SpaDES modules

A collection of available modules for use with the SpaDES R package (link).

Downloading modules from GitHub

The easiest way is to identify the original GitHub location of the module you want (e.g., PredictiveEcology/Biomass_core) to download and run this:

# Choose module and choose what folder to install it in. You will have to remember this folder.
# Choice 1 -- Simple install
# This is useful for most cases (e.g., don't want to clone the module via git)
# Get the function "getModule"
if (!require("Require")) {install.packages("Require"); library(Require)}
Require("PredictiveEcology/SpaDES.install") # install/load this package

modulePath = "modules" # Create one path for all modules for a project
getModule('PredictiveEcology/Biomass_core', modulePath = modulePath) 
getModule('PredictiveEcology/Biomass_regeneration', modulePath = modulePath) 

Or, a user can get the module through git, which has the benefit of maintaining version control, but is for more advanced use.

# Choice 2 -- Git install
# This has the advantage that your source code will be linked to the main source code
# Use git command line or your favorite Git client and fork/clone it with:
git clone git@github.com:PredictiveEcology/Biomass_core
git clone git@github.com:PredictiveEcology/Biomass_regeneration

Please see list of currently known modules `

Downloading modules from this repository

Another way to use modules is to get them from this repository is using the built-in functionality in the SpaDES package:

library(SpaDES)
saveTo <- "~/SpaDES-modules" # change this to suit your needs
downloadModule(name = "moduleName", path = saveTo)

This will download and unzip the module files in the directory specified by saveTo.

Example download -- Game of Life

#    # install.packages("SpaDES")
library(SpaDES)
setPaths() # sets 4 paths that SpaDES uses to temporary locations
# setPaths(modulePath = "~") # can try non-temporary locations too to keep between R sessions

moduleName <- "gameOfLife"
downloadModule(moduleName) # downloads to getPaths()$modulePath

modules <- list(moduleName)

######################
## Blinking
######################

X = c(10)
Y = c(10)
TYPE <- "blinker" ## see below for other types

parameters <- list(
  gameOfLife = list(X = X, Y = Y, initialType = TYPE)
)
times <- list(start = 1, end = 30) # only run for 10 steps

clearPlot()
dev() # creates new, faster window if in RStudio
mySim <- simInitAndSpades(times = times, params = parameters, modules = modules)

######################
# Do random starts on bigger map
######################

X = c(100)
Y = c(100)
TYPE <- NA ## random

parameters <- list(
  gameOfLife = list(X = X, Y = Y, initialType = TYPE)
)
clearPlot()
mySim <- simInitAndSpades(times = times, params = parameters, modules = modules)
####################
####################

Load documentation and source code

####################
#  Load Documentation and Source Code
####################
# Load the documentation .Rmd
file.edit(file.path(getPaths()$modulePath, moduleName, paste0(moduleName, ".Rmd")))

# Load the module source code .R
file.edit(file.path(getPaths()$modulePath, moduleName, paste0(moduleName, ".R")))

Known modules (existing or in development)

For a list of other modules currently in development, see here.