EIP

NAMESPACE

@@ -120,6 +120,7 @@ S3method(compute_terms,cohort)
 S3method(compute_terms,human)
 S3method(compute_terms,na)
 S3method(compute_terms,xde)
+S3method(dEIPdt,static)
 S3method(dHdt,numeric)
 S3method(dHdt,static)
 S3method(dLdt,basic)
@@ -314,6 +315,7 @@ export(compute_kappa_ty)
 export(compute_local_frac)
 export(compute_terms)
 export(compute_terms_steady)
+export(dEIPdt)
 export(dHdt)
 export(dLdt)
 export(dMYZdt)

R/adult-GeRM.R

@@ -109,7 +109,7 @@ dMYZdt.GeRM_dde <- function(t, y, pars, Lambda, kappa) {
     dGdt <- f*(M - G) - nu*G - (Omega %*% G)
     dYdt <- f*q*kappa*(M - Y) - (Omega %*% Y)
     dZdt <- Upsilon %*% diag(f_eip*q_eip*kappa_eip, nPatches) %*% (M_eip - Y_eip) - (Omega %*% Z)
-    dUdt <- as.vector((Omega_eip - Omega) %*% Upsilon)
+    dUdt <- as.vector(((1-dEIPdt(t,pars))*Omega_eip - Omega) %*% Upsilon)
 
     return(c(dMdt, dGdt, dYdt, dZdt, dUdt, kappa, f, q, g, sigma))
   })

R/adult-RM.R

@@ -105,7 +105,7 @@ dMYZdt.RM_dde <- function(t, y, pars, Lambda, kappa) {
     dPdt <- f*(M - P) - (Omega %*% P)
     dYdt <- f*q*kappa*(M - Y) - (Omega %*% Y)
     dZdt <- Upsilon %*% (fqkappa_eip * (M_eip - Y_eip)) - (Omega %*% Z)
-    dUdt <- as.vector((Omega_eip - Omega) %*% Upsilon)
+    dUdt <- as.vector(((1-dEIPdt(t,pars))*Omega_eip - Omega) %*% Upsilon)
 
     return(c(dMdt, dPdt, dYdt, dZdt, dUdt, f*q*kappa, g, sigma))
   })

R/eip.R

@@ -10,13 +10,30 @@ EIP <- function(t, pars) {
   UseMethod("EIP", pars$EIPmod)
 }
 
+#' @title Compute the derivative of the EIP as a function of time
+#' @description This method dispatches on the type of `pars$EIPmod`.
+#' @param t current simulation time
+#' @param pars a [list]
+#' @return [numeric]
+#' @export
+dEIPdt <- function(t, pars) {
+  UseMethod("dEIPdt", pars$EIPmod)
+}
+
 #' @title Modify parameters due to exogenous forcing by all kinds of control
 #' @description Implements [EIP] for the static model (the EIP is constant)
 #' @inheritParams EIP
 #' @return [list]
 #' @export
 EIP.static <- function(t, pars) {pars}
 
+#' @title This function computes the negative derivative of the EIP as a function of time
+#' @description Implements [EIP] for the static model (the dEIPdt=0)
+#' @inheritParams EIP
+#' @return [numeric]
+#' @export
+dEIPdt.static <- function(t, pars){0}
+
 #' @title Set up the static model for control forcing (do nothing)
 #' @param pars a [list]
 #' @return [list]

R/utils.R

@@ -73,18 +73,20 @@ get_inits <- function(pars){
 #' @export
 parse_deout <- function(deout, pars){
   varslist = list()
-  varslist$time = deout[,1]
   if ('Lpar' %in% names(pars)) {
     varslist$L = parse_deout_L(deout, pars)
+    varslist$L$time = deout[,1]
   }
   if ('MYZpar' %in% names(pars)) {
     varslist$MYZ = parse_deout_MYZ(deout, pars)
+    varslist$MYZ$time = deout[,1]
   }
   if ('Xpar' %in% names(pars)) {
     varslist$XH = parse_deout_X(deout, pars)
+    varslist$XH$time = deout[,1]
   }
   varslist$terms = compute_terms(varslist, deout, pars)
-  varslist$terms$time = varslist$time
+  varslist$terms$time = deout[,1]
   varslist$deout = deout
   return(varslist)
 }

_pkgdown.yml

@@ -93,6 +93,8 @@ reference:
   contents:
   - EIP
   - EIP.static
+  - dEIPdt
+  - dEIPdt.static
   - setup_eip_static
 - subtitle: Ztrace
   desc: |