Creating reports in R Materials for short, half-day workshops View on GitHub Learning Objectives Please submit a PR if you are interested in adding this feature.Creating reports in R | Training-modules Skip to the content. #Download rmarkdown code#Sos-rmarkdown does retain all global and code block options of RMarkdown documents as global and cell meta data in the resulting notebooks, but a SoS Notebook to RMarkdown converter is not planned. It aims to provide a lossless converter from RMarkdown to SoS Notebook so please submit a ticket if certain features of RMarkdown are not properly converted. Sos-rmarkdown is designed to convert Rmarkdown documents to Jupyter notebooks. Conversion from SoS Notebook to RMarkdown? Please refer to SoS Notebook templates for a list of templates. The hidden content could be displayed by selecting a dropdown box to the top right corner of the document. For example, template sos-report-toc-v2 outputs all cells but hides collapsed inputs and outputs by default. In addition, whereas the default templates from jupyter nbconvert does not respect the collasping status of cells and renders input and output of all cells, SoS Notebook provides templates that supports these features. SoS Notebook supports the use of multiple kernels in one notebook and can accommodate code blocks in multiple languages.įor example, code blocks such as ``` A Jupyter notebook with an ir kernel can only evaluate R scripts, and the use of magics such as %%python is rather limiting. Is converted to a markdown cell that is evaluated in a R kernel as followsĬode blocks in Rmarkdown supports multiple languages such as Python, Julia, and Stata. SoS Notebook addresses this problem with the use of a markdown kernel, which is essentially a markdown kernel that can be expanded with language-specific inline expressions.įor example, the following Rmarkdown text I counted `r sum(c(1,2,3))` blue cars on the highway. Jupyter cannot handle embedded expressions in its markdown cells because markdown cells are handled in its frontend and do not interact with the computing kernel. Rmarkdown supports inline expressions, which are R expressions embedded in markdown texts. SoS Notebook, especially its Jupyter Lab extension addresses most of the limitations and offers an almost perfect conversion from R markdown to Jupyter notebook. You can execute the notebook directly with command papermill -engine sos if you would like to use advanced features of papermill.Īlthough there are already a number of Rmd to Jupyter converters such as notedown, RMD-to-Jupyter, ipymd, and rmd2jupyter, they lack support for some of the Rmakdown features due to limitations of the Jupyter notebook platform. The -execute option essentially uses sos-papermill to execute the notebook with an SoS kernel. The resulting notebook will be a notebook with an R kernel. Rmd file does not have inline expressions and does not have codeīlocks using Python and other languages, and -execute option is not used, These steps could be combined with a Rmd -> HTML converter using the following command if you would only like to execute a Rmarkdown document with SoS Notebook, not knitr, and generate a SoS-style report: sos convert input.rmd output.html -execute -template sos-report-toc-v2 The resulting notebook could be converted to a HTML format using any of the jupyter or SoS Notebook templates using commands such as sos convert output.ipynb output.html -template sos-report-toc-v2 Rmd file to a Jupyter notebook with command sos convert input.Rmd output.ipynbĪnd optionally execute the resulting notebook with option -execute sos convert input.Rmd output.ipynb -execute #Download rmarkdown install#You will need to install additional kernels and language modules such as sos-python and sos-bash if the Rmarkdown documents use these languages. The conda installation of sos-r will install the conda version of R (e.g. Or conda install -c conda-forge sos-rmarkdown Sos-rmarkdown and related tools ( sos, sos-notebook, sos-r, markdown-kernel, papermill, sos-papermill) can be installed with command pip install sos-rmarkdown sos-rmarkdown is an extension module to SoS Workflow System and Polyglot Notebook and provides an almost lossless converter from Rmarkdown files to SoS notebooks using the sos file conversion mechanism. SoS Notebook is an extension to Jupyter Notebook that allows the use of multiple kernels in one notebook, and enables RMarkdown-like features such as markdown text with inline expressions and code blocks in multiple languages. The RMarkdown format is a markdown format with embedded R expressions and code blocks, and is extremely popular for R users. Sos-rmarkdown: an RMarkdown to SoS Notebook converter
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