Dev

NAMESPACE

@@ -96,7 +96,6 @@ S3method(IRSEffectSizes,none)
 S3method(LBaseline,basicL)
 S3method(LBaseline,trivial)
 S3method(LBionomics,basicL)
-S3method(LBionomics,static)
 S3method(LBionomics,trivial)
 S3method(LSM,none)
 S3method(MBaseline,GeRM)
@@ -108,7 +107,6 @@ S3method(MBionomics,GeRM)
 S3method(MBionomics,SI)
 S3method(MBionomics,basicM)
 S3method(MBionomics,macdonald)
-S3method(MBionomics,static)
 S3method(MBionomics,trivial)
 S3method(MassHealth,none)
 S3method(OtherBloodHosts,static)
@@ -231,12 +229,6 @@ S3method(make_function,sharkfin)
 S3method(make_function,sigmoid)
 S3method(make_function,sin)
 S3method(make_function,sum)
-S3method(make_indices_MYZ,GeRM)
-S3method(make_indices_MYZ,RM_dts)
-S3method(make_indices_MYZ,SI)
-S3method(make_indices_MYZ,basicM)
-S3method(make_indices_MYZ,macdonald)
-S3method(make_indices_MYZ,trivial)
 S3method(make_runtime,dts)
 S3method(make_runtime,xde)
 S3method(parse_Lorbits,basicL)
@@ -277,6 +269,8 @@ S3method(set_eir,cohort)
 S3method(setup_EIP,fixedlag_dts)
 S3method(setup_Linits,basicL)
 S3method(setup_Linits,trivial)
+S3method(setup_Lix,basicL)
+S3method(setup_Lix,trivial)
 S3method(setup_Lpar,basicL)
 S3method(setup_Lpar,trivial)
 S3method(setup_MYZinits,GeRM)
@@ -285,17 +279,23 @@ S3method(setup_MYZinits,SI)
 S3method(setup_MYZinits,basicM)
 S3method(setup_MYZinits,macdonald)
 S3method(setup_MYZinits,trivial)
+S3method(setup_MYZix,GeRM)
+S3method(setup_MYZix,RM_dts)
+S3method(setup_MYZix,SI)
+S3method(setup_MYZix,basicM)
+S3method(setup_MYZix,macdonald)
+S3method(setup_MYZix,trivial)
 S3method(setup_MYZpar,GeRM)
 S3method(setup_MYZpar,SI)
 S3method(setup_MYZpar,basicM)
 S3method(setup_MYZpar,macdonald)
 S3method(setup_MYZpar,trivial)
-S3method(setup_X_indices,SIS)
-S3method(setup_X_indices,hMoI)
-S3method(setup_X_indices,trivial)
 S3method(setup_Xinits,SIS)
 S3method(setup_Xinits,hMoI)
 S3method(setup_Xinits,trivial)
+S3method(setup_Xix,SIS)
+S3method(setup_Xix,hMoI)
+S3method(setup_Xix,trivial)
 S3method(setup_Xpar,SIS)
 S3method(setup_Xpar,hMoI)
 S3method(setup_Xpar,trivial)
@@ -306,8 +306,6 @@ S3method(setup_exposure_pois,dts)
 S3method(setup_exposure_pois,xde)
 S3method(setup_humidity,func)
 S3method(setup_hydrology,func)
-S3method(setup_indices_L,basicL)
-S3method(setup_indices_L,trivial)
 S3method(setup_rainfall,func)
 S3method(setup_shock,func)
 S3method(setup_temperature,func)
@@ -531,7 +529,6 @@ export(make_calU)
 export(make_eggs_laid)
 export(make_function)
 export(make_indices)
-export(make_indices_MYZ)
 export(make_kappa)
 export(make_local_frac)
 export(make_parameters_demography_null)
@@ -570,12 +567,14 @@ export(setup_EGG_LAYING)
 export(setup_EIP)
 export(setup_Hpar_static)
 export(setup_Linits)
+export(setup_Lix)
 export(setup_Lpar)
 export(setup_MYZinits)
+export(setup_MYZix)
 export(setup_MYZpar)
 export(setup_TRANSMISSION)
-export(setup_X_indices)
 export(setup_Xinits)
+export(setup_Xix)
 export(setup_Xpar)
 export(setup_care_seeking_no_behavior)
 export(setup_development)
@@ -589,7 +588,6 @@ export(setup_humidity)
 export(setup_humidity_func)
 export(setup_hydrology)
 export(setup_hydrology_func)
-export(setup_indices_L)
 export(setup_no_active_case_detection)
 export(setup_no_area_spray)
 export(setup_no_bednets)

