catch dev branch up with main

.devcontainer/devcontainer.json

@@ -13,9 +13,14 @@
 			"packages": "make,gcc,g++,cmake,clang-tidy,clang-format,clang,doxygen,ninja-build,libxtst6,libxt6"			
 		},
 		 "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-			"packages": "Matrix,cli,rlang,RcppEigen,TMB,ggplot2,dplyr,scales,covr",
-			 "installSystemRequirements": true
-		  }
+			"packages": "RcppEigen,dplyr,ggplot2,jsonlite,magrittr,methods,Rcpp,scales,TMB,usethis,devtools",
+			"installSystemRequirements": true
+		  },
+		 // option to run rstudio. you can type rserver into the command line to
+		 // get an session going (opens on a port, that you can open as a 
+		 // separate browser window).
+		 // more details: https://github.com/rocker-org/devcontainer-features/blob/main/src/rstudio-server/README.md
+		 "ghcr.io/rocker-org/devcontainer-features/rstudio-server:0": {}
 		},
 	// // if we want quarto cli
 	     // more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/quarto-cli/README.md

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,8 +2,6 @@ name: Bug Report
 description: Report a bug that causes the existing functionality to differ from what is described in the development plan
 title: "[Bug]: "
 labels: ["kind: bug", "triage_needed"]
-assignees:
-  - ChristineStawitz-NOAA
 body:
   - type: markdown
     attributes:

.github/ISSUE_TEMPLATE/developer_other_issue.yml

@@ -2,8 +2,6 @@ name: Developer (other issue)
 description: For FIMS implementation team members to document other types of issues
 title: "[Developer Issue]: "
 labels: ["status: triage_needed"]
-assignees:
-  - ChristineStawitz-NOAA
 body:
   - type: markdown
     attributes:

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -2,8 +2,6 @@ name: Feature Request
 description: Request new features or changes to features, such that the described functionality differs from what is currently in the development plan
 title: "[Feature]: "
 labels: ["kind: enhancement", "status: triage_needed"]
-assignees:
-  - ChristineStawitz-NOAA
 body:
   - type: markdown
     attributes:

.github/ISSUE_TEMPLATE/refactor_request.yml

@@ -2,8 +2,6 @@ name: Refactor
 description: Change the current structure of the code
 title: "[Refactor]: "
 labels: ["kind: refactor", "status: triage_needed"]
-assignees:
-  - ChristineStawitz-NOAA
 body:
   - type: markdown
     attributes:

DESCRIPTION

@@ -59,18 +59,17 @@ Imports:
     dplyr,
     ggplot2,
     jsonlite,
-    magrittr,
     methods,
     Rcpp,
     scales,
-    TMB (>= 1.8.0),
-    usethis
+    TMB (>= 1.8.0)
 Suggests: 
     covr,
     knitr,
     remotes,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    usethis
 LinkingTo: 
     Rcpp,
     RcppEigen,
@@ -83,5 +82,5 @@ Encoding: UTF-8
 LazyData: true
 NeedsCompilation: yes
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 SystemRequirements: GNU make

NAMESPACE

@@ -1,13 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(AgeComp)
 export(BevertonHoltRecruitment)
 export(CreateTMBModel)
 export(DoubleLogisticSelectivity)
 export(EWAAgrowth)
 export(FIMSFrame)
-export(FIMSFrameAge)
 export(Fleet)
 export(Index)
 export(LogisticMaturity)
@@ -19,17 +17,14 @@ export(TMBDmultinomDistribution)
 export(TMBDnormDistribution)
 export(clear)
 export(clear_logs)
-export(create_fims_rcpp_interface)
 export(get_fixed)
 export(get_random)
 export(m_agecomp)
 export(m_index)
 export(m_landings)
-export(mkObj)
 export(run_gtest)
 export(setup_and_run_gtest)
 export(setup_gtest)
-export(use_module)
 exportMethods(m_agecomp)
 exportMethods(m_index)
 exportMethods(m_landings)
@@ -38,8 +33,4 @@ import(stats)
 importFrom(Rcpp,sourceCpp)
 importFrom(TMB,MakeADFun)
 importFrom(ggplot2,.data)
-importFrom(magrittr,"%>%")
-importFrom(usethis,ui_stop)
-importFrom(usethis,use_template)
-importFrom(utils,head)
 useDynLib(FIMS, .registration = TRUE)

R/FIMS-package.R

@@ -1,11 +1,10 @@
 ## usethis namespace: start
 #' @useDynLib FIMS, .registration = TRUE
 #' @importFrom Rcpp sourceCpp
-#' @importFrom utils head
+#' @importFrom TMB MakeADFun
 #' @import stats
 #' @import methods
 #' @importFrom ggplot2 .data
-#' @importFrom usethis use_template ui_stop
 #' @export CreateTMBModel
 #' @export get_fixed
 #' @export get_random

R/data_mile1.R

@@ -1,9 +1,9 @@
-#' {FIMS} input data frame for milestone 1
+#' FIMS input data frame for milestone 1
 #'
 #' A dataset containing information necessary to run an age-structured stock
-#' assessment model in {FIMS} for milestone 1. This data was generated using
-#' the `ASSAMC` package written for the
-#' [model comparison project](www.github.com/Bai-Li-NOAA/Age_Structured_Stock_Assessment_Model_Comparison).
+#' assessment model in FIMS for milestone 1. This data was generated using
+#' the `ASSAMC` package written for the [model comparison project](
+#' www.github.com/Bai-Li-NOAA/Age_Structured_Stock_Assessment_Model_Comparison).
 #'
 #' @format A data frame with `r NROW(data_mile1)` observations of
 #' `r NCOL(data_mile1)` variables: