R2ucare

What it does (and does not do)

This package contains R functions to perform goodness-of-fit tests for capture-recapture models. It also has various functions to manipulate capture-recapture data. Please email all suggestions for improvements, questions, comments and bugs to olivier.gimenez[at]cefe[dot]cnrs[dot]fr.

For Cormack-Jolly-Seber models (single-state), we refer to Lebreton et al. (1992) and Pradel et al. (2005) for the theory. For Arnason-Schwarz models (multistate), have a look to Pradel et al. (2003). Chapter 5 of the Gentle Introduction to MARK also provides a good start for understanding goodness-of-fit tests.

Warning: to date, no goodness-of-fit test exists for models with individual covariates (unless you discretize them and use groups), individual time-varying covariates (unless you treat them as states) or temporal covariates; therefore, remove these covariates from your dataset before using it with R2ucare. For groups, just treat groups separately as in the Dipper example below.

To install the package

The latest stable version of the package can be downloaded from CRAN with the R command

install.packages("R2ucare")

The repository on GitHub https://github.com/oliviergimenez/R2ucare hosts the development version of the package, to install it:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("oliviergimenez/R2ucare")

Despite what its name might suggest, you do not need to download and install U-CARE to run the R2ucare package. This package is basically a Matlab to R translation of U-CARE (Choquet et al. 2009).

Getting started

The simplest way to get started is to have a look to the R2ucare vignette.

How to cite R2ucare?

Please, cite our (free access) paper if you use R2ucare:

Gimenez, O, Lebreton, J-D, Choquet, R, Pradel, R. (2018) R2ucare: An R package to perform goodness-of-fit tests for capture–recapture models. Methods in Ecology and Evolution 9: 1749-1754.

A bibtex entry is as follows:

@Article{,
  title = {R2ucare: An {R} package to perform goodness-of-fit tests for capture–recapture models},
  author = {{Gimenez} and {Olivier} and {Lebreton} and {Jean-Dominique} and {Choquet} and {Rémi} and {Pradel} and {Roger}},
  journal = {Methods in Ecology and Evolution},
  year = {2018},
  volume = {9},
  number = {7},
  pages = {1749-1754},
  url = {https://oliviergimenez.github.io/R2ucare/},
}

To-do list

  1. Fix bugs
  2. Add more tests (any help welcome)
    • gof test for recovery data
    • gof test for mixture of recapture and recoveries (based on Rachel McCrea’s work)
    • gof tests for heterogeneity in detection and in transition propensity, test for underlying state-structure (based on Anita Jeyam’s work)
    • Gof tests for closed pop models
    • Gof tests for occupancy models (relevant?)
  3. Make it more user-friendly
    • decision trees to suggest what to do when things go wrong
    • pass testMitec, testMltec and AS/JMV model fitting in C++ using Rcpp
    • mosaic plot for wbwa, and other ways to visually represent contingency tables for the other tests
    • class ucare

References