R/adult-GeRM.R

@@ -448,12 +448,12 @@ xde_steady_state_MYZ.GeRM = function(Lambda, kappa, MYZpar){with(MYZpar,{
 
 
 #' @title Add indices for adult mosquitoes to parameter list
-#' @description Implements [make_indices_MYZ] for the GeRM model.
-#' @inheritParams make_indices_MYZ
+#' @description Implements [setup_MYZix] for the GeRM model.
+#' @inheritParams setup_MYZix
 #' @return a [list]
 #' @importFrom utils tail
 #' @export
-make_indices_MYZ.GeRM <- function(pars, s) {with(pars,{
+setup_MYZix.GeRM <- function(pars, s) {with(pars,{
 
   M_ix <- seq(from = max_ix+1, length.out=nPatches)
   max_ix <- tail(M_ix, 1)

R/adult-RM-dts.R

@@ -99,12 +99,12 @@ make_MYZinits_RM_dts = function(nPatches, max_eip, MYZopts = list(),
 
 
 #' @title Add indices for adult mosquitoes to parameter list
-#' @description Implements [make_indices_MYZ] for the RM_dts model.
-#' @inheritParams make_indices_MYZ
+#' @description Implements [setup_MYZix] for the RM_dts model.
+#' @inheritParams setup_MYZix
 #' @return a [list]
 #' @importFrom utils tail
 #' @export
-make_indices_MYZ.RM_dts <- function(pars, s) {with(pars,{
+setup_MYZix.RM_dts <- function(pars, s) {with(pars,{
 
   M_ix <- seq(from = max_ix+1, length.out=nPatches)
   max_ix <- tail(M_ix, 1)

R/adult-basicM.R

@@ -267,12 +267,12 @@ set_MYZpars.GeRM <- function(pars, s=1, MYZopts=list()) {
   }))}
 
 #' @title Add indices for adult mosquitoes to parameter list
-#' @description Implements [make_indices_MYZ] for the basic M model.
-#' @inheritParams make_indices_MYZ
+#' @description Implements [setup_MYZix] for the basic M model.
+#' @inheritParams setup_MYZix
 #' @return none
 #' @importFrom utils tail
 #' @export
-make_indices_MYZ.basicM <- function(pars, s) {with(pars,{
+setup_MYZix.basicM <- function(pars, s) {with(pars,{
 
   M_ix <- seq(from = max_ix+1, length.out = nPatches)
   max_ix <- tail(M_ix, 1)

R/adult-interface.R

@@ -197,8 +197,8 @@ set_MYZinits <- function(pars, s=1, MYZopts=list()) {
 #' @param s the species index
 #' @return [list]
 #' @export
-make_indices_MYZ <- function(pars, s) {
-  UseMethod("make_indices_MYZ", pars$MYZpar[[s]])
+setup_MYZix <- function(pars, s) {
+  UseMethod("setup_MYZix", pars$MYZpar[[s]])
 }
 
 #' @title Parse the outputs and return the variables by name in a list

R/adult-macdonald.R

@@ -282,12 +282,12 @@ xde_steady_state_MYZ.macdonald = function(Lambda, kappa, MYZpar){with(MYZpar,{
 
 
 #' @title Add indices for adult mosquitoes to parameter list
-#' @description Implements [make_indices_MYZ] for the macdonald model.
-#' @inheritParams make_indices_MYZ
+#' @description Implements [setup_MYZix] for the macdonald model.
+#' @inheritParams setup_MYZix
 #' @return a [list]
 #' @importFrom utils tail
 #' @export
-make_indices_MYZ.macdonald <- function(pars, s) {with(pars,{
+setup_MYZix.macdonald <- function(pars, s) {with(pars,{
 
   M_ix <- seq(from = max_ix+1, length.out=nPatches)
   max_ix <- tail(M_ix, 1)

