refactor (*.R): Adhere to tidyverse principals

by cleaning up the R code

Removes functions
* mkObj
* create_rcpp_interface_object
* use_module
* %>%
* FIMSFrameAge

Adds importFrom(TMB, MakeADFun) to package b/c TMB is no longer
explicitly used in the codebase. And, experimented with removing usethis
b/c it was also used in ./R/ but is still used in data-raw. It is now a
suggested package. Uses :: instead of importing functions, e.g.,
utils::head().

* Constricts line width to 80 characters
* Use full stops at the end of sentences
* Implement more spacing in between roxygen tags
* Move export tag to the end in most instances
* Use explicit brackets for if statements
* Remove duplicated code in gtest by calling run_gtest()
* Parameter and object names to snake_case
* Parameter, function, and object names, largely, w/o abbreviations

fix(run_gtest): Use paste() instead of paste0() to ensure proper spacing
which is not explicit in the instructions. With paste()
they can input as many additional arguments as they want and they are
all automatically separated, e.g.,
`run_gtest("--something", "--something-else")`

Close #588
Close #564
Close #590

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,

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: