Input bread crumbs for Nathan to follow for fixing the code for RS

nmfs-fish-tools · May 22, 2024 · 6ee0820 · 6ee0820
1 parent 6f3069d
commit 6ee0820
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/RatioBiasEM.R b/R/RatioBiasEM.R
@@ -715,7 +715,7 @@ BiasEM <- function(EM_out_dir = NULL, init_loop = TRUE, OM_dat, verbose = FALSE,
   # new_OM_catch_list$catch_bio <- NULL
 
   if(!is.null(new_OM_catch_list$discards)){
-    tmp_discards <- base::merge(new_OM_catch_list$discards, sample_struct$EM2OMdiscard_bias, all.x=TRUE)
+    tmp_discards <- base::merge(abs(new_OM_catch_list$discards), abs(sample_struct$EM2OMdiscard_bias), all.x=TRUE) #need to sort to figure this out
     new_OM_catch_list$discards$Discard <- new_OM_catch_list$discards$Discard * tmp_discards$bias 
   }
 

diff --git a/R/parse_MS.R b/R/parse_MS.R
@@ -66,7 +66,7 @@ parse_MS <- function(MS, EM_out_dir = NULL, EM_init_dir = NULL,
     interim_struct = interim_struct,
     seed = seed
   )
-
+  # browser()
   new_catch_list <- do.call(MS, args = pars_list)
 
   # to do: need better checks on function name? Maybe be more explicit on