R/adult-si.R

@@ -355,12 +355,12 @@ put_MYZvars.SI <- function(MYZvars, y, pars, s){
 }
 
 #' @title Add indices for adult mosquitoes to parameter list
-#' @description Implements [make_indices_MYZ] for the `SI` model.
-#' @inheritParams make_indices_MYZ
+#' @description Implements [setup_MYZix] for the `SI` model.
+#' @inheritParams setup_MYZix
 #' @return a [list]
 #' @importFrom utils tail
 #' @export
-make_indices_MYZ.SI <- function(pars, s) {with(pars,{
+setup_MYZix.SI <- function(pars, s) {with(pars,{
 
   M_ix <- seq(from = max_ix+1, length.out=nPatches)
   max_ix <- tail(M_ix, 1)

R/adult-trivial.R

@@ -201,11 +201,11 @@ setup_MYZinits.trivial = function(pars, s, MYZopts=NULL){
 }
 
 #' @title Add indices for aquatic stage mosquitoes to parameter list
-#' @description Implements [make_indices_MYZ] for trivial (forced emergence) model.
-#' @inheritParams make_indices_MYZ
+#' @description Implements [setup_MYZix] for trivial (forced emergence) model.
+#' @inheritParams setup_MYZix
 #' @return none
 #' @export
-make_indices_MYZ.trivial <- function(pars, s) {
+setup_MYZix.trivial <- function(pars, s) {
   return(pars)
 }
 

R/aquatic-basicL.R

@@ -243,14 +243,25 @@ update_Linits.basicL <- function(pars, y, s) {
   return(pars)
 }
 
+
+#' @title Set **L** Component Initial Values
+#' @param pars an **`xds`** object
+#' @param s the vector species index
+#' @param Lopts a named list
+#' @return an `xds` object
+#' @export
+set_Linits <- function(pars, s=1, Lopts=list()) {
+  UseMethod("set_Linits", pars$Lpar[[s]])
+}
+
 #' @title Setup Variable Indices for `basicL` (**L** Component)
 #' @description Set the values of the indices for the **L** component variables
 #' for the `basicL` module
-#' @inheritParams setup_indices_L
+#' @inheritParams setup_Lix
 #' @return an **`xds`** object
 #' @importFrom utils tail
 #' @export
-setup_indices_L.basicL <- function(pars, s) {with(pars,{
+setup_Lix.basicL <- function(pars, s) {with(pars,{
 
   L_ix <- seq(from = max_ix+1, length.out = nHabitats)
   max_ix <- tail(L_ix, 1)
@@ -274,17 +285,6 @@ parse_Lorbits.basicL <- function(outputs, pars, s) {
   return(list(L=L))
 }
 
-
-#' @title Set **L** Component Initial Values
-#' @param pars an **`xds`** object
-#' @param s the vector species index
-#' @param Lopts a named list
-#' @return an `xds` object
-#' @export
-set_Linits <- function(pars, s=1, Lopts=list()) {
-  UseMethod("set_Linits", pars$Lpar[[s]])
-}
-
 #' @title Compute the Steady State of `dLdt.basicL` (**L** Component)
 #' @description Given an egg deposition rate `eta,`
 #' return a steady state value for the equations in [dLdt.basicL]

R/aquatic-interface.R

@@ -171,8 +171,8 @@ update_Linits <- function(pars, y, s) {
 #' @param s the species index
 #' @return an **`xds`** object
 #' @export
-setup_indices_L <- function(pars, s) {
-  UseMethod("setup_indices_L", pars$Lpar[[s]])
+setup_Lix <- function(pars, s) {
+  UseMethod("setup_Lix", pars$Lpar[[s]])
 }
 
 #' @title Parse **L** Component Outputs

R/aquatic-trivial.R

@@ -154,11 +154,11 @@ update_Linits.trivial<- function(pars, y, s) {
 }
 
 #' @title Setup Variable Indices for `trivial` (**L** Component)
-#' @description Implements [setup_indices_L] for trivial (forced emergence) model.
-#' @inheritParams setup_indices_L
+#' @description Implements [setup_Lix] for trivial (forced emergence) model.
+#' @inheritParams setup_Lix
 #' @return an **`xds`** object
 #' @export
-setup_indices_L.trivial <- function(pars, s) {
+setup_Lix.trivial <- function(pars, s) {
   return(pars)
 }
 

