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

DESCRIPTION

@@ -2,52 +2,45 @@ Package: hakedataUSA
 Title: Extract USA Data for Pacific Hake
 Version: 2022.0.1
 Authors@R: c(
-    person(given = c("Kelli", "F."),
-           family = "Johnson",
-           role = c("aut", "cre"),
-           email = "kelli.johnson@noaa.gov",
+    person(c("Kelli", "F."), "Johnson", , "kelli.johnson@noaa.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5149-451X")),
-    person(given = c("Aaron", "M."),
-           family = "Berger",
-           role = "aut"),
-    person(given = c("Ian", "G."),
-           family = "Taylor",
-           role = "ctb"),
-    person(given = c("Alan", "C."),
-           family = "Hicks",
-           role = "ctb"),
-    person(given = c("Andi"),
-           family = "Stephens",
-           role = "ctb"))
-Description: Extract data from the two data warehouses, i.e., North Pacific Database (NORPAC) and Pacific Fisheries Information Network (PacFIN), used to store data for the Pacific Fisheries Management Council (PFMC).
+    person(c("Aaron", "M."), "Berger", role = "aut"),
+    person(c("Ian", "G."), "Taylor", role = "ctb"),
+    person(c("Alan", "C."), "Hicks", role = "ctb"),
+    person("Andi", "Stephens", role = "ctb")
+  )
+Description: Extract data from the two data warehouses, i.e., North
+    Pacific Database (NORPAC) and Pacific Fisheries Information Network
+    (PacFIN), used to store data for the Pacific Fisheries Management
+    Council (PFMC).
 License: What license it uses
-Encoding: UTF-8
-LazyData: true
-Suggests:
-    knitr,
-    rmarkdown,
-    RODBC,
-    testthat
+Depends: 
+    R (>= 2.10)
 Imports:
-    magrittr,
     dplyr,
     fs,
     ggplot2,
     glue,
     graphics,
     grDevices,
+    magrittr,
     mapdata,
     maps,
     plyr,
-    RColorBrewer,
     r4ss,
+    RColorBrewer,
     readxl,
     stats,
     tidyr,
     tools
+Suggests:
+    knitr,
+    rmarkdown,
+    RODBC,
+    testthat
 Remotes:
-  github::r4ss/r4ss
-RoxygenNote: 7.2.3
+    github::r4ss/r4ss
+Encoding: UTF-8
+LazyData: true
 Roxygen: list(markdown = TRUE)
-Depends: 
-    R (>= 2.10)
+RoxygenNote: 7.2.3

R/plot_boxplot.R

@@ -39,7 +39,7 @@ get_depth_by_year <- function(d,
       median = 4,
       upperhinge = 5, upper95 = 6
     )
-  if(!is.null(yrs)){
+  if (!is.null(yrs)) {
     dpth <- dpth %>%
       dplyr::filter(year %in% yrs)
   }
@@ -62,7 +62,7 @@ get_rate_by_month <- function(d,
       median = 5,
       upperhinge = 6, upper95 = 7
     )
-  if(!is.null(yrs)){
+  if (!is.null(yrs)) {
     dpth <- dpth %>%
       dplyr::filter(year %in% yrs)
   }

R/process_age-.R

@@ -69,7 +69,7 @@ process_age_sea <- function(atsea.ages = get_local(file = "atsea.ages.Rdat"),
     dplyr::mutate(dplyr::across(
       dplyr::everything(),
       .fns = \(x) tidyr::replace_na(x, 0)
-    ))|>
+    )) |>
     tidyr::nest(gg = -"vesseltype") |>
     dplyr::mutate(
       lower_name = tolower(vesseltype),
@@ -153,7 +153,7 @@ process_age_shore <- function(page = get_local("page.Rdat"),
     dplyr::mutate(dplyr::across(
       dplyr::everything(),
       .fns = \(x) tidyr::replace_na(x, 0)
-    ))|>
+    )) |>
     utils::write.csv(
       file = fs::path(hakedata_wd(), "us-sb-age-raw.csv"),
       row.names = FALSE,

R/process_catch-.R

@@ -257,7 +257,6 @@ process_catch_norpac <- function(ncatch = get_local(file = "norpac_catch.Rdat"),
 process_catch_pacfin <- function(pcatch = get_local(file = "pacfin_catch.Rdat"),
                                  nyears = 5,
                                  savedir = hakedata_wd()) {
-
   # FLEET XXX is in the hake assessment as shore-based catches,
   # although 1986 differs from data used
   # database  1986 3431.9436

