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title : "Sharing modules and data"
author : "Alex M Chubaty & Eliot McIntire"
date : "December 9, 2016"
```{r setup, include=FALSE}
knitr::opts_chunk$set(cache = TRUE, echo = TRUE, eval = FALSE)
## `SpaDES` module repositories
A 'module repository' is simply a web site that serves files using a particular directory structure (the same directory structure used in a local `SpaDES` module repo).
Our module repo is at
This is the default repo in `SpaDES`.
- it's public
- it's easily accessible using `downloadModule()`
```{r module-repo-option, echo=TRUE, eval=TRUE}
getOption('spades.modulesRepo') ## default url prefix is GitHub
## Other `SpaDES` module repositories
Anybody can create their own repository as well (R has CRAN, Rforge, BioConductor and many lesser used ones)
`downloadModule()` has a `repo` argument.
## Our `SpaDES` module repository
- Initially, most `SpaDES` modules will not be there
- *e.g.*, SpaDES-LBM (SpaDES -- Landis Biomass Succession) is not there yet (we would like to publish it first)
## What is GitHub?
[]( is a free\* code archive and hosting service.
Allows hosting of public and private code repositories, build around `git` version control software.
GitHub provides:
- code archiving/distribution
- version control
- publication (code, html pages, and others)
- collaboration
- bug tracker
- **user friendly web interface and desktop client**
## Using GitHub for collaboration
We, and many others, use GitHub extensively for all our group's work
- Like Dropbox, in the sense that there is a cloud version, and potentially many local copies all over the place
- Unlike Dropbox, the copies on people's computers are not automatically there
- Requires manual intervention
## GitHub Client
- For your local copy of the files, you need an extra piece of software on your computer (like the "Dropbox client")
- `git` and GitHub both require a bit of learning:
- [tutorial](
- There are many other great `git` clients:
- **[Gitkraken](** is amazing and our group's prefered client (cross-platform)
- [SourceTree]( (Windows & Mac only)
- See for more
## `shiny` apps
- Massively powerful
- Allows the process of data wrangling, data visualization, data analysis, etc. to be made into interactive web (and mobile) apps
- By moving the web app development into R (instead of taking R outputs and putting them into a web development kit), means that the analysis power can be at the interactive stage
- Also, data analysts can be making web pages
## `shine` function
`SpaDES` has a simple function that takes any simList and makes a web app from it:
```{r shine}
<div class="centered">Try it!</div>
## Simple shiny apps
- hosted apps at [](
- *e.g.*, [Proof of concept](
## Themes
- Lots of developers making shiny themes
- Often they are wrappers on javascript code
- So your look can be easily modified without many web development skills
## Shiny maps with leaflet
- [leaflet package](
# Data sources
## Data sharing
- We have shown a way to specify default data sources
*Where was that?*
- We have shown a way to specify default data manipulations and data preparations of those default data
*Where was that?*
## If there are complex data sets?
- And from many sources?
- Can still use `sourceURL` in `defineModule` and create an `.inputObjects` function which will do all the manipulations
## How to adequately describe data?
- It is clear that there is not enough information contained in the metadata to fully describe everything about the required dataset(s) type(s)
- **Use the .Rmd** file to describe more for human eyes
- It is very difficult to algorithmically define data in a generic way
- There are standards, but `SpaDES` doesn't tap into those (yet!)
## Overriding default datasets
- If a *user* passes an object that a module requires (in 'defineModule' metadata)
- The default data will not be used
- checksums
- externally hosted data
- include data with your module code