Features

Execution engines

Supported notebook formats

Hiding cell inputs/outputs

You can hide inputs and or outputs of individual cells:

Papermill engine:

Within a jupyter notebook:

• edit cell metadata

• add one of the following tags: hide_input, hide_output, remove_cell

{
    "tags": [
        "remove_cell"
    ]
}

Rmarkdown engine:

• all native input control options (e.g. results=’hide’, include=FALSE, echo=FALSE) are supported. See the Rmarkdown documentation for more details.

Jupytext automatically converts the tags to Rmarkdown options for all supported formats.

Parametrized notebooks

Papermill engine:

• See the Papermill documentation

Example:

• Add the tag parameters to the metadata of a cell in a jupyter notebook.

• Declare default parameters in that cell:

input_file = '/path/to/default_file.csv'

• Use the variable as any other:

import pandas as pd
pd.read_csv(input_file)

Rmarkdown engine:

• See the documentation.

Example:

• Declare the parameter to the yaml frontmatter.

• You can set default parameters that will be used when the notebook is executed interactively in Rstudio. They will be overwritten when running through reportsrender.

---
title: My Document
output: html_document
params:
  input_file: '/path/to/default_file.csv'
---

• Access the parameters from the code:

read_csv(params$input_file)

Be compatible with both engines:

Yes it’s possible! You can execute the same notebook with both engines. Adding parameters is a bit more cumbersome though.

Example (Python notebook stored as .Rmd file using jupytext):

---
title: My Document
output: html_document
params:
  input_file: '/path/to/default_file.csv'
---

```{python tags=c("parameters")}
try:
    # try to get param from Rmarkdown using reticulate.
    input_file = r.params["input_file"]
except:
    # won't work if running papermill. Re-declare default parameters.
    input_file = "/path/to/default_file.csv"
```

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