Use 'stock' instead of 'taxa'

Author: arni-magnusson

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SOFIA
 Version: 2.0.0
-Date: 2022-08-04
+Date: 2022-08-08
 Title: Tools to Work with SOFIA Analyses
 Authors@R: c(person("Rishi", "Sharma", role="aut"),
              person("Arni", "Magnusson", role=c("aut","cre"), email="thisisarni@gmail.com"))

NEWS.md

@@ -1,4 +1,4 @@
-# SOFIA 2.0.0 (2022-08-04)
+# SOFIA 2.0.0 (2022-08-08)
 
 * Added functions gitRepos(), gitClone(), and gitCloneAll() to list and clone
   GitHub repositories.
@@ -7,6 +7,10 @@
 
 * Added errors and warnings if stock names in catch/effort/priors don't match.
 
+* Simplified addDriors() so it requires only the 'stock' name, not the 'taxa'
+  name. These names used to be identical, but only 'stock' will be used from now
+  on.
+
 * Improved plotCat() so it treats the first two columns of the input data frame
   as stock and year.
 

R/addDriors.R

@@ -2,8 +2,7 @@
 #'
 #' Add driors (data and priors) column to \sQuote{stocks} object.
 #'
-#' @param stocks \code{tibble} containing \code{stock}, \code{taxa}, and
-#'        \code{data}.
+#' @param stocks \code{tibble} containing \code{stock} and \code{data}.
 #' @param priors data frame containing \code{stock}, \code{initial_state},
 #'        \code{initial_state_cv}, \code{terminal_state}, and
 #'        \code{terminal_state_cv}.
@@ -73,7 +72,7 @@ addDriors <- function(stocks, priors, same.priors, shape_prior=2,
     p <- if(same.priors) match("All", priors$stock)
          else match(stocks$stock[i], priors$stock)
     driors[[i]] <- format_driors(
-      taxa = stocks$taxa[i],
+      taxa = stocks$stock[i],
       shape_prior = 2,
       catch = stocks$data[[i]]$capture,
       years = stocks$data[[i]]$year,