3 hours
Open your document in Rstudio. Click Knit. You’ll see a publish button in the item view pane - click it. You’ll be redirected to the rpubs web site. If you don’t have an account you’ll need to register. You’ll see a screen with basic metadata, but all is optional. Your document is published online!
Sign up for GitHub if you don’t have an account. Create a new repository (the
name doesn’t mater) and make sure to check the box for Initialize this repo
with a README file. Open Finder of Windows explorer on your computer.
Navigate to the FSCI directory and find the .html file you’ve been knitting.
Rename this file to index.html. On GitHub, Click on Upload a file. Drag
index.html to the box and click the green button at the bottom. Now go to
settings on GitHub. Scroll down to the GHPages section and click the dropbown
to select masster. Click Save. If you now scroll down to the GHPages section
you’ll see a github.io url. Copy this and go back to the code section of your
GitHub Repository. Click and add the url. If you clikc this link you’ll see
your report!
We need to copy all files used by knitter into our GitHub repository. Make a
copy of your .Rmd file that doesn’t include the ORCID section (The
authentication is a pain). Then we
need to tell Binder that we want to run R and what our dependencies are. In
GitHub, create a runtime.txt file that contains: r-2018-07-09. This
chooses a version of R at the date indicated. Next create a install.R file
that contains:
install.packages("rmarkdown")
install.packages("bitops")
install.packages("caTools")
install.packages("tidyverse")
install.packages("DT")
Now edit the README file in Github and add:
https://mybinder.org/v2/gh/AuthorCarpentry/R-Binder/master?urlpath=rstudio
replacing AuthorCarpentry with your GitHub account name and R-Binder with
your GitHub repository name. Click the Binder button and your environment will
load (it might take up to 20 mins the first time).
This final dynamic feature demonstrates the power of keeping your updated professional information in your ORCID profile, and copying information from it as you need it in your reproducible report.
To make this feature work its magic, we need to get an authentication token from ORCID in order to read your bio from your ORCID profile. This is a multi-step process, allowing RStudio and R to communicate with the ORCID system. Let’s proceed step by step.
In the exercise file, navigate to the section Principal Investigator’s
Biosketch. Open the file insert_orcid.R. Copy the first code chunk from
this file and paste into your exercise file under the Level 2 header
Principal Investigators Biosketch.
In this new code chunk in your exercise file, click the green arrow to the upper right corner to run the code. This will open up a web browser to the ORCID web site. Log into your ORCID account.
In your RStudio Environment window, you will see a variable called token
added. This is the authorization code issued by ORCID that allows R and
RStudio to read information from your ORCID account.
In the R console type token. This prints to the console the token value
you saw added to your Environment. We’ll be copying and pasting that token
string into a new file in Step 5 below.
This step creates an .Renviron file in your computer’s home directory
where you will store the ORCID token. By doing so, the authorization is able
to be reactivated every time your RStudio session communicates with ORCID to
refresh or add data from your profile.
Return to the file insert_orcid.R. Now copy and paste the second code chunk
into the console. (NOT into your exercise file!)
ORCID_TOKEN="1c7..."
where 1c7... is replaced by the token that we printed to the R console
earlier. You will need to copy everything after BEARER that was just
printed to the console. Paste it in after the = sign.
FYI, this .Renviron file will show up in your computer’s home directory
which is outside of your RStudio project directory. The exact “where” depends
on your computer’s operating system and configuration.
a. Add the following text under the header to give attribution to the
rorcid package:
_This is auto-populated from your ORCID profile using the @R-rorcid package._
b. Insert code to place the ORCID bio into the PI Biosketch section. Below
the code chunk, add `r bio`.
Save the changes, knit to HTML, and you’ll see the biography from your ORCID file now appear in the reproducible report.
To test that the biosketch will be auto-updated in your report when your ORCID bio is updated, go to your ORCID account and make a change to your biography. You might add a new accomplishment to the top of the bio, such as Master of Reproducible Reporting or Bends R Markdown to Their Will.
When you knit the document to HTML, the Principal Investigators Biosketch auto-updates!