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https://github.com/humburg/reportmd

Create multi-page HTML reports in R
https://github.com/humburg/reportmd

data-science r rmarkdown rstudio

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Create multi-page HTML reports in R

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README 

        
# ReportMD --- Writing Complex Scientific Reports in R

Release: [![Build Status](https://travis-ci.org/humburg/reportmd.svg?branch=master)](https://travis-ci.org/humburg/reportmd) 

Development: [![Build Status](https://travis-ci.org/humburg/reportmd.svg?branch=develop)](https://travis-ci.org/humburg/reportmd) 



It is common for complex analyses to be carried out in R. To improve the

reproducability of such analyses and provide the necessary documentation

it is increasingly common to use literate programming techniques. Although

R has had the ability to embed R code in long-form documents describing

the analysis and presenting the results via [*Sweave*](https://www.statistik.lmu.de/~leisch/Sweave/), 

it has been the introduction of [*RMarkdown*](http://rmarkdown.rstudio.com/) 

that has driven the increasing popularity of this approach. The relative

simplicity of authoring [*Markdown*](https://daringfireball.net/projects/markdown/) 

documents and the ability to convert these into a large variety of output formats

via [*pandoc*](http://pandoc.org/) combined with the tight integration with 

[*RStudio*](https://www.rstudio.com/) make this approach easy to use and

powerful at the same time. 



RStudio's support for RMarkdown templates and custom

document formats has enabled the community to provide templates that are

tailored towards specific use cases and integrate well with RStudio. The

document format provided by *reportMD* was inspired by, and is in part based on, [knitrBootstrap](https://github.com/jimhester/knitrBootstrap).



Unlike currently available tools used to

facilitate this literate programming approach to data analysis *reportMD* 

focuses specifically on complex data analyses that may not be well suited to the

monolithic document format typical of RMarkdown. Complex analysis are best split into smaller units

but are likely to depend on the results of earlier stages of the analysis.

This R package aims to provide a number of features to support analyses

that are split across multiple RMarkdown files with cross-file dependencies

and enables multi-page HTML output.



An example of a report generated with *reportMD* is available [online](https://humburg.github.io/reportmd/).



## Installation

To install *reportMD* and some of the dependancies requires [*devtools*](https://github.com/hadley/devtools).

Users of [*RStudio*](https://www.rstudio.com/) will already have this installed,

otherwise `install.packages('devtools')` will take care of that.



The latest version of *reportMD* can be installed:



```r

devtools::install_github('humburg/reportMD')

```



## Getting started

The [Multi-document Rmarkdown template](inst/rmarkdown/templates/multipart_report/skeleton/skeleton.Rmd)

included in this package has detailed instructions and examples. In *RStudio* select 



>    File > New File > R Markdown > From Template > Multi-part Report {reportMD}



This will create a copy of the template in the current project. Open the file

*skeleton.Rmd* and click on RStudio's *Knit* button to compile the template into

a webpage.



Alternatively the template is available as part of the installed R package

and can be located via the R command

`system.file('rmarkdown/templates/multipart_report/skeleton', package="reportMD")`.



## Features

Current and planned features include:

- [x] Ability to declare required RMarkdown documents in yaml header;

    - [x] Dependencies are resolved and rendered to the requested output

      format when the parent document is rendered.

    - [x] Make declared dependencies available as reference links so that

      links to these documents can easily inserted into the text using 

      Markdown syntax.

- [x] Ability to automatically load the results of cached chunks from other

  other documents;

- [x] Avoid recompiling child documents whenever possible;

- [ ] Providing a shorthand to include figures and tables generated by other

  documents;

- [ ] Automatic numbering of figures and tables

    - [x] within each document.

    - [ ] across linked documents.