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

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

Often we want to run a simulation with a variety of parameter values as inputs. This is sometimes called a simulation experiment. The experiment function gives us an easy interface to this.

We will use the establishment module that we created in exercise 4a.

Download a module

library(ggplot2)
library(SpaDES)

module.path <- file.path(dirname(tempdir()), "modules")
downloadModule("establishment", path = module.path)
setPaths(modulePath = module.path)

modules <- list("establishment")

mySim <- simInit(modules = modules)

# make sure the plotting device is clear
clearPlot()
spades(mySim)

Create an experiment

1. Find out which parameters are in this module. (Hint: where is the module? Can you open it easily from R?)
2. Pick one of the parameters and create a range of values for it.
3. Following the structure indicated in example 4 of ?experiment, use experiment to run a spades call for each parameter set (note that experiment is just a wrapper around spades).
4. Inspect the experiment structure using attributes(mySim).
5. Create a plot showing on the x axis your parameter values, and on the y-axis something like sum(mySim$establish[]), i.e., the number of pixels that had an establishment event.

Advanced - Create a two-parameter experiment

1. Repeat as above, but vary two parameters.

See a solution here

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