Merge pull request #125 from dd-harp/dev

Dev

NAMESPACE

@@ -75,6 +75,11 @@ S3method(F_fqZ,si)
 S3method(F_fqZ,trace)
 S3method(F_g,static)
 S3method(F_mu,static)
+S3method(F_ni,SEIS)
+S3method(F_ni,SEISd)
+S3method(F_ni,SIP)
+S3method(F_ni,SIS)
+S3method(F_ni,hMoI)
 S3method(F_nu,static)
 S3method(F_nu,type2)
 S3method(F_pr,SEIS)
@@ -176,11 +181,6 @@ S3method(ar2eir,nb)
 S3method(ar2eir,pois)
 S3method(compute_Omega,dts)
 S3method(compute_Omega,xde)
-S3method(compute_terms,cohort)
-S3method(compute_terms,dts)
-S3method(compute_terms,human)
-S3method(compute_terms,na)
-S3method(compute_terms,xde)
 S3method(dHdt,zero)
 S3method(dLdt,basicL)
 S3method(dLdt,trace)
@@ -218,8 +218,29 @@ S3method(get_Xinits,SIP)
 S3method(get_Xinits,SIS)
 S3method(get_Xinits,hMoI)
 S3method(get_Xinits,trace)
+S3method(get_f,RM)
+S3method(get_f,basicM)
+S3method(get_f,sei)
+S3method(get_f,si)
+S3method(get_f,trace)
+S3method(get_g,RM)
+S3method(get_g,basicM)
+S3method(get_g,sei)
+S3method(get_g,si)
+S3method(get_g,trace)
+S3method(get_q,RM)
+S3method(get_q,basicM)
+S3method(get_q,sei)
+S3method(get_q,si)
+S3method(get_q,trace)
+S3method(get_sigma,RM)
+S3method(get_sigma,basicM)
+S3method(get_sigma,sei)
+S3method(get_sigma,si)
+S3method(get_sigma,trace)
 S3method(list_Lvars,basicL)
 S3method(list_Lvars,trace)
+S3method(list_MYZvars,RM)
 S3method(list_MYZvars,RM_dts)
 S3method(list_MYZvars,basicM)
 S3method(list_MYZvars,sei)
@@ -279,20 +300,20 @@ S3method(make_indices_MYZ,si)
 S3method(make_indices_MYZ,trace)
 S3method(make_runtime,dts)
 S3method(make_runtime,xde)
-S3method(parse_outputs_L,basicL)
-S3method(parse_outputs_L,trace)
-S3method(parse_outputs_MYZ,RM)
-S3method(parse_outputs_MYZ,RM_dts)
-S3method(parse_outputs_MYZ,basicM)
-S3method(parse_outputs_MYZ,sei)
-S3method(parse_outputs_MYZ,si)
-S3method(parse_outputs_MYZ,trace)
-S3method(parse_outputs_X,SEIS)
-S3method(parse_outputs_X,SEISd)
-S3method(parse_outputs_X,SIP)
-S3method(parse_outputs_X,SIS)
-S3method(parse_outputs_X,hMoI)
-S3method(parse_outputs_X,trace)
+S3method(parse_Lorbits,basicL)
+S3method(parse_Lorbits,trace)
+S3method(parse_MYZorbits,RM)
+S3method(parse_MYZorbits,RM_dts)
+S3method(parse_MYZorbits,basicM)
+S3method(parse_MYZorbits,sei)
+S3method(parse_MYZorbits,si)
+S3method(parse_MYZorbits,trace)
+S3method(parse_Xorbits,SEIS)
+S3method(parse_Xorbits,SEISd)
+S3method(parse_Xorbits,SIP)
+S3method(parse_Xorbits,SIS)
+S3method(parse_Xorbits,hMoI)
+S3method(parse_Xorbits,trace)
 S3method(put_Lvars,trace)
 S3method(put_MYZvars,RM_dts)
 S3method(put_MYZvars,sei)
@@ -307,13 +328,13 @@ S3method(setup_exposure_nb,dts)
 S3method(setup_exposure_nb,xde)
 S3method(setup_exposure_pois,dts)
 S3method(setup_exposure_pois,xde)
-S3method(setup_setup,dynamic)
