Merge pull request #33 from pfmc-assessments/style-doc-code

I changed the github workflow that updated documentation with one that does all that as well as style the code (as discussed in nmfs-fish-tools/ghactions4r#131). So now we have nicely styled code.
pfmc-assessments · Jul 12, 2024 · 0f1186f · 0f1186f
2 parents 10eddd1 + 8ba9e0e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,102 +2,53 @@ Package: PEPtools
 Title: Tools for Stock Assessments used by the Population Ecology Program
 Version: 0.0.2.0001
 Authors@R: c(
-    person(
-      given = c("Kelli", "F."),
-      family = "Johnson",
-      role = c("aut", "cre"),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-5149-451X")
-    ),
-    person(
-      given = c("Ian", "G."),
-      family = "Taylor",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-4232-5669")
-    ),
-    person(
-      given = c("Chantel", "R."),
-      family = "Wetzel",
-      role = "aut",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-7573-8240")
-    ),
-    person(
-      given = c("John", "R."),
-      family = "Wallace",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-2333-1262")
-    ),
-    person(
-      given = c("Kiva"),
-      family = "Oken",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-5627-6837")
-    ),
-    person(
-      given = c("Kristin", "N."),
-      family = "Marshall",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-9769-2300")
-    ),
-    person(
-      given = c("Edward", "J."),
-      family = "Dick",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0001-7681-9176")
-    ),
-    person(
-      given = c("Melissa"),
-      family = "Monk",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0009-0007-6407-5131")
-    ),
-    person(
-      given = c("Jason"),
-      family = "Cope",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0001-7812-6728")
-    ),
-    person(
-      given = c("Brian", "J."),
-      family = "Langseth",
-      role = "ctb",
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-9901-6146")
-    )
-    )
-Description: The package contains various tools that are useful to 
-    scientists at the Northwest Fisheries Science Center (NWFSC)
-    in the Population Ecology Program (PEP). Users typically spend the
-    majority of their time producing assessments of groundfish stock off the
-    U.S. West Coast. Though, many of the tools will also be useful for
-    the general science they conduct as well. 
-Depends: R (>= 3.5.0)
+    person(c("Kelli", "F."), "Johnson", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-5149-451X")),
+    person(c("Ian", "G."), "Taylor", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-4232-5669")),
+    person(c("Chantel", "R."), "Wetzel", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-7573-8240")),
+    person(c("John", "R."), "Wallace", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-2333-1262")),
+    person("Kiva", "Oken", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-5627-6837")),
+    person(c("Kristin", "N."), "Marshall", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-9769-2300")),
+    person(c("Edward", "J."), "Dick", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0001-7681-9176")),
+    person("Melissa", "Monk", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0009-0007-6407-5131")),
+    person("Jason", "Cope", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0001-7812-6728")),
+    person(c("Brian", "J."), "Langseth", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-9901-6146"))
+  )
+Description: The package contains various tools that are useful to
+    scientists at the Northwest Fisheries Science Center (NWFSC) in the
+    Population Ecology Program (PEP). Users typically spend the majority
+    of their time producing assessments of groundfish stock off the U.S.
+    West Coast. Though, many of the tools will also be useful for the
+    general science they conduct as well.
+License: MIT + file LICENSE
+Depends: 
+    R (>= 3.5.0)
 Imports:
-  adnuts,
-  glue,
-  lubridate,
-  pkgbuild,
-  r4ss,
-  remotes,
-  stats,
-  usethis,
-  utils
+    adnuts,
+    glue,
+    lubridate,
+    pkgbuild,
+    r4ss,
+    remotes,
+    stats,
+    usethis,
+    utils
 Suggests:
-  devtools,
-  TMB
+    devtools,
+    TMB
 Remotes:
-  github::cole-monnahan-noaa/adnuts,
-  github::r4ss/r4ss
-License: MIT + file LICENSE
+    github::cole-monnahan-noaa/adnuts,
+    github::r4ss/r4ss
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
diff --git a/R/PEPmeeting.R b/R/PEPmeeting.R
@@ -11,7 +11,7 @@
 #' PEPtools::PEPmeeting()
 PEPmeeting <- function(year = format(Sys.time(), "%Y"),
                        people = c(
-                         "Aaron", "Brian", "Chantel", "Ian", "Jason", 
+                         "Aaron", "Brian", "Chantel", "Ian", "Jason",
                          "John", "Kelli", "Kiva", "Kristin", "Vlada"
                        )) {
   set.seed(year)

