madingleyr's Introduction

MadingleyR Package

Getting Started

Installing Madingley R

To install MadingleyR and MadingleyPlots (which is required for plotting the results of simulations), run the following commands:

library(devtools)
install_github("timnewbold/MadingleyR",subdir = "MadingleyR")
install_github("timnewbold/MadingleyPlots",subdir = "MadingleyPlots")

Running basic simulations

To get started with simple simulations of the Madingley Model, using default settings, you just need to run the following set of commands.

First, load the packages:

library(MadingleyR)
library(MadingleyPlots)

Then download the latest release of the Madingley Model:

codeDir <- "C:/Temp"
DownloadRelease(codeDir = codeDir)

Then download the necessary input data:

GetMadingleyData(codeDir = codeDir)

Now initialize the model, for a 50-year simulation in one grid cell:

init <- MadingleyInitialisation(duration = 50,
                                specific_locations = list(latitudes=2,longitudes=33))
params <- MadingleyParameters()

Finally, run the model:

madingleySim <- RunMadingley(codeDir = codeDir,init = init,params = params)

Plotting the basic simulations

To plot the time series of biomass densities by trophic level, simply run the following command:

PlotTemporal(resultsDir = madingleySim$outputDir,plotName = "BiomassDensity")

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madingleyr's Issues

ERROR: dependency ‘sds’ is not available for package ‘MadingleyPlots’

Hello,

I'm really exited to use this package but I can't find an 'sds' package for R (I'm using v3.3.3). Do you know of a way to solve this problem?

Here is the exact error:

install_github("timnewbold/MadingleyPlots",subdir = "MadingleyPlots")
Downloading GitHub repo timnewbold/MadingleyPlots@master
from URL https://api.github.com/repos/timnewbold/MadingleyPlots/zipball/master
Installing MadingleyPlots
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
'/tmp/RtmpYhasIx/devtools12063c6abf1/timnewbold-MadingleyPlots-412119d/MadingleyPlots'
--library='/home/bonobo/R/x86_64-pc-linux-gnu-library/3.3' --install-tests

ERROR: dependency ‘sds’ is not available for package ‘MadingleyPlots’