documentation.Rmd

# Documentation and Outputs

*Will someone understand this thing when I hand it over?*

Documentation is essential to collaboration and continuity for our work. Your
project should contain documentation to allow a project to be picked up by
another user. Documentation includes the following:

-   A **README** document in the top level of the project folder with a
    high-level explanation of project organization, purpose, and and contact
    info.
-   **Metadata** for your data set showing its origin and the type of data in
    each field in a table.
-   **Comments** in your computer code
-   **Written descriptions** of your analyses. The primary medium for this
    should be **R Markdown** documents, which allow you to combine code,
    results, and descriptive text in an easy to update and modify form. Shorter
    ephermal results can be posted as plots to your project Slack rooms.

## Learn

-   R Markdown is pretty straightforward to learn. You can create your first
    document and get the basics by going to File > New File > R Markdown
    in the RStudio menu. When you have time, dive in a bit more with [this great
    lesson on it](http://rpubs.com/marschmi/RMarkdown) with accompanying
    [video](https://www.youtube.com/watch?v=WFAHJ0NHOEQ&feature=youtu.be).
    Here's an [RStudio Reference
    Sheet](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
    for R Markdown.

## Install

-   (Very optional unless you are asked):
    [**ehastyle**](https://github.com/ecohealthalliance/ehastyle) is our
    internal EHA R package with R Markdown templates for some reports we
    produce.
    
## Library 

Once your project has been published, you should include the output in our EHA Library. Simply submit through [this google form](https://goo.gl/forms/pnJr4SGvlY8gyi2I3). The library database, along with full texts of both media and science publications, is stored on [DropBox](https://www.dropbox.com/sh/cdt1tvxddogw90m/AACH3HT9L5WDbpf2K_sOpy6Ta?dl=0). The purpose of the EHA Library is to store our work in a searchable, systematic database. A centralized location of EHA work is of use to our science and development teams. Additionaly, standardized analyses (stored in the [eha-library github repository](https://github.com/ecohealthalliance/eha-library)) create easy reporting to our board, our funding bodies, and the public. We have found this database particularly useful in the on-boarding of new staff. 

The current scope of the Library includes:

-   Scientific publications
-   Conference presentations
-   Layman publications by EHA staff 
-   EHA-mentored academic work
-   Media articles that highlight our work or our scientists