Join species IDs to fix dogfish

R/tidy-cpue-index.R

@@ -68,10 +68,10 @@ tidy_cpue_index <- function(dat, species_common,
   ), ]
   names(dat) <- tolower(names(dat))
 
-  if (!"species_common_name" %in% names(dat)) {
-    dat <- inner_join(dat, gfplot::pbs_species, by = "species_code")
-  }
-
+  # if (!"species_common_name" %in% names(dat)) {
+  dat$species_common_name <- NULL
+  dat <- inner_join(dat, gfplot::pbs_species, by = "species_code")
+  # }
   dat <- dat %>% mutate(year = lubridate::year(best_date))
 
   # create possibly alternate starting date:
@@ -163,6 +163,8 @@ tidy_cpue_index <- function(dat, species_common,
 
   # retain the data from our "fleet"
   d_retained <- semi_join(catch, fleet, by = "vessel_registration_number")
+
+
   if (return_raw_data) {
     return(d_retained)
   }