Merge branch 'main' of https://github.com/mrc-ide/YEP

mrc-ide · May 9, 2024 · a276fe0 · a276fe0
2 parents e3b852c + 1ae1bca
commit a276fe0
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Showing 4 changed files with 3 additions and 3 deletions.
diff --git a/R/main.R b/R/main.R
@@ -618,9 +618,9 @@ param_calc_enviro <- function(enviro_coeffs=c(),enviro_covar_values=c()){
   assert_that(length(enviro_coeffs) %in% c(n_env_vars,2*n_env_vars),msg="Wrong number of environmental coefficients")
 
   output=list(FOI=NA,R0=NA)
-  output$FOI=sum(enviro_coeffs[c(1:n_env_vars)]*enviro_covar_values)
+  output$FOI=max(0.0,sum(enviro_coeffs[c(1:n_env_vars)]*enviro_covar_values))
   if(length(enviro_coeffs)==2*n_env_vars){
-    output$R0=sum(enviro_coeffs[c(1:n_env_vars)+n_env_vars]*enviro_covar_values)
+    output$R0=max(0.0,sum(enviro_coeffs[c(1:n_env_vars)+n_env_vars]*enviro_covar_values))
     }
 
   return(output)

diff --git a/R/mcmc.R b/R/mcmc.R
@@ -255,7 +255,7 @@ single_posterior_calc <- function(log_params_prop=c(),input_data=list(),obs_sero
   if (is.finite(prior_prop)) {
 
     #Generate modelled data over all regions
-    if(p_rep_severe %in% names(consts$add_values)){
+    if("p_rep_severe" %in% names(consts$add_values)){
       dataset <- Generate_Dataset(input_data,FOI_values,R0_values,obs_sero_data,obs_case_data,vaccine_efficacy,
                                   consts$p_severe_inf,consts$p_death_severe_inf,p_rep_severe,p_rep_death,
                                   consts$mode_start,start_SEIRV=NULL,consts$dt,consts$n_reps,consts$deterministic,

diff --git a/src/YEP.dll b/src/YEP.dll
diff --git a/src/cpp11.o b/src/cpp11.o