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.
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).
The simplest way to get started is to have a look to the
R2ucare
vignette.
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/},
}
- Fix bugs
- 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?)
- 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
- Choquet, R., Lebreton, J.-D., Gimenez, O., Reboulet, A.-M., and R. Pradel. (2009). U-CARE: Utilities for performing goodness of fit tests and manipulating CApture-REcapture data. Ecography. 32: 1071-1074.
- Lebreton, J.-D. et al. (1992). Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecol. Monogr. 62: 67-118.
- Pradel, R., Gimenez O. and J.-D. Lebreton (2005). Principles and interest of GOF tests for multistate capture-recapture models. Animal Biodiversity and Conservation 28: 189–204.
- Pradel R., Wintrebert C.M.A. and Gimenez O. (2003). A proposal for a goodness-of-fit test to the Arnason-Schwarz multisite capture-recapture model. Biometrics 59: 43-53.