When posting R markdown (.rmd, or .Rmd files) to Kyso you will need to convert them to normal markdown (.md) files before they hit Kyso. That can be before you upload them, or before you commit them to your Github repository.

When you convert Rmd to normal markdown it will create run the code in the Rmd file, generate any images and tables needed, create a markdown file and an assets folder for any image files. You can them upload the markdown and assts folder to Kyso.

Converting

Installing knitr

Knitr is the package that we will use to convert the Rmd files to markdown in order to upload to Kyso, lets install it first using inside your R console:

install.packages("knitr")

Using the command line

In the directory of your .Rmd file just use the following command:

Rscript -e "library(knitr); knit('notebook.Rmd', 'notebook.md')"

Using R Studio

Make sure you set the working directory to the location of your .Rmd files.

Once you have your working directory set go to your R console inside R studio and enter the following commands, first to load knitr and then to convert the notebook:

library(knitr)
knit('notebook.Rmd', 'notebook.md')

Posting to Kyso

Then simply upload the generated files to Kyso, or commit them to your Github repo which is connected to Kyso. Be sure to select the generated .md file as the main file, not the .Rmd

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