style and docs: run devtools::document() and styler::style_pkg()

* styler is automatically creating four spaces for function argument indents when the tidyverse style guide only has 2 with the ) { on the next line. So, I went in and manually changed them all back. * Removed the latex code from the maturity vignette because it was leading to a failed build on R universe. * Fixed incorrect edit to call-calc_coverage with adding workflow_dispatch underneath a PR.
NOAA-FIMS · Jan 3, 2025 · cb222ec · cb222ec
1 parent 2338d23
commit cb222ec
Show file tree

Hide file tree

Showing 19 changed files with 156 additions and 256 deletions.
diff --git a/.github/workflows/call-calc-coverage.yml b/.github/workflows/call-calc-coverage.yml
@@ -4,8 +4,6 @@ name: call-calc_coverage
 # The default is to run the workflow on every push or pull request to every branch.
 on:
   workflow_dispatch:
-  push:
-    on: workflow_dispatch
     paths-ignore:
       - .devcontainer
       - .github

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,122 +2,44 @@ Package: FIMS
 Title: The Fisheries Integrated Modeling System
 Version: 0.3.0.0
 Authors@R: c(
-    person(
-      role = c("aut", "cre"),
-      family = "Johnson",
-      given = c("Kelli", "F."),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-5149-451X")
-    ),
-    person(
-      role = "aut",
-      family = "Brodziak",
-      given = c("Jon", "K.", "T."),
-      comment = c(ORCID = "0000-0001-8690-5588")
-    ),
-    person(
-      role = "aut",
-      family = "Doering",
-      given = c("Kathryn", "L."),
-      comment = c(ORCID = "0000-0002-0396-7044")
-    ),
-    person(
-      role = "aut",
-      family = "Havron",
-      given = c("Andrea", "M."),
-      comment = c(ORCID = "0000-0002-4080-448X")
-    ),
-    person(
-      role = "aut",
-      family = "Klasky",
-      given = c("Ronald"),
-      comment = c(ORCID = "0009-0004-7563-7716")
-    ),
-    person(
-      role = "aut",
-      family = "Kuriyama",
-      given = c("Peter", "T."),
-      comment = c(ORCID = "0000-0002-6971-4015")
-    ),
-    person(
-      role = "aut",
-      family = "Legault",
-      given = c("Christopher", "M."),
-      comment = c(ORCID = "0000-0002-0328-1376")
-    ),
-    person(
-      role = "aut",
-      family = "Li",
-      given = "Bai",
-      comment = c(ORCID = "0000-0002-8249-1442")
-    ),
-    person(
-      role = "aut",
-      family = "Miller",
-      given = c("Timothy", "J."),
-      comment = c(ORCID = "0000-0003-1411-1206")
-    ),
-    person(
-      role = "aut",
-      family = "Monnahan",
-      given = c("Cole", "C."),
-      comment = c(ORCID = "0000-0003-0871-6700")
-    ),
-    person(
-      role = "aut",
-      family = "Oshima",
-      given = c("Megumi", "C."),
-      comment = c(ORCID = "0009-0002-2239-1594")
-    ),
-    person(
-      role = "aut",
-      family = "Shertzer",
-      given = c("Kyle", "W."),
-      comment = c(ORCID = "0000-0001-7196-5959")
-    ),
-    person(
-      role = "aut",
-      family = "Stawitz",
-      given = c("Christine", "C."),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0003-3122-4501")
-    ),
