• Graduate student in Biology - UF
• Quantitative community ecologist
• ‘#rstats’ enthusiast
• This is my first presentation with R markdown
  • Resources to customize
  • I’d love some good/easy tutorials
  • It wasn’t a fun experience
    • Building a package is definitely easier

Twitter and Github @javirudolph

• To share
  • Easy to share a bundle
  • Code + data + documentation + tests
  • Anyone can download -> install -> use
• For you
  • Easy organization
    • set conventions make life easier
  • Documentation
    • can’t remember what that function was for?
    • forces you to write documentation
  • Load a package and have functions easily accessible
    • Reduce your ‘source()’ lines

• Hadley Wickham’s R packages
  - Second edition is in progress. Updates with usethis
• Emil Hvitfeldt’s blog post
• devtools
• This tutorial/presentation: https://github.com/javirudolph/short-tutorials/

We recommend using the RStudio IDE and start by installing these packages.

install.packages(c("devtools", "roxygen2", "usethis"))

• devtools simplify package development - cheatseet
• roxygen2 helps with the custom syntax used for package documentation
  
• usethis will set up components, directories, organize your package

# load the libraries
library(devtools)
library(roxygen2)
library(usethis)

Check your working directory, as this is were the package will be created.

getwd()

You can change your working directory and specify it with setwd() or within the package building function:

usethis::create_package("your path if not doing setwd/ your package name")

You don’t need to set up a project or anything, usethis takes care of the setup.

After running the following line of code, you will have a new RStudio window open.

usethis::create_package("rladiesgnv")

After you’ve created the package, you will want to start adding some functions.

As an example we will do a simple function that returns the color palette for R Ladies.

The advantage of the package usethis is that as you edit certain files, it will make sure to keep everything connected and update any necessary files in other areas of the directory.

library(usethis)

# Create the function file and edit
usethis::use_r("gimme_color_function")

You will notice that use_r automatically created the .R file for your function and placed it in the R/ directory.

In the new script that opens, you can write your function.

In our case, the function let’s us get the hex color codes for the R Ladies palette.

gimme_color_codes <- function(wantAll = TRUE){
  hex_palette <- c("#181818", "#D3D3D3", "#88398A", "#FFFFF", "#562457")
  if(wantAll == TRUE){
    print(hex_palette)
  }
  else{
    print("You should go for all of them.")
  }
}

And you are done with our minimal package!

# You can now press 'crt + shift + L'
# or

devtools::load_all()

This will ‘build’ and load the package. So you can test your new function by typing it in the console

gimme_color_codes()

[1] "#181818" "#D3D3D3" "#88398A" "#FFFFF" "#562457"

The roxygen2 package lets you write documentation in the same .R file where you’ve specified your function and then devtools generates the documentation.

You can write these comments before your function, which you can open using use_r("gimme_color_function") and start typing the comments with #'.

#' @title RLadies palette function
#'
#' @description This function will print out the hex codes for the RLadies palette
#' @param wantALL Do you want all the colors available in this palette? The default is TRUE
#' @keywords RLadies colors
#' @export
#' @examples
#' gimme_color_codes()
#'

Then type devtools::document() in the console, so it generates the documentation (.Rd files in the man/ directory). More info here

.
Open the NAMESPACE to check out the changes.

Now, in the console:

# 'ctrl + shift + b' or 
devtools::install()

# search for your function
?gimme_color_codes()

We have edited the documentation for the function, but not for the overall package.
To do that:

usethis::use_package_doc()

It will create an .R file used by devtools to create package documentation once we type devtools::document() in the console.

When we check our package documentation:

# 'ctrl + shift + b' or 
devtools::install()

?rladiesgnv

devtools::document()
devtools::install()
?rladiesgnv

and we can also add a license:

usethis::use_mit_license("Your Name Here")

Or link for version control and publish to Github:

usethis::use_git()
usethis::use_github()

If you get an error with that last line, you probably haven’t created an authorization token from Github:

usethis::browse_github_pat()
usethis::use_github(protocol = "https", 
                    auth_token = "the token number you get from the Github site")

Once you publish your package to github, you can create a README that will let your users know what this repo is all about.

usethis::use_readme_rmd()

check out this package at: https://github.com/javirudolph/rladiesgnv and even install it.

# In a new RStudio session:
library(devtools)
devtools::install_github("javirudolph/rladiesgnv")

.

You can follow me on twitter or github @javirudolph

Email: javirudolph@outlook.com