Merge branch 'main' into improve_interface_for_bayesian

R/obsSim_consistency.R

@@ -236,8 +236,10 @@ is_sim_inf_or_na <- function(sim_list, obs_list, param_values) {
  var_list <- lapply(names(sim_list[[sit]]), function(x) {
  if (any(is.infinite(sim_list[[sit]][!is.na(obs_list[[sit]][,x]),][[x]])) ||
  any(is.na(sim_list[[sit]][!is.na(obs_list[[sit]][,x]),][[x]]))) {
- return(list(sim_list[[sit]]$Date[is.infinite(sim_list[[sit]][!is.na(obs_list[[sit]][,x]),][[x]]) |
- is.na(sim_list[[sit]][!is.na(obs_list[[sit]][,x]),][[x]])]))
+ return(list(sim_list[[sit]]$Date[(is.infinite(sim_list[[sit]][[x]]) &
+ !is.na(obs_list[[sit]][,x])) |
+ (is.na(sim_list[[sit]][[x]]) &
+ !is.na(obs_list[[sit]][,x]))]))
  } else {
  return(NULL)
  }

tests/testthat/test-obsSim_consistency.R

@@ -69,20 +69,43 @@ test_that("Check is_sim_inf_or_na return FALSE when sim is not Inf neither NA wh
 sim_list <- obs_list
 sim_list$sit1$var1[[1]] <- Inf
 param_values <- c(p1=1.0, p2=2.0)
-res <- eval(parse(
- text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)"))
 test_that("Check is_sim_inf_or_na return TRUE when sim is Inf or NA when there is a corresponding observed value, case 1", {
- expect_true(res)
+ expect_warning(eval(parse(
+ text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)")))
+
+ withCallingHandlers(eval(parse(
+ text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)")),
+ warning = function(w) {
+ # Check if the warning message contains all expected substrings
+
+ expected_substrings <- c("var1", "2009-11-30", "sit1")
+
+ expect_true(all(stringr::str_detect(w$message,expected_substrings)),
+ info = paste("Not all expected substrings found in the warning message:", w$message))
+ }
+ )
 })
 
 # Check if is_sim_inf_or_na return TRUE when it must, missing values for several dates
 sim_list <- obs_list
 sim_list$sit3$var2 <- NA
 param_values <- c(p1=1.0, p2=2.0)
-res <- eval(parse(
- text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)"))
-test_that("Check is_sim_inf_or_na return TRUE when sim is Inf or NA when there is a corresponding observed value, case 2", {
- expect_true(res)
+test_that("Check is_sim_inf_or_na return TRUE when sim is Inf or NA when there is a corresponding observed value, case 1", {
+ expect_warning(eval(parse(
+ text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)")))
+
+ withCallingHandlers(eval(parse(
+ text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)")),
+ warning = function(w) {
+ # Check if the warning message contains all expected substrings
+
+ expected_substrings <- c("var2", "2010-10-03",
+ "2010-10-04", "sit3")
+
+ expect_true(all(stringr::str_detect(w$message,expected_substrings)),
+ info = paste("Not all expected substrings found in the warning message:", w$message))
+ }
+ )
 })
 
 
@@ -92,9 +115,22 @@ sim_list$sit1$var1[[1]] <- Inf
 sim_list$sit3$var1[[2]] <- NA
 sim_list$sit3$var2 <- NA
 param_values <- c(p1=1.0, p2=2.0)
-res <- eval(parse(
- text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)"))
-test_that("Check is_sim_inf_or_na return TRUE when sim is Inf or NA when there is a corresponding observed value, case 3", {
- expect_true(res)
+test_that("Check is_sim_inf_or_na return TRUE when sim is Inf or NA when there is a corresponding observed value, case 1", {
+ expect_warning(eval(parse(
+ text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)")))
+
+ withCallingHandlers(eval(parse(
+ text = "CroptimizR:::is_sim_inf_or_na(sim_list, obs_list, param_values)")),
+ warning = function(w) {
+ # Check if the warning message contains all expected substrings
+
+ expected_substrings <- c("var1", "2009-11-30", "sit1",
+ "var2", "2010-10-03",
+ "2010-10-04", "sit3")
+
+ expect_true(all(stringr::str_detect(w$message,expected_substrings)),
+ info = paste("Not all expected substrings found in the warning message:", w$message))
+ }
+ )
 })