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert eir to pr — xde_eir2pr","text":"","code":"xde_eir2pr(eir, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_eir2pr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert eir to pr — xde_eir2pr","text":"eir vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","text":"Add lines density infected individuals SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","text":"","code":"# S3 method for SEIR xde_lines_X(XH, pars, clrs = c(\"darkgreen\", \"darkred\", \"darkblue\"), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X.SEIR","text":"XH list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","text":"Add lines density infected individuals SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","text":"","code":"# S3 method for SIR xde_lines_X(XH, pars, clrs = c(\"darkred\", \"darkblue\"), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X.SIR","text":"XH list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","text":"Add lines density infected individuals Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","text":"","code":"# S3 method for garki xde_lines_X(XH, pars, clrs = viridisLite::turbo(7), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X.garki","text":"XH list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs character vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X_SEIR","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X_SEIR","text":"Add lines density infected individuals SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X_SEIR","text":"","code":"xde_lines_X_SEIR(   XH,   pars,   clrs = c(\"black\", \"darkgreen\", \"darkred\", \"darkblue\"),   llty = 1 )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SEIR model — xde_lines_X_SEIR","text":"XH list outputs parse_deout_X_SIS pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIR model — xde_lines_X_SIR","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X_SIR","text":"Add lines density infected individuals SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X_SIR","text":"","code":"xde_lines_X_SIR(XH, pars, clrs = c(\"black\", \"darkred\", \"darkblue\"), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIR model — xde_lines_X_SIR","text":"XH list outputs parse_deout_X_SIS pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the Garki model — xde_lines_X_garki","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X_garki","text":"Add lines density infected individuals Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X_garki","text":"","code":"xde_lines_X_garki(XH, pars, clrs = viridisLite::turbo(7), llty = 1)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_lines_X_garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the Garki model — xde_lines_X_garki","text":"XH list outputs parse_deout_X_SIS pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","title":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","text":"Plot density infected individuals SEIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","text":"","code":"# S3 method for SEIR xde_plot_X(   pars,   i,   clrs = c(\"black\", \"darkgreen\", \"darkred\", \"darkblue\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SEIR model — xde_plot_X.SEIR","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","title":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","text":"Plot density infected individuals SIR model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","text":"","code":"# S3 method for SIR xde_plot_X(   pars,   i,   clrs = c(\"black\", \"darkred\", \"darkblue\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.SIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SIR model — xde_plot_X.SIR","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.garki.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","title":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","text":"Plot density infected individuals Garki model","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.garki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","text":"","code":"# S3 method for garki xde_plot_X(   pars,   i,   clrs = viridisLite::turbo(7),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_plot_X.garki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the Garki model — xde_plot_X.garki","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2eir.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to eir — xde_pr2eir","title":"Convert pr to eir — xde_pr2eir","text":"Use outputs$eirpr table convert set pr values eir values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to eir — xde_pr2eir","text":"","code":"xde_pr2eir(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to eir — xde_pr2eir","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2lambda.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to lambda — xde_pr2lambda","title":"Convert pr to lambda — xde_pr2lambda","text":"Use outputs$lambdapr table convert set pr values lambda values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2lambda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to lambda — xde_pr2lambda","text":"","code":"xde_pr2lambda(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2lambda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to lambda — xde_pr2lambda","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2m.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to mosquito density — xde_pr2m","title":"Convert pr to mosquito density — xde_pr2m","text":"Use outputs$eirpr table convert set pr values scaled mosquito density values","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2m.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to mosquito density — xde_pr2m","text":"","code":"xde_pr2m(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2m.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to mosquito density — xde_pr2m","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2ni.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert pr to ni — xde_pr2ni","title":"Convert pr to ni — xde_pr2ni","text":"Use outputs$eirpr table interpolate","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2ni.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert pr to ni — xde_pr2ni","text":"","code":"xde_pr2ni(pr, model, extend = FALSE)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_pr2ni.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert pr to ni — xde_pr2ni","text":"pr vector model list extend logical option determine whether extend outside range","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct an eirpr object for an arbitary model — xde_scaling","title":"Construct an eirpr object for an arbitary model — xde_scaling","text":"takes model uses XH component define eirpr relationship using xde_scaling_eir calls xde_scaling_lambda","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct an eirpr object for an arbitary model — xde_scaling","text":"","code":"xde_scaling(model, N = 25, F_eir = NULL)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct an eirpr object for an arbitary model — xde_scaling","text":"model list defines exDE model (e.g.,  generated xde_setup()) N size mesh aEIR F_eir function compute EIR function time","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_Z.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eir-pr scaling relationships — xde_scaling_Z","title":"Compute eir-pr scaling relationships — xde_scaling_Z","text":"function computes average annual values eir, pr, interesting terms returns table. computed model class \"human\"","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_Z.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eir-pr scaling relationships — xde_scaling_Z","text":"","code":"xde_scaling_Z(model, N = 25)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_Z.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eir-pr scaling relationships — xde_scaling_Z","text":"model list defines exDE model generated xde_setup_human() N integer, size mesh aEIR","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_eir.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eir-pr scaling relationships — xde_scaling_eir","title":"Compute eir-pr scaling relationships — xde_scaling_eir","text":"function computes average annual values eir, pr, interesting terms returns table. computed model class \"cohort\"","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eir-pr scaling relationships — xde_scaling_eir","text":"","code":"xde_scaling_eir(model, N = 25)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eir-pr scaling relationships — xde_scaling_eir","text":"model list defines exDE model generated xde_setup_cohort() N integer","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_lambda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","title":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","text":"function computes m lambda output one xde_scaling_eir xde_scaling_Z.  outputs attached eirpr","code":""},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_lambda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","text":"","code":"xde_scaling_lambda(model)"},{"path":"https://dd-harp.github.io/mobwork/reference/xde_scaling_lambda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute lambda from an eirpr object using the Ross-Macdonald model — xde_scaling_lambda","text":"model list defines exDE model (e.g.,  generated xde_setup())","code":""}]
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index cc411e7..d633156 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -18,6 +18,15 @@
   
