From 2afad88ae7b493f55493072c2f4e1a7e89634c10 Mon Sep 17 00:00:00 2001
From: Arni Magnusson <thisisarni@gmail.com>
Date: Mon, 8 Aug 2022 20:31:21 +1100
Subject: [PATCH] Use 'stock' instead of 'taxa'

---
 DESCRIPTION      | 2 +-
 NEWS.md          | 6 +++++-
 R/addDriors.R    | 5 ++---
 man/addDriors.Rd | 3 +--
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a386bec..6f65239 100644
--- a/DESCRIPTION
+++ b/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"))
diff --git a/NEWS.md b/NEWS.md
index 30da13d..45c30c9 100644
--- a/NEWS.md
+++ b/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.
 
diff --git a/R/addDriors.R b/R/addDriors.R
index 6d0fbc4..0adcd92 100644
--- a/R/addDriors.R
+++ b/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,
diff --git a/man/addDriors.Rd b/man/addDriors.Rd
index e77bada..eef35c0 100644
--- a/man/addDriors.Rd
+++ b/man/addDriors.Rd
@@ -8,8 +8,7 @@ addDriors(stocks, priors, same.priors, shape_prior = 2, b_ref_type = "k",
   growth_rate_prior = NA, growth_rate_prior_cv = 0.2, ...)
 }
 \arguments{
-\item{stocks}{\code{tibble} containing \code{stock}, \code{taxa}, and
-\code{data}.}
+\item{stocks}{\code{tibble} containing \code{stock} and \code{data}.}
 
 \item{priors}{data frame containing \code{stock}, \code{initial_state},
 \code{initial_state_cv}, \code{terminal_state}, and