-    person(
-      role = "aut",
-      family = "Sullivan",
-      given = c("Jane", "Y."),
-      comment = c(ORCID = "0000-0002-8094-1673")
-    ),
-    person(
-      role = "aut",
-      family = "Supernaw",
-      given = "Matthew",
-      comment = c(ORCID = "0009-0007-3681-7433")
-    ),
-    person(
-      role = "aut",
-      family = "Taylor",
-      given = c("Ian", "G."),
-      comment = c(ORCID = "0000-0002-4232-5669")
-    ),
-    person(
-      role = "aut",
-      family = "Vaughan",
-      given = c("Nathan", "R."),
-      comment = c(ORCID = "0009-0000-3054-6950")
-    ),
-    person(
-      role = "ctb",
-      family = "Blackhart",
-      given = "Kristan",
-      comment = c(ORCID = "0000-0003-4232-2510")
-    ),
-    person(
-      role = "ctb",
-      family = "Ianelli",
-      given = c("James", "N."),
-      comment = c(ORCID = "0000-0002-7170-8677")
-    )
+    person(c("Kelli", "F."), "Johnson", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-5149-451X")),
+    person(c("Jon", "K.", "T."), "Brodziak", role = "aut",
+           comment = c(ORCID = "0000-0001-8690-5588")),
+    person(c("Kathryn", "L."), "Doering", role = "aut",
+           comment = c(ORCID = "0000-0002-0396-7044")),
+    person(c("Andrea", "M."), "Havron", role = "aut",
+           comment = c(ORCID = "0000-0002-4080-448X")),
+    person("Ronald", "Klasky", role = "aut",
+           comment = c(ORCID = "0009-0004-7563-7716")),
+    person(c("Peter", "T."), "Kuriyama", role = "aut",
+           comment = c(ORCID = "0000-0002-6971-4015")),
+    person(c("Christopher", "M."), "Legault", role = "aut",
+           comment = c(ORCID = "0000-0002-0328-1376")),
+    person("Bai", "Li", role = "aut",
+           comment = c(ORCID = "0000-0002-8249-1442")),
+    person(c("Timothy", "J."), "Miller", role = "aut",
+           comment = c(ORCID = "0000-0003-1411-1206")),
+    person(c("Cole", "C."), "Monnahan", role = "aut",
+           comment = c(ORCID = "0000-0003-0871-6700")),
+    person(c("Megumi", "C."), "Oshima", role = "aut",
+           comment = c(ORCID = "0009-0002-2239-1594")),
+    person(c("Kyle", "W."), "Shertzer", role = "aut",
+           comment = c(ORCID = "0000-0001-7196-5959")),
+    person(c("Christine", "C."), "Stawitz", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0003-3122-4501")),
+    person(c("Jane", "Y."), "Sullivan", role = "aut",
+           comment = c(ORCID = "0000-0002-8094-1673")),
+    person("Matthew", "Supernaw", role = "aut",
+           comment = c(ORCID = "0009-0007-3681-7433")),
+    person(c("Ian", "G."), "Taylor", role = "aut",
+           comment = c(ORCID = "0000-0002-4232-5669")),
+    person(c("Nathan", "R."), "Vaughan", role = "aut",
+           comment = c(ORCID = "0009-0000-3054-6950")),
+    person("Kristan", "Blackhart", role = "ctb",
+           comment = c(ORCID = "0000-0003-4232-2510")),
+    person(c("James", "N."), "Ianelli", role = "ctb",
+           comment = c(ORCID = "0000-0002-7170-8677"))
   )
 Description: The Fisheries Integrated Modeling System is a next-generation
     framework of stock assessment models, assisting fishery managers with