     https://dd-harp.github.io/mobwork/index.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/F_H.SEIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/F_H.SIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/F_H.garki.html
+  
   
     https://dd-harp.github.io/mobwork/reference/F_X.SEIR.html
   
@@ -39,6 +48,9 @@
   
     https://dd-harp.github.io/mobwork/reference/F_eggs.RMG.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/F_fqM.RMG.html
+  
   
     https://dd-harp.github.io/mobwork/reference/F_fqZ.RMG.html
   
@@ -66,12 +78,18 @@
   
     https://dd-harp.github.io/mobwork/reference/dMYZdt.RMG.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/dXdt.SEIR.html
+  
   
     https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdX.html
   
   
     https://dd-harp.github.io/mobwork/reference/dXdt.SEIRdXdH.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/dXdt.SIR.html
+  
   
     https://dd-harp.github.io/mobwork/reference/dXdt.SIRdX.html
   
@@ -255,6 +273,12 @@
   
     https://dd-harp.github.io/mobwork/reference/setup_MYZ.RMG.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/setup_MYZinits.RMG.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/setup_MYZpar.RMG.html
+  
   
     https://dd-harp.github.io/mobwork/reference/setup_X.SEIR.html
   
@@ -264,6 +288,24 @@
   
     https://dd-harp.github.io/mobwork/reference/setup_X.garki.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/setup_Xinits.SEIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/setup_Xinits.SIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/setup_Xinits.garki.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/setup_Xpar.SEIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/setup_Xpar.SIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/setup_Xpar.garki.html
+  
   
     https://dd-harp.github.io/mobwork/reference/split_stratum_by_biting.SIS.html
   
@@ -300,6 +342,15 @@
   
     https://dd-harp.github.io/mobwork/reference/xde_lines_X.garki.html
   
+  
+    https://dd-harp.github.io/mobwork/reference/xde_lines_X_SEIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/xde_lines_X_SIR.html
+  
+  
+    https://dd-harp.github.io/mobwork/reference/xde_lines_X_garki.html
+  
   
