This course will assist you with recreating work that a previous coworker completed, revisiting a project you abandoned some time ago, or simply reproducing a document with a consistent format and workflow. Incomplete information about how the work was done, where the files are, and which is the most recent version can give rise to many complications. This course focuses on the proper documentation creation process, allowing you and your colleagues to easily reproduce the components of your workflow. Throughout this course, you'll receive helpful demonstrations of RStudio and the R Markdown language and engage in active learning opportunities to help you build a professional online portfolio.
Create an R Package with an R Markdown Template
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Из курса от партнера Emory University
Reproducible Templates for Analysis and Dissemination
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Из урока
Leveraging Custom Templates from Leading Scientific Journals
This module delves into custom templates available for websites, books, and scientific publishers, such as Elsevier and the IEEE, with the chance to create your first R Package.
Познакомьтесь с преподавателями
Melinda HigginsAssociate Research Professor/Senior Biostatistician
School of Nursing
For this lesson, since we're creating in R package,
we're going to begin with a new GitHub repository and a new RStudio project.
Let's go ahead and create a new GitHub repository.
So we're going to call the repository WCtemplatePackage and
we'll type in a description.
Weather Check- R package with an R Markdown Template.
However, this time we are not going to create a README file, so
leave that unchecked.
And then click Create repository, next we're going to go into RStudio and
close any previous projects that you're working on.
You can do this by clicking File > Close Project.
Next in the Console window, we're going to change to the RepTemplate folder on
our computer using the set working directory function.
We type in the following, setwd followed by the file location.
Go ahead and run the set working directory command.
You can also set the working directory in RStudio
by clicking on Sessions > Set Working Directory > Choose Directory.
We're going to need the devtools Package to create a new R package.
Go ahead and click on Tools > Install Packages to install the devtools package.
Then in the Console window,
we need to load the devtools package using the library command, then click Enter.
Now that we have got devtools loaded we are going to create a package named
the same name as the GitHub repository that you just created, WCtemplate package.
To do this, we need to type in the following command.
So from devtools we type in the command create
followed by the name of the GitHub repository that we just created.
So type in devtoolscreate::("WCtemplatePackage") and
click Enter.
You'll notice in the file viewer at the right,
when you click Refresh, we now have a new folder called WCtemplatePackage.
This is in your RepTemplates folder.
If you don't see it right away, be sure to click to the Refresh button shown up here
as a little circle with an arrow.
Go ahead and click on this folder so you can view the files in this new directory.
Next, let's click on the WCtemplatePackage.Rproj file.
This is going to open the project in a new R session and
it says do you want to open it?
Say Yes.
So this opens a new R session for this project.
Let's go ahead and click on Tools > Project Options and
click on the tab for Git/SVN and
you'll notice that it currently says version control system is done.
We want to switch to Git, click the down arrow and select Git.
It's going to say,
do you want to initialize this with the new Git repository?
Click Yes.
It also says that you need to restart RStudio.
Click Yes.
Once RStudio restarts,
you'll notice up here at the top right, we now have a tab for Git.
Now that you have a basic skeleton of an R package created and
we've initialized it using Git,
we need to link this folder back to the GitHub repository that you've created.
So open your Git Bash window and
make sure that you're in the new folder for WCTemplatesPackage.
Type in the following commands, we're going to use the git add command to
stage the files, and we'll add git commit and this is our first commit.
Click Enter.
Remember that we are going to have to copy the URL from the GitHub repository to
the clipboard so that we can put it in here, git remote add origin,
followed by the URL, and click Enter.
Then we're going to push everything using the modified push command that
you've seen before.
We type in git push -u origin master, and click Enter.
We can also type in git status as a quick check and then go to your GitHub
repository and click Refresh to make sure that everything synced back up.
It's worth noting that the workflow that we're going to use to setup the rest of
our R package with the R Markdown Template
is based on the basic template tutorial by Chester Ismay.
The link is provided in the Read Ahead materials.
Now that your basic R package is created,
we need to create the skeleton directory for your article.
So let's name the R Markdown Template, weather.
In the console window in RStudio, we're going to type in an R command
to create the skeleton folder for the weather template.
This is provided in your Read Ahead materials.
So this command is going to create a new directory called,
inst/rmarkdown/templates/weather/skeleton under the WCTemplatePackage directory.
To confirm that this worked,
you will notice over here in the Files window, if we click on inst,
we now see all of that, rmarkdown > templates > weather > skeleton.
