Added flag for noncontiguous samples. Should check output to make sure it still plots with NAs

Author: slucey

MultisppRec2024.Rmd

@@ -539,11 +539,15 @@ calc_rec <- function(survdat,
                         COMNAME, SCINAME)
       }
     } %>%
-    dplyr::mutate(recruits_biom_lead1 = dplyr::lead(recruits_biom,
+    dplyr::mutate(bad_pair = !is.na(lead(YEAR)) &
+                    ((YEAR +1 != lead(YEAR)) | (SEASON != lead(SEASON))),
+                  recruits_biom_lead1 = dplyr::lead(recruits_biom,
                                                     n = 1),
                   recruits_abund_lead1 = dplyr::lead(recruits_abund,
-                                                     n = 1),
-                  rs         = recruits_abund_lead1/
+                                                     n = 1)) %>%
+    dplyr::mutate(across(c(recruits_biom_lead1, recruits_abund_lead1),
+                         ~ ifelse(bad_pair, NA, .))) %>%
+    dplyr::mutate(rs         = recruits_abund_lead1/
                                spawners_biom,
                   rs_abund   = recruits_abund_lead1/
                                 spawners_abund,