-S3method(setup_setup,setup)
-S3method(setup_setup,static)
 S3method(setup_travel_static,dts)
 S3method(setup_travel_static,xde)
 S3method(travel_malaria,dts)
 S3method(travel_malaria,xde)
+S3method(trigger_setup,dynamic)
+S3method(trigger_setup,setup)
+S3method(trigger_setup,static)
 S3method(update_Linits,basicL)
 S3method(update_Linits,trace)
 S3method(update_MYZinits,RM)
@@ -390,6 +411,7 @@ export(F_fqM)
 export(F_fqZ)
 export(F_g)
 export(F_mu)
+export(F_ni)
 export(F_nu)
 export(F_p)
 export(F_pr)
@@ -449,8 +471,6 @@ export(change_habitat_weights)
 export(checkIt)
 export(compute_B)
 export(compute_EIR)
-export(compute_NI)
-export(compute_NI_ix)
 export(compute_Omega)
 export(compute_Omega_dts)
 export(compute_Omega_xde)
@@ -464,13 +484,6 @@ export(compute_calU)
 export(compute_eggs_laid)
 export(compute_kappa)
 export(compute_local_frac)
-export(compute_terms)
-export(compute_terms_steady)
-export(compute_vars_aqua)
-export(compute_vars_cohort)
-export(compute_vars_full)
-export(compute_vars_human)
-export(compute_vars_mosy)
 export(create_Linits_basicL)
 export(create_Lpar_basicL)
 export(create_Lpar_trace)
@@ -524,7 +537,17 @@ export(get_MYZinits)
 export(get_Omega)
 export(get_Upsilon)
 export(get_Xinits)
+export(get_bionomics)
+export(get_bionomics_s)
+export(get_f)
+export(get_ft)
+export(get_g)
 export(get_inits)
+export(get_last)
+export(get_q)
+export(get_qt)
+export(get_sigma)
+export(get_terms)
 export(last_to_inits)
 export(list_Lvars)
 export(list_MYZvars)
@@ -561,14 +584,16 @@ export(metric_calD)
 export(metric_calR)
 export(metric_calV)
 export(metric_calZ)
-export(parse_outputs)
-export(parse_outputs_L)
-export(parse_outputs_MYZ)
-export(parse_outputs_X)
-export(parse_outputs_vec)
+export(parse_Lorbits)
+export(parse_MYZorbits)
+export(parse_Xorbits)
+export(parse_orbits)
+export(parse_y)
 export(put_Lvars)
 export(put_MYZvars)
 export(put_Xvars)
+export(reset_state)
+export(reset_state_i)
 export(runt)
 export(set_Dday)
 export(setup_BLOOD_FEEDING)
@@ -604,7 +629,6 @@ export(setup_rainfall_no_forcing)
 export(setup_relative_humidity_no_forcing)
 export(setup_resources_forced)
 export(setup_resources_static)
-export(setup_setup)
 export(setup_sugar_baits_null)
 export(setup_sugar_static)
 export(setup_temperature_no_forcing)
@@ -617,6 +641,7 @@ export(setup_weather_forced)
 export(setup_weather_no_forcing)
 export(shapeIt)
 export(travel_malaria)
+export(trigger_setup)
 export(update_Linits)
 export(update_MYZinits)
 export(update_MYZpar_RM)
@@ -634,6 +659,7 @@ export(xde_steady_state_M)
 export(xde_steady_state_MYZ)
 export(xde_steady_state_X)
 export(xde_steady_state_XH)
+export(xds_flatten)
 export(xds_lines_EIR)
 export(xds_lines_M)
 export(xds_lines_PR)

