Merge pull request #145 from dd-harp/dev

Dev
dd-harp · Aug 29, 2024 · c8c2e83 · c8c2e83
2 parents 8b53889 + e6adf04
commit c8c2e83
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Showing 10 changed files with 129 additions and 90 deletions.
diff --git a/R/blood_feeding.R b/R/blood_feeding.R
@@ -208,7 +208,7 @@ make_WB <- function(t, pars, y=0){
 
     if(pars$nHosts > 1){
       for(i in 2:pars$nHosts){
-        H = F_H(y, pars, i)
+        H = F_H(t, y, pars, i)
         TaR = pars$TaR[[s]][[i]]
         wts = pars$BFpar$search_weights[[s]][[i]]
         Wi = compute_W(wts, H, TaR)

diff --git a/R/human-SIS.R b/R/human-SIS.R
@@ -96,8 +96,6 @@ create_Xpar_SIS = function(nStrata, Xopts=list(),
   })}
 
 
-
-
 #' @title Size of effective infectious human population
 #' @description Implements [F_X] for the SIS model.
 #' @inheritParams F_X

diff --git a/R/outputs-make.R b/R/outputs-make.R
@@ -14,7 +14,7 @@ make_outputs = function(pars, de_vars, tm){
 make_outputs.full = function(pars, de_vars, tm){
   pars$outputs$time <- tm
   pars$outputs$last_y <- tail(de_vars, 1)
-  pars$outputs$bionomics <- get_bionomics(tm, de_vars, pars)
+#  pars$outputs$bionomics <- get_bionomics(tm, de_vars, pars)
   pars$outputs$orbits <- parse_orbits(de_vars, pars)
   pars$outputs$terms <- get_terms(tm, de_vars, pars)
   return(pars)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -107,6 +107,7 @@ reference:
   contents:
   - xde_solve
   - xde_stable_orbit
+  - xde_solve_cohort
   - xde_steady
   - dts_solve
   - dts_steady

diff --git a/docs/articles/GettingStarted.html b/docs/articles/GettingStarted.html
diff --git a/docs/articles/aqua_trace.html b/docs/articles/aqua_trace.html