R/bionomics.R

@@ -36,21 +36,3 @@ Bionomics <- function(t, y, pars){
   }
   return(pars)
 }
-
-#' @title Set mosquito bionomics to baseline
-#' @description Implements [MBionomics] for models with no forcing
-#' @inheritParams MBionomics
-#' @return an `xds` object
-#' @export
-MBionomics.static <- function(t, y, pars, s) {
-  return(pars)
-}
-
-#' @title Set mosquito bionomics to baseline
-#' @description Implements [LBionomics] for models with no forcing
-#' @inheritParams LBionomics
-#' @return the model as a [list]
-#' @export
-LBionomics.static <- function(t, y, pars, s) {
-  return(pars)
-}

R/human-SIS.R

@@ -228,12 +228,12 @@ get_Xinits.SIS <- function(pars, i=1){pars$Xinits[[i]]}
 
 
 #' @title Add indices for human population to parameter list
-#' @description Implements [setup_X_indices] for the SIS model.
-#' @inheritParams setup_X_indices
+#' @description Implements [setup_Xix] for the SIS model.
+#' @inheritParams setup_Xix
 #' @return none
 #' @importFrom utils tail
 #' @export
-setup_X_indices.SIS <- function(pars, i) {with(pars,{
+setup_Xix.SIS <- function(pars, i) {with(pars,{
 
   S_ix <- seq(from = max_ix+1, length.out=nStrata[i])
   max_ix <- tail(S_ix, 1)

R/human-hMoI.R

@@ -191,12 +191,12 @@ HTC.hMoI <- function(pars, i) {
 }
 
 #' @title Add indices for human population to parameter list
-#' @description Implements [setup_X_indices] for the hybrid MoI model.
-#' @inheritParams setup_X_indices
+#' @description Implements [setup_Xix] for the hybrid MoI model.
+#' @inheritParams setup_Xix
 #' @return none
 #' @importFrom utils tail
 #' @export
-setup_X_indices.hMoI <- function(pars, i) {with(pars,{
+setup_Xix.hMoI <- function(pars, i) {with(pars,{
   m1_ix <- seq(from = max_ix+1, length.out=nStrata[i])
   max_ix <- tail(m1_ix, 1)
 

R/human-interface.R

@@ -108,8 +108,8 @@ setup_Xinits = function(pars, H, i, Xopts=list()){
 #' @param i the host species index
 #' @return an **`xds`** object
 #' @export
-setup_X_indices <- function(pars, i) {
-  UseMethod("setup_X_indices", pars$Xpar[[i]])
+setup_Xix <- function(pars, i) {
+  UseMethod("setup_Xix", pars$Xpar[[i]])
 }
 
 #' @title Return the variables as a list

R/human-trivial.R

@@ -140,12 +140,12 @@ setup_Xinits.trivial = function(pars, H, i, Xopts=list()){
 }
 
 #' @title Add indices for human population to parameter list
-#' @description Implements [setup_X_indices] for the trivial model.
-#' @inheritParams setup_X_indices
+#' @description Implements [setup_Xix] for the trivial model.
+#' @inheritParams setup_Xix
 #' @return none
 #' @importFrom utils tail
 #' @export
-setup_X_indices.trivial <- function(pars, i) {
+setup_Xix.trivial <- function(pars, i) {
   return(pars)
 }
 

R/utils.R

@@ -9,17 +9,17 @@ make_indices <- function(pars) {
   s = length(pars$Linits)
   if(s>0)
     for(ix in 1:s)
-      pars = setup_indices_L(pars, ix)
+      pars = setup_Lix(pars, ix)
 
   s = length(pars$MYZinits)
   if(s>0)
     for(ix in 1:s)
-      pars = make_indices_MYZ(pars, ix)
+      pars = setup_MYZix(pars, ix)
 
   i = length(pars$Xinits)
   if(i>0)
     for(ix in 1:i)
-      pars = setup_X_indices(pars, ix)
+      pars = setup_Xix(pars, ix)
 
   return(pars)
 }