first commit

Author: eeholmes

.Rbuildignore

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

.gitignore

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 # 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", , "eli.holmes@noaa.gov", role = c("aut", "cre"))
+Maintainer: Elizabeth Holmes <eli.holmes@noaa.gov>
+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

LICENSE

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

NAMESPACE

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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.

NEWS.md

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

R/import_packages.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/samplefunction.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))
+}

R/sampleplot.R

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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")
+```
+
+