We need to go ahead and put something here in the skeleton directory.
So we're going to copy the wcarticle RMD file that we created in the last lesson
and put it into this new skeleton directory.
So we need to install it in the inst > rmarkdown > templates > weather >
skeleton directory.
However, we need to change the name of the file from wcarticle to skeleton.rmd.
Back in RStudio, let's also create a template.yaml file.
So click on File > New File > Text File, and we're
going to type in the following information provided in the Read Ahead materials.
We're going to put in name Weather Check Report.
Let's click Save and we're going to save it as template.yaml.
However, we want to make sure that we put this
in the directory just above the skeleton directory that we just created.
So we need to go to inst > rmarkdown > templates > weather and
put it in this folder which is right above the skeleton directory.
Click Save.
To see everything worked we actually need to install R package,
which at the moment it's only is locally.
First though we need to change our working directory.
So Click on Session > Set Working Directory > Directory.
We actually need to go up one level and
make sure we're in the RepTemplate folder directory, and click Open.
Then we need to go back to the RStudio console window and
we're going to use another devtools command to install R package.
So go ahead and run this command.
You'll notice that it says it's installing our WCtemplatePackage.
Next we're going to restart your R session.
Click on Session > Restart R.
To check to make sure that we actually can see our new template that we created,
let's go to File > New File > R Markdown, and click on From Template.
If we scroll down, we should now see the Weather Check Report
listed as a template from our new WCtemplatePackage.
Click on this WC Check Report template and
let's create a new R Markdown file based on it, click OK.
Let's go ahead and save this under a different file name.
Click on File > Save As, and we're going to call this
wcArticleMountains for the mountains region.
After you save the file, go ahead and click on NIT with Parameters and
in the pull down box click Mountain and click Net.
When it finishes, you should now have a report for
weather information preferences in the United States for the Mountain region.
Now that we've made several changes, let's go ahead and
back everything up to your GitHub account.
Open your Git Bash window and make sure that you're in the RepTemplates folder for
the WCtemplatePackage, then type in git add, to add all of the new files and
git commit, then type in the command to push everything up to the repository.
We'll type in get status to check that there is nothing left to commit.
The working tree is clean, you can go back to the GitHub repository and
click Refresh.
Now everything is synced up with your GitHub account.
Finally let's make one last edition.
In your GitHub repository, there's a button at the bottom for
adding a README file.
Click on Add a README.
Type in the following instructions to your readers on how to install and
use your new R package within your weather check template.
But be sure to put in your username for your GitHub account in this README file.
The instructions for doing this are provided in your Read Ahead materials.
So we've typed in some information here that says that this is an R package
that provides an R Markdown Template for
creating a report from the weather check data set.
And then we've also provided some information on how to install
the development version of this package.
Next we show the code to the reader for
installing this package using the devtools install GitHub command.
Now that we've updated the README file here, go ahead and
add a comment that we created a new readme file and click Commit New File.
We now have a new readme file for anyone that's reading your new GitHub repository.
However, now that we've made this change in the GitHub repository,
we need to sync it with your local drive.
This time, let's open the Git Bash window,
and instead of typing in git push, we're actually going to do a pull.
Type in git pull.
Now you can check your file folder for the WCtemplatePackage and
you'll notice that we have a README file installed on your local drive.
So now that we've done all of this,
let's actually try installing the package from your GitHub repository.
First we need to remove the previous local installation.
So click on the packages tab in the bottom right and
scroll down to find where your new package was installed.
You'll notice that we see the listing here for the WCtemplatePackage.
There's a little x at the right, if we click on that it will remove the package.
It says, do you want to permanently uninstall, this can't be undone.
Click Yes.
Now if you try to create an R Markdown package with this template,
it's no longer shown.
So if I click on File > New File > R Markdown from Template, and
scroll through the list, I no longer see the template with the WCtemplatePackage.
This time we're going to install it from your GitHub repository.
To do this, go to the R Studio console window, and
type in the devtools command that you had written on your README file.
Remember, that part of this command includes your GitHub user ID.
So your ID will look slightly different than mine, and then click Enter.
It's now installing the WCtemplatePackage off of your GitHub repository.
To check to make sure that this worked, let's go back to File > New File >
R Markdown from Template and scroll down, and you should again see
the weather check report template from your WCtemplatePackage.
Congratulations, you've now created your very first basic R package
with an R Markdown Template.
And you've deployed it by via GitHub for
others who install and use within the RStudio environment.
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