Merge pull request #134 from dd-harp/dev

parse_deout_X returns pr
dd-harp · Oct 13, 2023 · b610b68 · b610b68
2 parents ac95168 + 174084c
commit b610b68
Show file tree

Hide file tree

Showing 4 changed files with 7 additions and 3 deletions.
diff --git a/R/human-SIP.R b/R/human-SIP.R
@@ -138,6 +138,7 @@ make_Xinits_SIP = function(pars, Xopts = list(),
 parse_deout_X.SIP <- function(varslist, deout, pars) {
   varslist$X = deout[,pars$Xpar$X_ix+1]
   varslist$P = deout[,pars$Xpar$P_ix+1]
+  varslist$pr = varslist$X/varslist$H
   return(varslist)
 }
 

diff --git a/R/human-SIS.R b/R/human-SIS.R
@@ -109,6 +109,7 @@ make_Xinits_SIS = function(pars, Xopts = list(), X0=1){with(Xopts,{
 #' @export
 parse_deout_X.SIS <- function(varslist, deout, pars) {
   varslist$X = deout[,pars$Xpar$X_ix+1]
+  varslist$pr = varslist$X/varslist$H
   return(varslist)
 }
 

diff --git a/R/human-hMoI.R b/R/human-hMoI.R
@@ -171,6 +171,8 @@ make_inits_X_hMoI <- function(pars, m10, m20) {
 parse_deout_X.hMoI <- function(varslist, deout, pars) {
   varslist$m1 = deout[,pars$Xpar$m1_ix+1]
   varslist$m2 = deout[,pars$Xpar$m2_ix+1]
+  varslist$pr = 1-exp(-varslist$m1)
+  varslist$pr_apparent = 1-exp(-varslist$m2)
   return(varslist)
 }
 

diff --git a/R/utils.R b/R/utils.R
@@ -82,12 +82,12 @@ parse_deout <- function(deout, pars){
   if ('MYZpar' %in% names(pars)) {
     varslist = parse_deout_MYZ(varslist, deout, pars)
   }
-  if ('Xpar' %in% names(pars)) {
-    varslist = parse_deout_X(varslist, deout, pars)
-  }
   if ('Hpar' %in% names(pars)) {
     varslist = parse_deout_H(varslist, deout, pars)
   }
+  if ('Xpar' %in% names(pars)) {
+    varslist = parse_deout_X(varslist, deout, pars)
+  }
   return(varslist)
 }