R/adult-RM-bionomics.R

@@ -30,9 +30,15 @@ create_MYZpar_RM_static = function(nPatches, MYZopts=list(), eip=12,
     MYZpar$f      <- checkIt(f, nPatches)
     MYZpar$q      <- checkIt(q, nPatches)
     MYZpar$nu     <- checkIt(nu, nPatches)
+
     MYZpar$eggsPerBatch <- eggsPerBatch
     MYZpar$calK <- diag(nPatches)
 
+    MYZpar$es_f       <- rep(1, nPatches)
+    MYZpar$es_q       <- rep(1, nPatches)
+    MYZpar$es_g       <- rep(1, nPatches)
+    MYZpar$es_sigma   <- rep(1, nPatches)
+
     Omega <- diag(g, nPatches)
     MYZpar$Omega <- Omega
     MYZpar$Upsilon <- expm::expm(-Omega*eip)

R/adult-RM-dts.R

@@ -162,21 +162,20 @@ put_MYZvars.RM_dts <- function(MYZvars, y, pars, s){
 
 
 #' @title Parse the output of deSolve and return variables for the RM_dts model
-#' @description Implements [parse_outputs_MYZ] for the RM_dts model
-#' @inheritParams parse_outputs_MYZ
+#' @description Implements [parse_MYZorbits] for the RM_dts model
+#' @inheritParams parse_MYZorbits
 #' @return a [list]
 #' @export
-parse_outputs_MYZ.RM_dts <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
-  time = outputs[,1]
-  M = outputs[,M_ix+1]
-  P = outputs[,P_ix+1]
-  U = outputs[,U_ix+1]
-  Y = rowSums(outputs[,Y_ix+1])
-  Z = outputs[,Z_ix+1]
+parse_MYZorbits.RM_dts <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
+  M = outputs[,M_ix]
+  P = outputs[,P_ix]
+  U = outputs[,U_ix]
+  Y = rowSums(outputs[,Y_ix])
+  Z = outputs[,Z_ix]
   y = Y/M
   z = Z/M
   parous = P/M
-  return(list(time=time, M=M, P=P, U=U, Y=Y, Z=Z, y=y, z=z, parous=parous))
+  return(list(M=M, P=P, U=U, Y=Y, Z=Z, y=y, z=z, parous=parous))
 })}
 
 #' @title Return initial values as a vector

R/adult-RM.R

@@ -218,24 +218,38 @@ update_MYZinits.RM <- function(pars, y0, s) {
     return(pars)
   })}
 
-
+#' @title Return the variables as a list
+#' @description This method dispatches on the type of `pars$MYZpar[[s]]`
+#' @inheritParams list_MYZvars
+#' @return a [list]
+#' @export
+list_MYZvars.RM <- function(y, pars, s){
+  with(pars$ix$MYZ[[s]],
+       return(list(
+         M = y[M_ix],
+         P = y[P_ix],
+         Y = y[Y_ix],
+         Z = y[Z_ix]
+       )))
+}
 
 
 #' @title Parse the output of deSolve and return variables for the RM model
-#' @description Implements [parse_outputs_MYZ] for the RM model
-#' @inheritParams parse_outputs_MYZ
+#' @description Implements [parse_MYZorbits] for the RM model
+#' @inheritParams parse_MYZorbits
 #' @return a [list]
 #' @export
-parse_outputs_MYZ.RM <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
-  time = outputs[,1]
-  M = outputs[,M_ix+1]
-  P = outputs[,P_ix+1]
-  Y = outputs[,Y_ix+1]
-  Z = outputs[,Z_ix+1]
+parse_MYZorbits.RM <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
+  M = outputs[,M_ix]
+  P = outputs[,P_ix]
+  Y = outputs[,Y_ix]
+  Z = outputs[,Z_ix]
+  f = get_ft(pars, s)
+  q = get_qt(pars, s)
   y = Y/M
   z = Z/M
   parous = P/M
-  return(list(time=time, M=M, P=P, Y=Y, Z=Z, y=y, z=z, parous))
+  return(list(M=M, P=P, Y=Y, Z=Z, y=y, z=z, parous=parous, fqZ=f*q*Z, fqM=f*q*M))
 })}
 
 #' @title Compute the steady states as a function of the daily EIR

R/adult-basicM.R

@@ -185,16 +185,15 @@ make_indices_MYZ.basicM <- function(pars, s) {with(pars,{
   return(pars)
 })}
 
