Refactor scalar case_when() branches in convert_output() to if/else

R/convert_output.R

@@ -475,12 +475,7 @@ convert_output <- function(
               if ("sexes" %in% colnames(df3)) {
                 df3 <- df3 |>
                   # add in case if sexes is present and add sex as na if so
-                  dplyr::mutate(
-                    sex = dplyr::case_when(
-                      any(grepl("^sexes$", colnames(df3))) ~ sexes,
-                      TRUE ~ NA
-                    )
-                  ) |>
+                  dplyr::mutate(sex = if (any(grepl("^sexes$", colnames(df3)))) sexes else NA) |>
                   dplyr::select(-sexes)
               } else {
                 df3 <- dplyr::mutate(df3, sex = NA)
@@ -667,7 +662,7 @@ convert_output <- function(
                   label == "f" ~ "fishing_mortality",
                   TRUE ~ label
                 ),
-                estimate = as.numeric(estimate)
+                estimate = suppressWarnings(as.numeric(estimate))
                   # dplyr::if_else(
                   # grepl("-|_", as.numeric(estimate)),
                   # NA,
@@ -1425,10 +1420,7 @@ convert_output <- function(
     out_new <- Reduce(rbind, out_list)
     out_new <- out_new |>
       dplyr::mutate(
-        fleet = dplyr::case_when(
-          any(unique(out_new$fleet) %in% fleet_names) ~ fleet,
-          TRUE ~ fleet_names[fleet]
-        ),
+        fleet = if (any(unique(out_new$fleet) %in% fleet_names)) fleet else fleet_names[fleet],
         era = dplyr::case_when(
           !is.na(era) ~ era,
           year < start_year ~ "init",
@@ -2395,7 +2387,14 @@ convert_output <- function(
       var_names_sheet <- var_names_sheet |> dplyr::select(-module_name)
       out_new <- dplyr::left_join(out_new, var_names_sheet, by = "label")
     } else {
-      out_new <- dplyr::left_join(out_new, var_names_sheet, by = c("module_name", "label"))
+      var_names_sheet <- var_names_sheet |>
+        dplyr::distinct(module_name, label, .keep_all = TRUE)
+      out_new <- dplyr::left_join(
+        out_new,
+        var_names_sheet,
+        by = c("module_name", "label"),
+        relationship = "many-to-one"
+      )
     }
     out_new <- out_new |>
       dplyr::mutate(label = dplyr::case_when(

R/utils_plot.R

@@ -375,10 +375,7 @@ plot_aa <- function(
     dplyr::mutate(
       age = as.numeric(age),
       # zvar = .data[[z]],
-      zvar = dplyr::case_when(
-        proportional ~ sqrt(.data[[z]]),
-        TRUE ~ .data[[z]]
-      )
+      zvar = if (proportional) sqrt(.data[[z]]) else .data[[z]]
     )
   # Caclaulate x-axis breaks
   x_n_breaks <- axis_breaks(dat[[x]])

tests/testthat/test-convert_output.R

@@ -25,6 +25,12 @@ test_that("convert_output works for SS3", {
   expect_equal(dim(output)[2], 34)
 })
 
+test_that("convert_output does not emit scalar case_when deprecation warning", {
+  expect_no_warning(convert_output(
+    file = fs::path("fixtures", "ss3_models", "models", "Hake_2018", "Report.sso")
+  ))
+})
+
 
 test_that("convert_output saves model ss3 hake output file", {
   dir.create(fs::path("fixtures", "ss3_models_converted", "Hake_2018"), recursive = TRUE)

tests/testthat/test-utils_plot.R

@@ -78,7 +78,7 @@ test_that("plot_aa and helper line builders return expected outputs", {
     group_var = "1"
   )
 
-  proportional_plot <- plot_aa(aa_dat, proportional = TRUE)
+  expect_no_warning(proportional_plot <- plot_aa(aa_dat, proportional = TRUE))
   expect_s3_class(proportional_plot, "gg")
   expect_equal(proportional_plot$theme$legend.position, "none")