first commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+Readme.Rmd
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^pkgdownTemplate\.Rcheck$
+^pkgdownTemplate.*\.tar\.gz$
+^pkgdownTemplate.*\.tgz$
+^DataProduct\.Rcheck$
+^DataProduct.*\.tar\.gz$
+^DataProduct.*\.tgz$

.github/.gitignore

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+*.html

.github/workflows/R-CMD-check.yaml

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+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Turned of check/build of vignettes
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Check
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes"), error_on = "error", build_args = "--no-build-vignettes")
+        shell: Rscript {0}

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+*.Rproj
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+inst/doc
+pkgdownTemplate.Rcheck/
+pkgdownTemplate*.tar.gz
+pkgdownTemplate*.tgz
+DataProduct.Rcheck/
+DataProduct*.tar.gz
+DataProduct*.tgz

DESCRIPTION

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+Package: DataProduct
+Title: A NMFS Data Product
+Date: 2022-02-14
+Version: 1.0
+Authors@R: c(person("Elizabeth", "Holmes", , "[email protected]", role = c("aut", "cre")), person("Another", "Contributor", role="aut"))
+URL: https://rverse-tutorials.github.io/DataProduct, https://github.com/rverse-tutorials/DataProduct
+BugReports: https://github.com/rverse-tutorials/DataProduct/issues
+Description: This is an expample NMFS branded R data package with a pkgdown website.
+Depends: R (>= 4.0.0)
+Suggests: 
+    rmarkdown,
+    knitr
+Imports: stats, graphics
+License: GPL-3 + file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.2
+Roxygen: list(markdown = TRUE)
+VignetteBuilder: knitr

LICENSE

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+Software code created by U.S. Government employees is not subject to
+copyright in the United States (17 U.S.C. §105). The United State
+s/Department of Commerce reserve all rights to seek and obtain copyright
+protection in countries other than the United States for Software authored
+in its entirety by the Department of Commerce. To this end, the Department
+of Commerce hereby grants to Recipient a royalty-free, nonexclusive license
+to use, copy, and create derivative works of the Software outside of the
+United States.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(samplefunction)
+export(sampleplot)
+import(graphics)
+import(stats)

NEWS.md

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+# pkgdownTemplate
+
+# Version 1.0
+
+This is a basic template with NMFS branding. It has NMFS palette and the NMFS footer, license, and **pkgdown** structure.

R/data-cars.R

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+#' @title a dataset of horsepower for different cars
+#'
+#' @description First 4 columns of the mtcars dataset.
+#'
+#' \itemize{
+#'   \item mpg. miles per gallon
+#'   \item cyl. cylinders
+#'   \item disp. displacement
+#'   \item hp. horse poser
+#' }
+#'
+#' @docType data
+#' @name cars
+#' @usage data(cars)
+#' @references R base package.
+#' @format A data frame.
+#' @keywords datasets
+NULL

R/data-iris2.R

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+#' @title sepal length for differen species of iris
+#'
+#' @description The Species and Sepal.Length from the iris data set from base R.
+#'
+#' \itemize{
+#'   \item Species. species
+#'   \item Sepal.Length. sepal length
+#' }
+#'
+#' @docType data
+#' @name iris2
+#' @usage data(iris2)
+#' @references from R base package.
+#' @format A data frame.
+#' @keywords datasets
+NULL

R/import_packages.R

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+#' @import stats
+#' @import graphics
+NULL

R/samplefunction.R

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+#' Sample Function Title
+#'
+#' This part is the description. It can be as long as you want but usually is one paragraph.
+#'
+#' @param x This is a required argument and has no default value.
+#' @param y Has a default value of 10.
+#' @param z Although this looks like it is a default string, the function `match.arg()` is
+#' used to set it in the function. With `match.arg()`, the string specifies what values are allowed and it will throw an error if not one of those. The default is the first value.
+#' @return A string with the values.
+#' @examples
+#' samplefunction(1)
+#' @export
+samplefunction <- function(x, y=10, z=c("yellow", "red", "green")){
+  z <- match.arg(z)
+  return(paste(x, y, z))
+}

R/sampleplot.R

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+#' Sample plot
+#'
+#' This shows how you need to use `::` with all your functions that are not in base R.
+#'
+#' @param x The x variables.
+#' @param y The y response values.
+#' @return the coefficient of the linear regression
+#' @examples
+#' x <- 1:10
+#' y <- 10+3*x + stats::rnorm(10, 0, 10)
+#' sampleplot(x, y)
+#' @export
+sampleplot <- function(x, y){
+  the.lm <- stats::lm(y ~ x)
+  plot(x, y)   
+  graphics::abline(the.lm)
+  return(coef(the.lm))
+}

