Merge remote-tracking branch 'origin/main' into exp_comps

pfmc-assessments · Aug 23, 2024 · 35b5846 · 35b5846
2 parents 2838578 + 9593eb3
commit 35b5846
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Showing 2 changed files with 28 additions and 21 deletions.
diff --git a/R/est_weight_length.R b/R/est_weight_length.R
@@ -67,9 +67,10 @@ estimate_weight_length <- function(
     female = . %>% dplyr::filter(sex %in% c("F", "Female", "f")),
     male = . %>% dplyr::filter(sex %in% c("M", "Male", "m")),
     all = . %>% dplyr::filter(sex %in% c(NA, "F", "M", "U", "H", "Male", "Female", "Unsexed", "m", "f", "u"))
-    ) |>
+  ) |>
     purrr::map_dfr(~ tidyr::nest(.x(data), data = everything()),
-      .id = "group") |>
+      .id = "group"
+    ) |>
     dplyr::mutate(
       fits = purrr::map(data, ~ stats::lm(log(weight) ~ log(length_cm),
         data = .x
@@ -83,7 +84,7 @@ estimate_weight_length <- function(
       SD = purrr::map_dbl(fits, ~ sd(.x$residuals)),
       A = purrr::map_dbl(fits, ~ exp(.x$coefficients[1]) * exp(0.5 * sd(.x$residuals)^2)),
       B = purrr::map_dbl(fits, ~ .x$coefficients[2])
-      ) |>
+    ) |>
     data.frame()
 
   if (verbose) {

diff --git a/R/plot_bio_patterns.R b/R/plot_bio_patterns.R
@@ -138,29 +138,35 @@ plot_bio_patterns <- function(
     )
 
   # plot 1
-  cowplot::plot_grid(ll, ld, nrow = 2)
-  if (!is.null(dir)) {
-    ggsave(
-      filename = file.path(dir, "plots", paste0(col_name, "_by_lat_depth.png")),
-      width = width, height = height, units = "in"
-    )
+  if (1 %in% plot) {
+    print(cowplot::plot_grid(ll, ld, nrow = 2))
+    if (!is.null(dir)) {
+      ggsave(
+        filename = file.path(dir, "plots", paste0(col_name, "_by_lat_depth.png")),
+        width = width, height = height, units = "in"
+      )
+    }
   }
 
   # plot 2
-  print(ldy)
-  if (!is.null(dir)) {
-    ggsave(
-      filename = file.path(dir, "plots", paste0(col_name, "_by_year_depth.png")),
-      width = width + 3, height = height + 3, units = "in"
-    )
+  if (2 %in% plot) {
+    print(ldy)
+    if (!is.null(dir)) {
+      ggsave(
+        filename = file.path(dir, "plots", paste0(col_name, "_by_year_depth.png")),
+        width = width + 3, height = height + 3, units = "in"
+      )
+    }
   }
 
   # plot 3
-  print(lly)
-  if (!is.null(dir)) {
-    ggsave(
-      filename = file.path(dir, "plots", paste0(col_name, "_by_year_lat.png")),
-      width = width + 3, height = height + 3, units = "in"
-    )
+  if (3 %in% plot) {
+    print(lly)
+    if (!is.null(dir)) {
+      ggsave(
+        filename = file.path(dir, "plots", paste0(col_name, "_by_year_lat.png")),
+        width = width + 3, height = height + 3, units = "in"
+      )
+    }
   }
 }