-#' @title Parse the output of deSolve and return variables for the basicM model
-#' @description Implements [parse_outputs_MYZ] for the basicM model.
-#' @inheritParams parse_outputs_MYZ
+#' @title Parse outputs for basicM
+#' @description Implements [parse_MYZorbits] for the basicM model.
+#' @inheritParams parse_MYZorbits
 #' @return [list]
 #' @export
-parse_outputs_MYZ.basicM <- function(outputs, pars, s) {
-  time = outputs[,1]
+parse_MYZorbits.basicM <- function(outputs, pars, s) {
   with(pars$ix$MYZ[[s]],{
-    M = outputs[,M_ix+1]
-    P = outputs[,P_ix+1]
+    M = outputs[,M_ix]
+    P = outputs[,P_ix]
     parous = P/M
-    return(list(time=time, M=M, P=P, parous=parous))
+    return(list(M=M, P=P, parous=parous))
 })}

R/adult-interface.R

@@ -170,8 +170,8 @@ make_indices_MYZ <- function(pars, s) {
 #' @param s the species index
 #' @return [list]
 #' @export
-parse_outputs_MYZ <- function(outputs, pars, s) {
-  UseMethod("parse_outputs_MYZ", pars$MYZpar[[s]])
+parse_MYZorbits <- function(outputs, pars, s) {
+  UseMethod("parse_MYZorbits", pars$MYZpar[[s]])
 }
 
 #' @title Return initial values as a vector

R/adult-sei.R

@@ -187,18 +187,19 @@ make_indices_MYZ.sei <- function(pars, s) {with(pars,{
 
 
 #' @title Parse the output of deSolve and return variables for the sei model
-#' @description Implements [parse_outputs_MYZ] for the sei model
-#' @inheritParams parse_outputs_MYZ
+#' @description Implements [parse_MYZorbits] for the sei model
+#' @inheritParams parse_MYZorbits
 #' @return a [list]
 #' @export
-parse_outputs_MYZ.sei <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
-  time = outputs[,1]
-  M = outputs[,M_ix+1]
-  Y = outputs[,Y_ix+1]
-  Z = outputs[,Z_ix+1]
+parse_MYZorbits.sei <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
+  M = outputs[,M_ix]
+  Y = outputs[,Y_ix]
+  Z = outputs[,Z_ix]
+  f = get_ft(pars,s)
+  q = get_ft(pars,s)
   y = Y/M
   z = Z/M
-  return(list(time=time, M=M, Z=Z, Y=Y, y=y, z=z))
+  return(list(M=M, Z=Z, Y=Y, y=y, z=z, fqZ=f*q*Z, fqM=f*q*M))
 })}
 
 #' @title Return initial values as a vector

R/adult-si.R

@@ -180,18 +180,19 @@ make_indices_MYZ.si <- function(pars, s) {with(pars,{
 
 
 #' @title Parse the output of deSolve and return variables for the si model
-#' @description Implements [parse_outputs_MYZ] for the si model
-#' @inheritParams parse_outputs_MYZ
+#' @description Implements [parse_MYZorbits] for the si model
+#' @inheritParams parse_MYZorbits
 #' @return a [list]
 #' @export
-parse_outputs_MYZ.si <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
-  time = outputs[,1]
-  M = outputs[,M_ix+1]
-  Y = outputs[,Z_ix+1]
+parse_MYZorbits.si <- function(outputs, pars, s) {with(pars$ix$MYZ[[s]],{
+  M = outputs[,M_ix]
+  Y = outputs[,Z_ix]
   Z = t(with(pars$MYZpar[[1]], Upsilon %*% t(Y)))
+  ff = get_ft(pars,s)
+  qq = get_qt(pars,s)
   y = Y/M
   z = Z/M
-  return(list(time=time, M=M, Z=Z, Y=Y, y=y, z=z))
+  return(list(M=M, Z=Z, Y=Y, y=y, z=z, fqZ=ff*qq*Z, fqM=ff*qq*M))
 })}
 
 #' @title Return initial values as a vector