first commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+Readme.Rmd
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.gitignore

@@ -4,6 +4,7 @@
 
 # Session Data files
 .RData
+*.Rproj
 
 # User-specific files
 .Ruserdata
@@ -37,3 +38,5 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+inst/doc
+docs

DESCRIPTION

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+Package: pkgdownTemplate
+Title: pkgdown Template Package
+Date: 2021-07-04
+Version: 1.0
+Authors@R: person("Holmes", "Elizabeth", , "[email protected]", role = c("aut", "cre"))
+Maintainer: Elizabeth Holmes <[email protected]>
+URL: https://RWorkflow-Workshop-2021.github.io/pkgdown-template, https://github.com/RWorkflow-Workshop-2021/pkgdown-template
+BugReports: https://github.com/RWorkflow-Workshop-2021/pkgdown-template/issues
+Description: This is a template package for a NMFS branded R 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: 7.1.1
+Roxygen: list(markdown = TRUE)
+VignetteBuilder: knitr

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/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 -->
+
+# pkgdown template <img src="man/figures/logo.png" align="right" style="padding: 10px"/>
+
+This is a template for a NMFS branded GitHub repository, 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.
+
+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 editted 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
+
+pkgdown::build_favicon
+
+<!-- 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")
+```
+
+

README.md

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-# pkgdown-template
-Clone this repo to create a NMFS branded pkgdown website
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# pkgdown template <img src="man/figures/logo.png" align="right" style="padding: 10px"/>
+
+This is a template for a NMFS branded GitHub repository, 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 &gt; Project Options… &gt; 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.
+
+1.  On the Build tab, click Install and Restart to make sure it builds.
+2.  On the Build tab, click Check to make sure it passes all the checks.
+3.  Type the code `pkgdown::build_site()` and make sure the **pkgdown**
+    building works.
+
+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 editted 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
+
+pkgdown::build\_favicon
+
+<!-- Do not edit below. This adds the Disclaimer and NMFS footer. -->
+
+------------------------------------------------------------------------
+
+## Disclaimer
+
+The United States Department of Commerce (DOC) GitHub project code is
+provided on an ‘as is’ basis and the user assumes responsibility for its
+use. DOC has relinquished control of the information and no longer has
+responsibility to protect the integrity, confidentiality, or
+availability of the information. Any claims against the Department of
+Commerce stemming from the use of its GitHub project will be governed by
+all applicable Federal law. Any reference to specific commercial
+products, processes, or services by service mark, trademark,
+manufacturer, or otherwise, does not constitute or imply their
+endorsement, recommendation or favoring by the Department of Commerce.
+The Department of Commerce seal and logo, or the seal and logo of a DOC
+bureau, shall not be used in any manner to imply endorsement of any
+commercial product or activity by DOC or the United States Government.”
+
+------------------------------------------------------------------------
+
+<img src="https://raw.githubusercontent.com/nmfs-general-modeling-tools/nmfspalette/main/man/figures/noaa-fisheries-rgb-2line-horizontal-small.png" height="75" alt="NOAA Fisheries">
+
+[U.S. Department of Commerce](https://www.commerce.gov/) \| [National
+Oceanographic and Atmospheric Administration](https://www.noaa.gov) \|
+[NOAA Fisheries](https://www.fisheries.noaa.gov/)

pkgdown/_pkgdown.yml

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+navbar:
+  structure:
+    left:
+    - home
+    - reference
+    - sourcecode
+    - issue
+    - articles
+    - documents
+    - news
+    right: github
+
+  components:
+    home:
+      icon: fas fa-home fa-lg
+      href: index.html
+
+    reference:
+      text: Functions
+      icon: far fa-file-code fa-lg
+      href: reference/index.html
+
+    sourcecode:
+      text: Source Code
+      icon: fab fa-github fa-lg
+      href: https://github.com/RWorkflow-Workshop-2021/pkgdown-template
+
+    issue:
+      text: Issues
+      icon: fas fa-question-circle fa-lg
+      href: https://github.com/RWorkflow-Workshop-2021/pkgdown-template/issues/
+
+    articles:
+      text: Vignettes
+      icon: fas fa-file-contract fa-lg
+      href: articles/index.html
+
+    documents:
+      text: References
+      icon: fas fa-book fa-lg
+      menu:
+      - text: Scoping Document
+        href: Scoping.pdf
+      - text: Background Page
+        href: Article.html
+
+reference:
+- title: Plot functions
+  contents:
+  - contains("plot")
+- title: Function functions
+  contents:
+  - contains("function")
+
+news:
+  releases:
+  - text: "Version 1.0"
+    href: https://github.com/RWorkflow-Workshop-2021/pkgdown-template/releases/tag/v1.0
+

pkgdown/extra.css

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+@import url("https://nmfs-general-modeling-tools.github.io/nmfspalette/extra.css");

vignettes/.gitignore

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+*.html
+*.R

vignettes/samplevignette.Rmd

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+---
+title: "samplevignette"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{samplevignette}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r setup}
+library(pkgdownTemplate)
+```
+
+Here you can show uses worked up examples for your package. The easiest way to make a new package is to use `usethis::use_vignette("nameofvignette")`.
+
+## Let's make a plot!
+
+```{r fig.align="center"}
+require(stats)
+x <- runif(10)
+y <- 10 + 3*x + rnorm(10)
+sampleplot(x, y)
+title(samplefunction("x versus y", y="10 vals", z="green"))
+```