In cmartin/PopulationViabilityAnalysis: An R implementation of count-based multi-site population viability analysis

This package implements a stochastic simulation for a count-based multi-site population viability analysis as described in chapter 11 of Quantitative Conservation Ecology (Morris & Doak, 2002).

Code is highly inspired from the MatLab implementation described in the book.

Installation

You have two options here.

Install package from github.com

This allows you to easily install updates, have access to the function help files etc.

library(devtools)
devtools::install_github("cmartin/msPVA")
library(msPVA)

Or you download the source file and run it directly

In this case, you need download the raw R file and then execute :

source("MultisitePVA.R")

This is a quicker, but dirtier way!

Try some examples

With the same Clapper rail data as in Morris & Doak

Definining parameters manually :

library(msPVA)
library(knitr)
read_chunk("inst/examples/ms.Example.R")
read_chunk("inst/examples/ss.Example.R")
read_chunk("inst/examples/params.Example.R")

Or ask the package to calculate most of them automatically from a time-series :

With a two-populations polar bear time series from Stirling et al. 2004

Run it for a single population

Read the book

If you are to use this package, I highly recommend that you first read chapter 11 from Quantitative Conservation Ecology (Morris & Doak, 2002), so you understand limitations and assumptions from the underlying model. Managing animal populations should not be taken lightly.

Problems

Please report any bugs to the GitHub issue tracker and write any questions to [e-mail]

Citation

If this code is useful to you, please cite as :

cat(citation("msPVA")$textVersion)

cmartin/PopulationViabilityAnalysis documentation built on May 13, 2019, 8:23 p.m.