fix: select with .data deprecated

see https://www.tidyverse.org/blog/2022/10/tidyselect-1-2-0/#using-data-inside-selections
nmfs-fish-tools · Apr 1, 2024 · ba9ef37 · ba9ef37
1 parent bfb64a8
commit ba9ef37
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Showing 3 changed files with 8 additions and 10 deletions.
diff --git a/R/MS_functions.R b/R/MS_functions.R
@@ -249,19 +249,19 @@ get_EM_catch_df <- function(EM_dir, dat) {
     dplyr::summarise(catch = sum(.data[["catch"]])) %>%
     merge(se, all.x = TRUE, all.y = FALSE) %>%
     dplyr::ungroup() %>%
-    dplyr::select(.data[["year"]], .data[["seas"]], .data[["fleet"]], .data[["catch"]], .data[["catch_se"]])
+    dplyr::select(dplyr::all_of(c("year", "seas", "fleet", "catch","catch_se")))
   catch_bio_df <- catch_bio_df %>%
     dplyr::group_by(.data[["year"]], .data[["seas"]], .data[["fleet"]]) %>%
     dplyr::summarise(catch = sum(.data[["catch"]])) %>%
     merge(se, all.x = TRUE, all.y = FALSE) %>%
     dplyr::ungroup() %>%
-    dplyr::select(.data[["year"]], .data[["seas"]], .data[["fleet"]], .data[["catch"]], .data[["catch_se"]])
+    dplyr::select(dplyr::all_of(c("year", "seas", "fleet", "catch", "catch_se")))
   catch_F_df <- catch_F_df %>%
     dplyr::group_by(.data[["year"]], .data[["seas"]], .data[["fleet"]]) %>%
     dplyr::summarise(catch = sum(.data[["catch"]])) %>%
     merge(se, all.x = TRUE, all.y = FALSE) %>%
     dplyr::ungroup() %>%
-    dplyr::select(.data[["year"]], .data[["seas"]], .data[["fleet"]], .data[["catch"]], .data[["catch_se"]])
+    dplyr::select(dplyr::all_of(c("year","seas","fleet","catch","catch_se")))
 
   catch_df <- as.data.frame(catch_df)
   catch_bio_df <- as.data.frame(catch_bio_df)

diff --git a/R/calc_F.R b/R/calc_F.R
@@ -183,7 +183,7 @@ get_retained_catch <- function(timeseries, units_of_catch) {
   retain_catch_df <- retain_catch_df %>%
     dplyr::group_by(.data[["Yr"]], .data[["Era"]], .data[["Seas"]], .data[["Units"]], .data[["Fleet"]]) %>%
     dplyr::summarise(retained_catch = sum(.data[["retained_catch"]])) %>%
-    dplyr::select(.data[["Yr"]], .data[["Era"]], .data[["Seas"]], .data[["Units"]], .data[["Fleet"]], .data[["retained_catch"]])
+    dplyr::select(dplyr::all_of(c("Yr","Era","Seas","Units","Fleet","retained_catch")))
   retain_catch_df <- as.data.frame(retain_catch_df) # want as df and not tibble
   # units are not as concise as they could be, but leave for now.
   retain_catch_df
@@ -242,10 +242,8 @@ get_dead_catch <- function(timeseries, units_of_catch) {
   dead_catch_df <- dead_catch_df %>%
     dplyr::group_by(.data[["Yr"]], .data[["Era"]], .data[["Seas"]], .data[["Units"]], .data[["Fleet"]]) %>%
     dplyr::summarise(retained_catch = sum(.data[["retained_catch"]])) %>%
-    dplyr::select(
-      .data[["Yr"]], .data[["Era"]], .data[["Seas"]], .data[["Units"]], .data[["Fleet"]],
-      .data[["retained_catch"]]
-    )
+    dplyr::select(dplyr::all_of(c("Yr", "Era", "Seas", "Units", "Fleet",
+     "retained_catch")))
   dead_catch_df <- as.data.frame(dead_catch_df)
   # units are not as concise as they could be, but leave for now.
 }
diff --git a/R/initOM_create_devs_list.R b/R/initOM_create_devs_list.R
@@ -409,8 +409,8 @@ add_dev_changes <- function(fut_list, scen, iter, parlist, dat, vals_df, nyrs, c
       custom_vals <- fut_list[["input"]][fut_list[["input"]][["scen"]] %in% c("all", scen) &
         fut_list[["input"]][["par"]] == i &
         fut_list[["input"]][["iter"]] == iter, ]
-      custom_vals <- dplyr::select(custom_vals, .data[["yr"]], .data[["value"]]) %>%
-        dplyr::rename(yrs = .data[["yr"]])
+      custom_vals <- dplyr::select(custom_vals, dplyr::all_of(c("yr","value"))) %>%
+        dplyr::rename(yrs = "yr")
       vals_df <- dplyr::left_join(vals_df, custom_vals, by = "yrs") %>%
         tidyr::replace_na(replace = list(value = tmp_base))
       vals_df[[i]] <- vals_df[["value"]] # move to the correct column