diff --git a/R/create_default_parameters.R b/R/create_default_parameters.R
@@ -344,8 +344,7 @@ create_default_fleet <- function(fleets,
     dplyr::arrange(dplyr::desc(type)) |>
     dplyr::pull(uncertainty)
 
-  index_distribution_default <- switch(
-    index_distribution,
+  index_distribution_default <- switch(index_distribution,
     "DnormDistribution" = create_default_DnormDistribution(
       value = index_uncertainty,
       input_type = "data",
@@ -367,8 +366,8 @@ create_default_fleet <- function(fleets,
   default <- list(c(
     selectivity_default,
     process_default,
-    index_distribution_default)
-  )
+    index_distribution_default
+  ))
 
   names(default) <- fleet_name
   return(default)
@@ -523,7 +522,7 @@ create_default_DlnormDistribution <- function(
 }
 
 #' Create default recruitment parameters
-#'#'
+#'
 #' @description
 #' This function sets up default parameters for a recruitment module.
 #'
@@ -541,7 +540,8 @@ create_default_DlnormDistribution <- function(
 create_default_recruitment <- function(
   recruitment,
   data,
-  input_type = "BevertonHoltRecruitment") {
+  input_type = "BevertonHoltRecruitment"
+) {
   # Input checks
   if (!is.list(recruitment)) {
     cli::cli_abort(c(
@@ -554,8 +554,7 @@ create_default_recruitment <- function(
   # NOTE: All new forms of recruitment must be placed in the vector of default
   # arguments for `form` and their methods but be placed below in the call to
   # `switch`
-  process_default <- switch(
-    form,
+  process_default <- switch(form,
     "BevertonHoltRecruitment" = create_default_BevertonHoltRecruitment(data)
   )
   names(process_default) <- paste0(form, ".", names(process_default))
@@ -564,8 +563,7 @@ create_default_recruitment <- function(
   distribution_input <- recruitment[["process_distribution"]]
   distribution_default <- NULL
   if (!is.null(distribution_input)) {
-    distribution_default <- switch(
-      distribution_input,
+    distribution_default <- switch(distribution_input,
       "DnormDistribution" = create_default_DnormDistribution(
         data = data,
         input_type = "process"
@@ -614,7 +612,7 @@ update_parameters <- function(current_parameters, modified_parameters) {
   # Check if current_parameters is a list with required components
   if (
     !is.list(current_parameters) ||
-    !all(c("parameters", "modules") %in% names(current_parameters))
+      !all(c("parameters", "modules") %in% names(current_parameters))
   ) {
     cli::cli_abort(c(
       "i" = "{.var current_parameters} argument must be a list containing

diff --git a/R/distribution_formulas.R b/R/distribution_formulas.R
@@ -71,7 +71,7 @@ check_distribution_validity <- function(args) {
   }
   if (
     !(family[["family"]] %in% available_distributions) ||
-    "unavailable data type" %in% available_distributions
+      "unavailable data type" %in% available_distributions
   ) {
     ifelse_type <- ifelse(
       is.null(data_type),
@@ -120,7 +120,7 @@ check_distribution_validity <- function(args) {
     }
     if (
       length(sd[["estimated"]]) > 1 &&
-      length(sd[["value"]]) != length(sd[["estimated"]])
+        length(sd[["value"]]) != length(sd[["estimated"]])
     ) {
       sd_length <- length(sd[["value"]])
       est_length <- length(sd[["estimated"]])
@@ -236,7 +236,7 @@ get_expected_name <- function(family, data_type) {
 #'   ),
 #'   data_type = "index"
 #' )
-#' 
+#'
 #' # Set up a new process distribution
 #' # Create a new recruitment module
 #' recruitment <- methods::new(BevertonHoltRecruitment)
@@ -263,7 +263,7 @@ initialize_data_distribution <- function(
   # FIXME: Make the available families a data object
   # Could also make the matrix of distributions available per type as a
   # data frame where the check could use the stored object.
-  
+
 
   # validity check on user input
   args <- list(
@@ -303,7 +303,7 @@ initialize_data_distribution <- function(
 
     # populate logged standard deviation parameter with log of input
     new_module$log_sd$resize(length(sd[["value"]]))
-    for (i in seq_along(sd[["value"]])){
+    for (i in seq_along(sd[["value"]])) {
       new_module$log_sd[i]$value <- log(sd[["value"]][i])
     }
 
@@ -318,7 +318,7 @@ initialize_data_distribution <- function(
   }
 
   if (family[["family"]] == "multinomial") {
-    #create new Rcpp module
+    # create new Rcpp module
     new_module <- methods::new(DmultinomDistribution)
   }
 
@@ -366,7 +366,7 @@ initialize_process_distribution <- function(
       log(sd[["value"]]),
       length(sd[["value"]])
     )
-    #setup whether or not sd parameter is estimated
+    # setup whether or not sd parameter is estimated
     if (length(sd[["value"]]) > 1 && length(sd[["estimated"]]) == 1) {
       new_module$log_sd$set_all_estimable(sd[["estimated"]])
     } else {
@@ -382,11 +382,11 @@ initialize_process_distribution <- function(
 
     # populate logged standard deviation parameter with log of input
     new_module$log_sd$resize(length(sd[["value"]]))
-    for (i in seq_along(sd[["value"]])){
+    for (i in seq_along(sd[["value"]])) {
       new_module$log_sd[i]$value <- log(sd[["value"]][i])
     }
 
-    #setup whether or not sd parameter is estimated
+    # setup whether or not sd parameter is estimated
     if (length(sd[["value"]]) > 1 && length(sd[["estimated"]]) == 1) {
       new_module$log_sd$set_all_estimable(sd[["estimated"]])
     } else {