Added get_XH and get_MYZ; conventional output location for xde_solve_…

…cohort

NAMESPACE

@@ -475,10 +475,12 @@ export(get_EIR)
 export(get_H)
 export(get_Linits)
 export(get_Lpars)
+export(get_MYZ)
 export(get_MYZinits)
 export(get_MYZpars)
 export(get_Omega)
 export(get_Upsilon)
+export(get_XH)
 export(get_Xinits)
 export(get_Xpars)
 export(get_bionomics)

R/get.R

@@ -45,3 +45,26 @@ get_terms <- function(tm, de_vars, pars) {
 get_EIR = function(pars, i){
   pars$outputs$terms$EIR
 }
+
+#' @title Get **XH** outputs
+#' @param pars an **`xds`** object
+#' @param i the host species index
+#' @export
+get_XH = function(pars, i=1){
+  got = pars$outputs$orbits$XH[[i]]
+  got$time = pars$outputs$orbits$time
+  got$eir = pars$outputs$terms$EIR[[i]]
+  return(got)
+}
+
+#' @title Get **MYZ** outputs
+#' @param pars an **`xds`** object
+#' @param s the vector species index
+#' @export
+get_MYZ = function(pars, s=1){
+  got = pars$outputs$orbits$MYZ[[s]]
+  got$time = pars$outputs$orbits$time
+  got$kappa = pars$outputs$terms$kappa[[s]]
+  return(got)
+}
+

R/outputs-get.R

@@ -0,0 +1 @@
+get_EIR

R/xde_cohort.R

@@ -77,8 +77,9 @@ xds_solve_cohort = function(pars, bday=0, A = 10, da = 10){
   pars$outputs$last_y <- tail(de_vars, 1)
   pars$outputs$orbits$age <- age
   pars$outputs$orbits$time <- age+bday
-  pars$outputs$orbits$terms <- list()
-  pars$outputs$orbits$terms$EIR<- with(pars, F_eir(age, bday))
+  pars$outputs$terms <- list()
+  pars$outputs$terms$EIR <- list()
+  pars$outputs$terms$EIR[[1]] <- with(pars, F_eir(age, bday))
   return(pars)
 }
 

_pkgdown.yml

@@ -131,6 +131,8 @@ reference:
   - parse_y
   - get_inits
   - get_H
+  - get_XH
+  - get_MYZ
   - make_indices
   - trigger_setup
 - subtitle: Examine

docs/pkgdown.yml

@@ -9,7 +9,6 @@ articles:
   Contributing: Contributing.html
   ex_534: ex_534.html
   Exposure: Exposure.html
-  Forcing: Forcing.html
   GettingStarted: GettingStarted.html
   History: History.html
   human_hmoi: human_hmoi.html
@@ -23,9 +22,8 @@ articles:
   SpatialTransmissionDynamics: SpatialTransmissionDynamics.html
   TraceFunctions: TraceFunctions.html
   Understanding_ramp.xds: Understanding_ramp.xds.html
-  VectorControl: VectorControl.html
   Working: Working.html
-last_built: 2024-10-09T14:34Z
+last_built: 2024-10-14T15:07Z
 urls:
   reference: https://dd-harp.github.io/ramp.xds/reference
   article: https://dd-harp.github.io/ramp.xds/articles