Merge pull request #54 from dd-harp/dev

Dev

R/diffeqn.R

@@ -37,7 +37,7 @@ xDE_diffeqn <- function(t, y, pars, EIR_delta = NULL, kappa_delta = NULL) {
   # bloodmeal
 
   # EIR: entomological inoculation rate
-  EIR <- F_EIR(t, y, pars)
+  EIR <- F_EIR(t, y, pars, MosyBehavior)
   if (!is.null(EIR_delta)) {
     EIR <- EIR + EIR_delta
   }

R/human-SIP.R

@@ -2,15 +2,13 @@
 
 #' @title Entomological inoculation rate on human strata
 #' @description Implements [F_EIR] for the SIP model.
-#' @param t current simulation time
-#' @param y state vector
-#' @param pars an [environment]
+#' @inheritParams F_EIR
 #' @return a [numeric] vector of length `nStrata`
 #' @export
-F_EIR.SIP <- function(t, y, pars) {
+F_EIR.SIP <- function(t, y, pars, MosyBehavior) {
   Z <- F_Z(t, y, pars)
-  f <- pars$MYZpar$f # may want to use wrapper compute_f/q
-  q <- pars$MYZpar$q
+  f <- MosyBehavior$f[1]
+  q <- MosyBehavior$q[1]
   beta <- F_beta(t, y, pars)
   as.vector(beta %*% diag(f*q, nrow = pars$nPatches) %*% Z)
 }

R/human-SIS.R

@@ -2,15 +2,13 @@
 
 #' @title Entomological inoculation rate on human strata
 #' @description Implements [F_EIR] for the SIS model.
-#' @param t current simulation time
-#' @param y state vector
-#' @param pars an [environment]
+#' @inheritParams F_EIR
 #' @return a [numeric] vector of length `nStrata`
 #' @export
-F_EIR.SIS <- function(t, y, pars) {
+F_EIR.SIS <- function(t, y, pars, MosyBehavior) {
   Z <- F_Z(t, y, pars)
-  f <- pars$MYZpar$f # may want to use wrapper compute_f/q
-  q <- pars$MYZpar$q
+  f <- MosyBehavior$f[1]
+  q <- MosyBehavior$q[1]
   beta <- F_beta(t, y, pars)
   as.vector(beta %*% diag(f*q, nrow = pars$nPatches) %*% Z)
 }

R/human-hMoI.R

@@ -2,15 +2,13 @@
 
 #' @title Entomological inoculation rate on human strata
 #' @description Implements [F_EIR] for the hybrid MoI model.
-#' @param t current simulation time
-#' @param y state vector
-#' @param pars an [environment]
+#' @inheritParams F_EIR
 #' @return a [numeric] vector of length `nStrata`
 #' @export
-F_EIR.hMoI <- function(t, y, pars) {
+F_EIR.hMoI <- function(t, y, pars, MosyBehavior) {
   Z <- F_Z(t, y, pars)
-  f <- pars$MYZpar$f # may want to use wrapper compute_f/q
-  q <- pars$MYZpar$q
+  f <- MosyBehavior$f[1]
+  q <- MosyBehavior$q[1]
   beta <- F_beta(t, y, pars)
   as.vector(beta %*% diag(f*q, nrow = pars$nPatches) %*% Z)
 }

R/human-interface.R

@@ -5,9 +5,10 @@
 #' @param t current simulation time
 #' @param y state vector
 #' @param pars an [environment]
+#' @param MosyBehavior values returned by [exDE::MosquitoBehavior], potentially modified by control [exDE::VectorControl]
 #' @return a [numeric] vector of length `nStrata`
 #' @export
-F_EIR <- function(t, y, pars) {
+F_EIR <- function(t, y, pars, MosyBehavior) {
   UseMethod("F_EIR", pars$Xpar)
 }
 

vignettes/vc_lemenach.Rmd

@@ -125,14 +125,14 @@ theta <- (eta - psi*L - phi*L)/(L^2)
 
 ## Setup
 
-Now that all state variables have been solved at equilibrium, we can set up the parameters and components of the system. We also need to set up a time-varying function to compute the coverage of ITNs at any time point. We use a sine curve with a period of 365 days which goes from 0 to 1 over that period. This must be a function that takes a single argument `t` (time) and returns a scalar value.
+Now that all state variables have been solved at equilibrium, we can set up the parameters and components of the system. We also need to set up a time-varying function to compute the coverage of ITNs at any time point. We use a sine curve with a period of 365 days which goes from 0 to 1 over that period, with the phase shifted so that at 0 it returns 0. The function also returns 0 for any $t<0$. This must be a function that takes a single argument `t` (time) and returns a scalar value.
 
 ```{r}
 pars$calU <- calU
 pars$calN <- calN
 
 # ITN coverage
-ITN_cov <- function(t) {(sin(2*pi*t / 365) + 1) / 2}
+ITN_cov <- function(t) {ifelse(t < 0, 0, (sin(2*pi*(t-365/4) / 365) + 1) / 2)}
 
 # set parameters
 make_parameters_exogenous_null(pars)