In PredictiveEcology/SpaDES.Workshops: Training workshops for ecological modeling with SpaDES

knitr::opts_chunk$set(cache = TRUE, echo = TRUE, eval = FALSE)
library(SpaDES)

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 https://github.com/PredictiveEcology/SpaDES-modules

This is the default repo in SpaDES.

- it's public
- it's easily accessible using `downloadModule()`

getOption('spades.moduleRepo') ## default url prefix is GitHub.com

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?

Github.com 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 https://git-scm.com/downloads/guis 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.shiny (on GitHub) has a simple function that takes any simList and makes a web app from it:

?shine

Try it!

Simple shiny apps

• hosted apps at shinyapps.io

  • 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

PredictiveEcology/SpaDES.Workshops documentation built on Jan. 30, 2021, 6:52 p.m.