What is SpaDES?

A high-level introduction to the SpaDES framework that can help with reproducible, reusable research.

Introduction to SpaDES as a tool for decision making in Ecology

SpaDES as a simulation platform

Here we look at an existing simulation model, LandR-Biomass ā€“> This one is a rewrite of LANDIS-II Biomass Succession

Vegetation simulation model: LandR-Biomass

SpaDES as a workflow platform

Here we continue with LandR-Biomass ā€“> But we add a module that estimates all parameters and gets all data. The module, Biomass_borealDataPrep, has been tested widely in the boreal forest of Canada. It uses open datasets.

Using Biomass_borealDataPrep with Biomass_core to estimate input data layers

Hands on: From R to SpaDES

In this section we will present examples of how to bring both static and dynamic R scripts into SpaDES, by creating modules from scratch and linking them

Converting R code to a `SpaDES` module - seed establishment
Dynamic modelling in SpaDES - a simple example
Modules -- Thinking in a modular way

A simple, landscape fire model: https://github.com/PredictiveEcology/scfm/blob/development/scfm.Rmd

This model, based on Steve Cummingā€™s work, is a percolation simulation model, that contains all the necessary aparatus to estimate the parameters for a fire regime that is statistically correct, i.e., given an input dataset of historical fires, this module will reproduce the fire size distribution on the same landscape. There are ~8 modules in this model. This module has been used in a variety of places in Canada, but its implementation is still in alpha state, so unexpected behaviour may result.

https://github.com/PredictiveEcology/scfm/blob/development/scfm.Rmd Landscape Fire Model

SpaDES anatomy

A SpaDES module is the primary unit of organization for a SpaDES workflow. The key features of the SpaDES anatomy are: 1. Metadata 2. simList Everything else derives from these two structures

My first `SpaDES` module - from `R` to `SpaDES`
Modules -- The nitty gritty details
simList -- What is in it?
Exercises: Building `SpaDES` modules
Modules -- Integrating among modules

Taking control

To become more advanced with R, reproducible workflows, profiling etc. we provide some general tips and content to improve skills. These are concentrated on applications with SpaDES, but they are not unique to SpaDES.

R -- developing powerful skills
R -- Profiling code
Caching
Debugging

Useful Cheatsheets

We provide some links to useful Cheatsheets

Cheatsheets