     https://dd-harp.github.io/mobwork/reference/xde_plot_X.SEIR.html
   
diff --git a/man/lines_eirVpr.Rd b/man/lines_eirVpr.Rd
index 300eb17..3af6f58 100644
--- a/man/lines_eirVpr.Rd
+++ b/man/lines_eirVpr.Rd
@@ -4,12 +4,14 @@
 \alias{lines_eirVpr}
 \title{Add lines for the EIR(t) \emph{vs.} the PR(t)}
 \usage{
-lines_eirVpr(terms, pars, clrs = "black", llty = 1)
+lines_eirVpr(eir, pr, nStrata, clrs = "black", llty = 1)
 }
 \arguments{
-\item{terms}{a \link{list} with the outputs of \code{exDE::parse_deout()}}
+\item{eir}{the daily EIR}
 
-\item{pars}{a \link{list} that defines an \code{exDE} model (\emph{e.g.},  generated by \code{exDE::xde_setup()})}
+\item{pr}{the parasite rate}
+
+\item{nStrata}{the number of population strata}
 
 \item{clrs}{a \link{character} vector of colors}
 
diff --git a/man/plot_eirVpr.Rd b/man/plot_eirVpr.Rd
index 48cafdd..c072619 100644
--- a/man/plot_eirVpr.Rd
+++ b/man/plot_eirVpr.Rd
@@ -4,11 +4,20 @@
 \alias{plot_eirVpr}
 \title{Plot EIR(t) \emph{vs.} the PR(t)}
 \usage{
-plot_eirVpr(pars, clrs = "black", llty = 1, stable = FALSE, add_axes = TRUE)
+plot_eirVpr(
+  pars,
+  i = 1,
+  clrs = "black",
+  llty = 1,
+  stable = FALSE,
+  add_axes = TRUE
+)
 }
 \arguments{
 \item{pars}{a \link{list} that defines an \code{exDE} model (\emph{e.g.},  generated by \code{exDE::xde_setup()})}
 
+\item{i}{the host species index}
+
 \item{clrs}{a \link{character} vector of colors}
 
 \item{llty}{an \link{integer} that specifies \code{lty} for plotting}
diff --git a/man/split_stratum_by_biting.Rd b/man/split_stratum_by_biting.Rd
index 3ac44a7..cdbc866 100644
--- a/man/split_stratum_by_biting.Rd
+++ b/man/split_stratum_by_biting.Rd
@@ -4,12 +4,14 @@
 \alias{split_stratum_by_biting}
 \title{Split a stratum into two strata, assigning}
 \usage{
-split_stratum_by_biting(pars, i, p, fac)
+split_stratum_by_biting(pars, i, j, p, fac)
 }
 \arguments{
 \item{pars}{a \link{list} defining a model}
 
-\item{i}{the stratum to split}
+\item{i}{the host species index}
+
+\item{j}{the stratum to split}
 
 \item{p}{the fraction in the higher exposure stratum}
 
diff --git a/man/split_stratum_by_biting.SIS.Rd b/man/split_stratum_by_biting.SIS.Rd
index b1b7968..94a1958 100644
--- a/man/split_stratum_by_biting.SIS.Rd
+++ b/man/split_stratum_by_biting.SIS.Rd
@@ -4,12 +4,14 @@
 \alias{split_stratum_by_biting.SIS}
 \title{Split a stratum into two strata, assigning a fraction \code{p} a new biting weight that is multiplied by a factor \code{fac} compared with the old one. The biting weight for the remaining \code{1-p} gets a new factor \code{1/fac}}
 \usage{
-\method{split_stratum_by_biting}{SIS}(pars, i, p, fac)
+\method{split_stratum_by_biting}{SIS}(pars, i, j, p, fac)
 }
 \arguments{
 \item{pars}{a \link{list} defining a model}
 
-\item{i}{the stratum to split}
+\item{i}{the host species index}
+
+\item{j}{the stratum to split}
 
 \item{p}{the fraction that gets multiplied by \code{fac}}