README.md

offsetsim

OffsetSim is an iterative model that simulates the landscape under a set of user-defined offset conservation actions and gains structures to yield an assessment of the gains and losses at the site scale, where the loss of biodiversity from a particular development site is mitigated by an associated gain from one more offset sites, the program scale, comprising all sites in the development-offset program, and the landscape scale, comprising all sites in the landscape, i.e. the sites within the development-offset program as well as those not included. The model requires a set of GIS data layers to be defined as feature layers, as well as a set of response functions that describe the effect of each action on each feature layer. The features can represent any user defined spatial layer including species occupation, habitat types, vegetation classes, environmental domains, ecosystems, and ecosystem services. Actions such as development, protection, restoration etc. are defined and linked to these features. The responses to these actions include the characteristics of the offset action (e.g. the characteristics of the offset restoration function) and are provided as user defined functions.

How to install

Download and install the latest version of R. On Ubuntu or another debian-based linux system, this can be done on the terminal as follows:

sudo apt-get update
sudo apt-get install r-base
sudo apt-get install git

You will then require the R devtools package in order to install offsetsim. To install devtools, from inside R do:

install.packages('devtools')

To now install the offsetsim package, from inside R do:

devtools::install_github("isaacpeterson/offset_simulator")

This may take a while as R downloads, builds, and installs the package and all its dependencies.

How to run

Once offsetsim is installed, the easiest way to get started is to generate an offset simulation example that you can customise. To create the user example from inside R do:

library(offsetsim)
osim.create.example('./my-osim-example')

This will download the example files (make sure you have an active internet connection) into the directory ./my-osim-example. To now run the example from inside R do:

setwd('./my-osim-example'); source('offsetsim_example.R')

How to get more help

You can get more information on offsetsim functionality, from inside R do:

??offsetsim

Description on the files

initialise_params_defaults.R

run_offsets_simulation.R

plot_collated_realisations.R

Model outputs

Code should be in a directory called /offset_simulator

Outputs will be written into a directory called /offset_data

offset_data has the following structure:

Within this directory there are the following directories

Points to note

This script can occasionally create runaway processes if the runs are stopped before completion by the user. By default the script will utilize all available processors on your machine. So if you terminate the script while it's running, it may leave some R processes running. This can be terminated by just quitting R, or manually killing those remaining processes.



isaacpeterson/offset_simulator documentation built on May 12, 2018, 10:11 a.m.