README.md

In david-borchers/LCE_paper: Latent Capture History estimation package

Contents

This is code to go with the paper A latent capture history model for digital aerial surveys by D. L. Borchers, P. Nightingale, B. C. Stevenson, and R. M. Fewster, to appear in the journal Biometrics.

It contains source code for an R package called "twoplane" and a folder called "usercode". You will need to build the package before using it.

It is a standard R package, and has been tested (most recently) with R version 4.0.2.

The package contains a small component written in C++, so it requires a C++ compiler toolchain to be installed.

Building and installing in R

To build and install the package in R using devtools, you may use the following commands:

Start R and set the working directory to the directory containing this file

install.packages("devtools")

library(devtools)

build()

install()

Now the package should be ready to load:

library(twoplane)

Building and installing in RStudio

Alternatively, to build and install the package in RStudio: 1. Open the project file: LCE_paper.Rproj 2. Open the Build tab 3. Under "More", select "Clean and Rebuild"

Usercode

The usercode folder contains three files:

1. porpoiseFit.R contains code to load and fit to the semi-synthetic porpoise data used in the paper,

2. sim-longlag.r contains code to do the long-lag simulations, and

3. sim-shortlag.r contains code to do the long-lag simulations.

twoplane package

Estimates animal density and related parameters from a mark-recapture line transect survey using two cameras, on which recaptures are not identified, there is animal movement and animals' availability is governed by a Markov model.

RStudio

If you are an RStudio user, you might want to use the R project file LCE_paper.Rproj as your RStudio project file.

david-borchers/LCE_paper documentation built on Nov. 15, 2020, 1:33 p.m.