clean up documentation and create pkgdown site

.Rbuildignore

@@ -6,3 +6,6 @@
 ^data-raw$
 ^vignettes/get-all-cache
 ^vignettes/knitr-cache
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -53,4 +53,5 @@ inst/shortraker-kni*
 figs/*
 inst/pcod-vb.html
 *~
-*.dll
+*.dll
+docs

DESCRIPTION

@@ -35,5 +35,5 @@ Suggests:
     sf
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
-URL: https://github.com/pbs-assess/gfdata
+URL: https://github.com/pbs-assess/gfdata, https://pbs-assess.github.io/gfdata/
 BugReports: https://github.com/pbs-assess/gfdata/issues

R/correct-ssids.R

@@ -1,9 +1,9 @@
-#' Custom fixes for problem surveys with shared trip ids resulting in assignment to wrong ssid
-#'
-#' @param dat df containing these columns: fishing_event_ids, survey_series_id, survey_id,
-#'  major_stat_area_code, minor_stat_area_code
-#' @param specimens Defaults to FALSE where checks for duplication of fishing_event_ids
-#'
+# Custom fixes for problem surveys with shared trip ids resulting in assignment to wrong ssid
+#
+# @param dat df containing these columns: fishing_event_ids, survey_series_id, survey_id,
+#  major_stat_area_code, minor_stat_area_code
+# @param specimens Defaults to FALSE where checks for duplication of fishing_event_ids
+#
 correct_ssids <- function(dat, specimens = FALSE) {
   try(dat[dat$survey_series_id %in% c(6, 7), ]$survey_id <- NA, silent = TRUE)
   try(dat[((dat$survey_series_id == 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_id <- 7, silent = TRUE)

R/parent-level-counts.R

@@ -1,9 +1,9 @@
-#' summarize sub/minor level counts from fishing event data at the parent event level
-#' includes correction for a typo in dataframe
-#' retrieves missing fishing_event_ids for sablefish surveys using major_level_ids
-#'
-#' @param fe df retrieved with get-event-data.sql
-#'
+# summarize sub/minor level counts from fishing event data at the parent event level
+# includes correction for a typo in dataframe
+# retrieves missing fishing_event_ids for sablefish surveys using major_level_ids
+#
+# @param fe df retrieved with get-event-data.sql
+#
 get_parent_level_counts <- function(fe) {
   # just actual parent-level events
   fe_A_no_parent <- filter(fe, is.na(FE_PARENT_EVENT_ID), is.na(FE_MINOR_LEVEL_ID), is.na(FE_SUB_LEVEL_ID))

R/skate-level-counts.R

@@ -1,9 +1,8 @@
-#' summarize fishing event data at the skate level
-#' retrieves missing fishing_event_ids for sablefish surveys using major_level_ids
-#'
-#' @param fe df retrieved with get-event-data.sql
-#'
-
+# summarize fishing event data at the skate level
+# retrieves missing fishing_event_ids for sablefish surveys using major_level_ids
+#
+# @param fe df retrieved with get-event-data.sql
+#
 get_skate_level_counts <- function(fe) {
   fe <- fe |> distinct()
 

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://pbs-assess.github.io/gfdata/
+template:
+  bootstrap: 5
+

inst/CITATION

@@ -1,22 +1,22 @@
 citHeader("To cite gfdata in publications use:")
 
-citEntry(
-  entry    = "manual",
+bibentry(
+  bibtype    = "manual",
   title    = "{gfdata}: Data Extraction for {DFO} {PBS} Groundfish Stocks",
-  year     = "2022",
-  note     = "R package version 0.0.0.9000",
-  author = "Keppel, E. A. and Anderson, S.C. and Edwards, A. M. and Grandin, C.",
+  year     = "2024",
+  note     = "R package version 0.1.3",
+  author = "Keppel, E. A. and Anderson, S.C. and Edwards, A. M. and Grandin, C. and English, P. A.",
   url      = "https://github.com/pbs-assess/gfdata",
   textVersion = paste(
-  "Keppel, E.A., S.C. Anderson, A.M. Edwards, and C. Grandin. 2022.
+  "Keppel, E.A., S.C. Anderson, A.M. Edwards, C. Grandin, and P.A. English. 2024.
   gfdata: Data Extraction for DFO PBS Groundfish Stocks. R package version
-  0.0.0.9000. https://github.com/pbs-assess/gfdata"
+  0.1.3. https://github.com/pbs-assess/gfdata"
   )
 )
 
 
-citEntry(
-  entry    = "article",
+bibentry(
+  bibtype    = "article",
   title    = "A Reproducible Data Synopsis for over 100 Species of {British Columbia} Groundfish",
   author = "Anderson, S.C. and Keppel, E. A. and Edwards, A. M.",
   year     = "2019",

vignettes/01-gfdata-vignette.Rmd

@@ -1,17 +1,19 @@
 ---
-title: "gfdata Vignette"
+title: "Introduction to gfdata"
 author: "Elise Keppel"
 date: "2024-10-15"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{gfdata Vignette}
+  %\VignetteIndexEntry{Introduction to gfdata}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 
-
-
-
+<style type="text/css">
+  body{
+  font-size: 11pt;
+}
+</style>
 
 # Setup
 

vignettes/02-gfdata-vignette-get-all.Rmd

@@ -1,15 +1,19 @@
 ---
-title: "gfdata `get_all` vignette"
+title: "Using 'get_all' functions"
 author: "Philina English"
 date: "2024-10-11"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{gfdata `get_all' Vignette}
+  %\VignetteIndexEntry{Using 'get_all' functions}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 
-
+<style type="text/css">
+  body{
+  font-size: 11pt;
+}
+</style>
 
 ## Why use a `get_all_*()` function?
 

vignettes/gfdata-vignette-get-all.Rmd.orig

@@ -1,14 +1,20 @@
 ---
-title: "gfdata `get_all` vignette"
+title: "Using 'get_all' functions"
 author: "Philina English"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{gfdata `get_all' Vignette}
+  %\VignetteIndexEntry{Using 'get_all' functions}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 
+<style type="text/css">
+  body{
+  font-size: 11pt;
+}
+</style>
+
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(
   collapse = FALSE,