add error message for missing strata

R/est.incidence.by.R

@@ -49,7 +49,7 @@
 #'   curve_params = curve,
 #'   noise_params = noise %>% filter(Country == "Pakistan"),
 #'   antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
-#'   #num_cores = 8 # Allow for parallel processing to decrease run time
+#'   # num_cores = 8 # Allow for parallel processing to decrease run time
 #'   iterlim = 5 # limit iterations for the purpose of this example
 #' )
 #'
@@ -101,6 +101,36 @@ est.incidence.by <- function(
     return(to_return)
   }
 
+  if (!all(is.element(strata, pop_data %>% names()))) {
+    # accommodate multiple strata
+    combined_pattern <- paste(strata, collapse = "|")
+
+    # search strata variable from pop_data
+    present_vars <-
+      grep(
+        x = pop_data %>% names(),
+        value = TRUE,
+        pattern = combined_pattern,
+        ignore.case = TRUE
+      )
+
+    not_present_vars <- setdiff(
+      x = strata,
+      y = present_vars
+    )
+
+    cli::cli_abort(
+      class = "missing_var",
+      message = c(
+        "x" = "Can't stratify with the provided strata.",
+        "i" = "The {.arg strata} option{?s} {.arg {not_present_vars}} {?is/are} missing in {.arg pop_data}.",
+        if (length(present_vars) > 0) {
+          "i" <- "Did you mean {.var {present_vars}}?"
+        }
+      )
+    )
+  }
+
   .checkStrata(data = pop_data, strata = strata)
 
   .errorCheck(

tests/testthat/test-est.incidence.R

@@ -79,3 +79,36 @@ test_that("`est.incidence()` produces expected results", {
 
   expect_equal(est_true, est_false)
 })
+
+test_that("est.incidence() aborts when strata is missing in `pop_data`", {
+  # get pop data
+  xs_data <- load_pop_data(
+    file_path = "https://osf.io/download//n6cp3/",
+    age = "Age",
+    value = "result",
+    id = "index_id",
+    standardize = TRUE
+  ) %>%
+    filter(Country == "Pakistan") %>%
+    slice_head(n = 100)
+
+  # get noise data
+  noise <- load_noise_params("https://osf.io/download//hqy4v/") %>%
+    filter(Country == "Pakistan")
+
+  # get curve data
+  curve <- load_curve_params("https://osf.io/download/rtw5k/")
+
+  expect_error(
+    object = est.incidence.by(
+      strata = c("catch"),
+      pop_data = xs_data %>% filter(Country == "Pakistan"),
+      curve_params = curve,
+      noise_params = noise %>% filter(Country == "Pakistan"),
+      antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
+      # num_cores = 8 # Allow for parallel processing to decrease run time
+      iterlim = 5 # limit iterations for the purpose of this example
+    ),
+    class = "missing_var"
+  )
+})