diff --git a/R/buffer_fxn.R b/R/buffer_fxn.R
@@ -1,52 +1,50 @@
 #' Buffer calculation for West Coast groundish assessments
-#' 
-#' @details 
+#'
+#' @details
 #' Buffer calculation for U.S. West Coast Groundfish Stocks
 #' Applies the time-varying sigma approach based on the 2019
-#' approach described in: 
+#' approach described in:
 #' Wetzel, C.R. and O.S. Hamel, 2023. Applying a probability harvest control rule
 #' to account for increased uncertainty in setting precautionary harvest limits
-#' from past stock assessments. Fisheries Research 262: 106659. 
-#' 
+#' from past stock assessments. Fisheries Research 262: 106659.
+#'
 #' @param years Years to generate buffer values. The first year should align with
 #' the year of the assessment. Input should be vector of years to calulculate
 #' West Coast groundfish buffers for (e.g., years = 2021:2032).
 #' @param sigma The initial sigma value to use based on West Coast groundfish
 #' assessment categories (cat 1 = 0.50, cat 2 = 1.0, cat 3 = 2.0). For categories
-#' 1 and 2 the sigma will be time-varying. 
+#' 1 and 2 the sigma will be time-varying.
 #' @param pstar The management risk tolerance determined by the PFMC (i.e., 0.45, 0.40).
-#' 
+#'
 #' @examples
 #' get_buffer(years = 2011:2032, sigma = 1.0, pstar = 0.4)
 #' @author written by Chantel Wetzel
 #' @export
 #'
-get_buffer <- function(years, sigma, pstar){
-
-	y <- 1:(length(years) - 1)
-	if (sigma != 2.0) {
-	  # the rate of change in sigma approved by the SSC in 2019
-	  r <- 0.075	  
-	} else {
+get_buffer <- function(years, sigma, pstar) {
+  y <- 1:(length(years) - 1)
+  if (sigma != 2.0) {
+    # the rate of change in sigma approved by the SSC in 2019
+    r <- 0.075
+  } else {
     r <- 0
-	}
-
-	# This is the equation for the rate of change in sigma
-	sigma_calc <-  c(sigma, sigma * (1+(y-1)*r))
-	buffer <- exp(stats::qnorm(pstar, 0, sigma_calc))
-	max_buffer <- exp(stats::qnorm(pstar, 0, 2.0))
-	# Set the buffer for fixed catch years to 1.0
-	buffer[1:2] <- 1
-	category_3 <- which(buffer < max_buffer)
-	if (length(category_3) > 0) {
-	  buffer[category_3] <- max_buffer 
-	}
-
-	out <- data.frame(
-	  year = years, 
-	  buffer = round(buffer, 3)
-	  )
-
-	return(out)
-}
+  }
 
+  # This is the equation for the rate of change in sigma
+  sigma_calc <- c(sigma, sigma * (1 + (y - 1) * r))
+  buffer <- exp(stats::qnorm(pstar, 0, sigma_calc))
+  max_buffer <- exp(stats::qnorm(pstar, 0, 2.0))
+  # Set the buffer for fixed catch years to 1.0
+  buffer[1:2] <- 1
+  category_3 <- which(buffer < max_buffer)
+  if (length(category_3) > 0) {
+    buffer[category_3] <- max_buffer
+  }
+
+  out <- data.frame(
+    year = years,
+    buffer = round(buffer, 3)
+  )
+
+  return(out)
+}
diff --git a/R/check_filename.R b/R/check_filename.R
@@ -38,9 +38,8 @@
 #' check_filename(tempdir())
 #'
 check_filename <- function(paths) {
-
   # Check for spaces
   stopifnot(all(!grepl("\\s", paths)))
 
   return(paths)
-}
+}
diff --git a/R/check_install_TMB.R b/R/check_install_TMB.R
@@ -34,12 +34,16 @@ check_install_TMB <- function() {
   stopifnot(pkgbuild::find_rtools())
   packages <- utils::installed.packages()
   if (!"TMB" %in% packages[, "Package"]) {
-    stop("Use the following code to install TMB\n",
-      "install.packages('TMB')")
+    stop(
+      "Use the following code to install TMB\n",
+      "install.packages('TMB')"
+    )
   }
   if (!"TMBhelper" %in% packages[, "Package"]) {
-    stop("Use the following code to install TMBhelper\n",
-      "remotes::install_github('kaskr/TMB_contrib_R/TMBhelper')")
+    stop(
+      "Use the following code to install TMBhelper\n",
+      "remotes::install_github('kaskr/TMB_contrib_R/TMBhelper')"
+    )
   }
 
   wd <- getwd()