R/process_weight_at_age-.R

@@ -13,8 +13,8 @@ process_weight_at_age_survey <- function(savedir = hakedata_wd()) {
   # Custom function only needed inside this function for survey data
   read_mutate_join <- function(x, y) {
     if (!grepl("xlsx", x)) {
-        x_data <- suppressWarnings(readxl::read_xls(x))
-        y_data <- suppressWarnings(readxl::read_xls(y))
+      x_data <- suppressWarnings(readxl::read_xls(x))
+      y_data <- suppressWarnings(readxl::read_xls(y))
     } else {
       x_data <- suppressWarnings(readxl::read_excel(x))
       y_data <- suppressWarnings(readxl::read_excel(y))
@@ -48,24 +48,24 @@ process_weight_at_age_survey <- function(savedir = hakedata_wd()) {
       yy,
       by = "haul"
     ) |>
-    dplyr::transmute(
-      Source = dplyr::case_when(
-        basename(dirname(x)) == "US" ~ "U.S. Acoustic",
-        basename(dirname(x)) == "CAN" ~ "Canada Acoustic",
-        TRUE ~ "Unknown Acoustic"
-      ),
-      Weight_kg = weight,
-      Sex = Sex2,
-      Age_yrs = age,
-      Length_cm = length,
-      Month = as.numeric(format(as.Date(hb_date_time, f = "%m/%d/%Y"), "%m")),
-      Year = as.numeric(format(as.Date(hb_date_time, f = "%m/%d/%Y"), "%Y"))
-    ) |>
-    dplyr::mutate(
-      Year = ifelse(Year < 2000, Year + 2000, Year)
-    ) |>
-    dplyr::filter(!is.na(Age_yrs)) |>
-    dplyr::filter(!is.na(Weight_kg))
+      dplyr::transmute(
+        Source = dplyr::case_when(
+          basename(dirname(x)) == "US" ~ "U.S. Acoustic",
+          basename(dirname(x)) == "CAN" ~ "Canada Acoustic",
+          TRUE ~ "Unknown Acoustic"
+        ),
+        Weight_kg = weight,
+        Sex = Sex2,
+        Age_yrs = age,
+        Length_cm = length,
+        Month = as.numeric(format(as.Date(hb_date_time, f = "%m/%d/%Y"), "%m")),
+        Year = as.numeric(format(as.Date(hb_date_time, f = "%m/%d/%Y"), "%Y"))
+      ) |>
+      dplyr::mutate(
+        Year = ifelse(Year < 2000, Year + 2000, Year)
+      ) |>
+      dplyr::filter(!is.na(Age_yrs)) |>
+      dplyr::filter(!is.na(Weight_kg))
     stopifnot(!any(is.na(together[["Year"]])))
     return(together)
   }
@@ -84,7 +84,7 @@ process_weight_at_age_survey <- function(savedir = hakedata_wd()) {
         "/20[12][0-9]/[CANUS]{2,3}|/2009/[CANUS]{2,3}",
         value
       )
-    ) |> 
+    ) |>
     dplyr::mutate(
       bio_file = purrr::map_chr(
         value,
@@ -223,9 +223,9 @@ process_weight_at_age <- function(dir = hakedata_wd(),
   # save on size, contains all US samples in LWAdata_1975to2007.csv, so
   # eliminated that file.
   files_weights <- fs::path(
-      ext = "csv",
-      dir,
-      c("survey-weight-at-age", "us-weight-at-age", "can-weight-at-age")
+    ext = "csv",
+    dir,
+    c("survey-weight-at-age", "us-weight-at-age", "can-weight-at-age")
   )
   dat <- purrr::map_dfr(
     files_weights,

README.Rmd

@@ -32,15 +32,15 @@ for the assessment of Pacific Hake.
 1. Next, load the package. This can be accomplished through GitHub (first
    chunk) or using a local clone (second chunk).
    ```{r installation-github}
-   chooseCRANmirror(ind = 1)
-   # install.packages("pak")
-   pak::pak("pacific-hake/hakedataUSA")
-   library(hakedataUSA)
+chooseCRANmirror(ind = 1)
+# install.packages("pak")
+pak::pak("pacific-hake/hakedataUSA")
+library(hakedataUSA)
    ```
    ```{r installation-local}
-   chooseCRANmirror(ind = 1)
-   stopifnot(basename(getwd()) == "hakedataUSA")
-   devtools::load_all()
+chooseCRANmirror(ind = 1)
+stopifnot(basename(getwd()) == "hakedataUSA")
+devtools::load_all()
    ```
 1. The path to where all of the raw output will be saved is stored in an 
    internal function, i.e., `hakedata_wd()`. Try it out, see if it works for