From e76c39db5f4c03baf37e8e7cecdd252f09c987c8 Mon Sep 17 00:00:00 2001
From: Kevin See <kevin.see@dfw.wa.gov>
Date: Fri, 23 Feb 2024 13:48:36 -0800
Subject: [PATCH] updated package dependencies in DESCRIPTION (and in a couple
 functions)

---
 DESCRIPTION       | 31 +++++++++++++++++--------------
 R/prepJAGS.R      |  3 +--
 R/queryTrapRate.R |  2 +-
 3 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8157689..ad6a3a0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,25 +9,28 @@ URL: https://github.com/KevinSee/STADEM
 BugReports: https://github.com/KevinSee/STADEM/issues
 Description: Estimate wild, hatchery and hatchery no-clip escapement for Chinook or steelhead (focused on Lower Granite dam) in a given year, accounting for error in window counts, re-ascension and night-time passage rates and uncertain trap rates.
 Depends: 
-  R (>= 3.2.3),
+  R (>= 4.0.0),
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: TRUE
 Imports:
+    boot (>= 1.3.28),
+    coda (>= 0.19.4),
     dplyr (>= 1.1.2),
+    ggplot2 (>= 3.4.2),
+    httr (>= 1.4.6),
+    janitor (>= 2.2.0),
+    lubridate (>= 1.9.2),
+    readr (>= 2.1.2),
+    rjags (>= 4.12),
     stringr (>= 1.5.0),
-    boot,
-    httr (>= 1.2.1),
-    lubridate (>= 1.3.3),
-    rjags (>= 4-6),
-    Hmisc (>= 4.2-0),
-    janitor (>= 2.0.0)
+    tidyr (>= 1.3.0)
 RoxygenNote: 7.2.3
-Suggests: 
-  knitr,
-  rmarkdown,
-  ggplot2,
-  ggpubr,
-  jagsUI (>= 1.4.4),
-  kableExtra
 VignetteBuilder: knitr
+Suggests: 
+    ggpubr (>= 0.4.0),
+    Hmisc (>= 4.6.0),
+    jagsUI (>= 1.5.2),
+    kableExtra (>= 1.3.4),
+    knitr (>= 1.42),
+    rmarkdown (>= 2.20)
diff --git a/R/prepJAGS.R b/R/prepJAGS.R
index bf461d5..7d66a9d 100644
--- a/R/prepJAGS.R
+++ b/R/prepJAGS.R
@@ -10,7 +10,6 @@
 #' @param wild_tags Should only wild PIT tags be used to estimate daytime passage and re-ascension rates? Default is \code{FALSE}.
 #'
 #' @import dplyr
-#' @importFrom plyr dlply
 #' @export
 #' @return NULL
 #'
@@ -37,7 +36,7 @@ prepJAGS = function(lgr_weekly = NULL,
 
   # is ladder open? 1 if yes, 0 if no
   ladder = lgr_weekly %>%
-    transmute(open = if_else(window_open | trap_open,
+    mutate(open = if_else(window_open | trap_open,
                              1, 0)) %>%
     pull(open)
 
diff --git a/R/queryTrapRate.R b/R/queryTrapRate.R
index 141459e..dd5dbf3 100644
--- a/R/queryTrapRate.R
+++ b/R/queryTrapRate.R
@@ -10,7 +10,7 @@
 #'
 #' @source \url{http://www.cbr.washington.edu/dart}
 #'
-#' @import lubridate dplyr
+#' @import lubridate dplyr readr
 #' @export
 #' @return NULL