README.Rmd

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+---
+output: 
+  md_document:
+    variant: gfm
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# DataProduct <img src="man/figures/logo.png" align="right" style="padding: 10px"/>
+
+<!-- badges: start -->
+[![GitHub release (latest by date)](https://img.shields.io/github/v/release/RVerse-Tutorials/DataProduct)](https://github.com/RVerse-Tutorials/DataProduct/releases)
+[![R-CMD-check](https://github.com/RVerse-Tutorials/DataProduct/workflows/R-CMD-check/badge.svg)](https://github.com/RVerse-Tutorials/DataProduct/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+This is a template for a NMFS branded R package and pkgdown website. It will have a NMFS palette, appropriate license and disclaimer, and a NMFS footer with logo.
+
+The instructions will use the **usethis** and **pkgdown** packages. So install those.
+
+## Step 1 Make sure the package builds
+
+1. Clone this GitHub repository and then open the new repository (on your computer).
+2. Set-up your RStudio project to use Roxygen for documentation and NAMESPACE
+  * Tools > Project Options... > Build Tools  Click the checkbox that says "Build documentation with Roxygen".
+  * The Configure popup box for Roxygen will probably appear, if not click the Configure button. Check all the checkboxes.
+3. On the Build tab, click Install and Restart to make sure it builds.
+4. On the Build tab, click Check to make sure it passes all the checks.
+5. Type the code `pkgdown::build_site()` and make sure the **pkgdown** building works. If on RStudio Cloud, you will need to use `pkgdown::build_site(override = list(destination = "~/docs"))` to 
+
+Note steps 3 and 4 are to make sure your computer is set up to build and check packages. As long as you haven't edited the package yet, it will build and pass check.
+
+## Step 2 Customize your package
+
+1. Edit the DESCRIPTION file (change Title, Description, urls for repo, Authors)
+2. Add any required packages to Depends (or Imports* or Suggests*).
+3. Edit the Readme.Rmd file.
+4. Add your functions to the R folder. There are some template functions there already.
+5. Don't touch the man folder. Roxygen2 will make your Rd files.
+
+## Step 3 Make some vignettes (optional)
+
+Vignettes are longform examples and are Rmd files in the `vignettes` folder. Easiest way to start a new vignette is `usethis::use_vignette("vignettename")`.
+
+## Step 4 Customize your **pkgdown** site and build
+
+1. Structure of the upper navbar. Edit `_pkgdown.yml` in the `pkddown` folder to change the look of the upper navbar. There are endless options. Find examples from other peoples' pkgdown sites.
+2. Update your logo and favicons. Logo is in `man/figures`. After updating run `pkgdown::build_favicon()` to remake the favicons.
+3. Add material to the `docs` folder as needed. See the example for the References tab in the `_pkgdown.yml`.
+4. Build your site with `pkgdown::build_site()`.
+
+## Step 5 Make your site live on GitHub
+
+1. Push the changes to GitHub.
+2. Click on Settings for the repository.
+3. Scroll way down to the GitHub Pages section.
+4. In the **Source** section, change branch to Main and folder to `docs`. There are other ways to set up GitHub Pages but this will get you started.
+5. I always add my GitHub Pages URL to the repo description (on right when on your main repo page).
+
+## NMFS Branding
+
+This template has the following branding elements.
+
+1. `extra.css` in the `pkgdown` folder sources the **nmfspalette** css. This get you the colors.
+2. The `Readme.Rmd` file sources the NMFS Disclaimer and footer with NMFS logo from the [FIT Resources](https://github.com/nmfs-fish-tools/Resources).
+3. The LICENSE is set to that used by [FIT packages](https://github.com/nmfs-fish-tools).
+
+## GitHub Actions and Badges
+
+In the `.github` folder is just one action, to run R CMD check on the package.
+
+## Readme File
+
+**pkgdown** uses `Readme.md` but to pull in the Disclaimer and footer from FIT, you need a Rmd file. When you update the `Readme.Rmd` file, **you need to remember to knit the file** to update `Readme.md`. 
+
+<!-- Do not edit below. This adds the Disclaimer and NMFS footer. -->
+
+****
+
+```{r add-disclaimer, echo=FALSE, results='asis'}
+url <- "https://raw.githubusercontent.com/nmfs-fish-tools/Resources/master/Disclaimer.md"
+childtext <- readLines(url)
+cat(childtext, sep="\n")
+```
+
+****
+
+```{r footer, echo=FALSE, results='asis'}
+url <- "https://raw.githubusercontent.com/nmfs-fish-tools/Resources/master/footer.md" 
+childtext <- readLines(url)
+cat(childtext, sep="\n")
+```
+
+