ucare: Goodness-of-fit tests for the Cormack-Jolly-Seber model

In openCR: Open Population Capture-Recapture

Goodness-of-fit tests for the Cormack-Jolly-Seber model

Description

The package R2ucare (Gimenez et al. 2018, 2022) provides the standard tests for CJS models from Burnham et al. (1987) along with tests for multi-state models as described by Pradel et al. (2005). This function is a wrapper for the tests relevant to openCR (see Details). Original papers and the vignette for R2ucare should be consulted for interpretation.

Usage

ucare.cjs(CH, tests = "all", by = NULL, verbose = TRUE, rounding = 3, ...)

Arguments

CH	capthist object suitable for openCR
tests	character vector with the names of specific tests (see Details) or ‘all’
by	character name of covariate in CH used to split rows of CH into separate groups
verbose	logical; if TRUE then additional details are tabulated
rounding	integer number of decimal places in output
...	other arguments passed to split.capthist if needed

Details

The possible tests are “test3sr", “test3sm", “test2ct", “test2cl", and “overall_CJS".

If CH is a multi-session object then it will first be collapsed to a single-session object with join as usual in openCR. If CH has an intervals attribute indicating that the data are from a robust design (some intervals zero) then it will first be collapsed to one secondary session per primary session, with a warning.

If by is specified it should point to a categorical variable (factor or character) in the covariates attribute of CH. Separate tests will be conducted for each group.

R2ucare was removed from CRAN in May 2022, but will return at some point. In the meantime, it may be necessary to install from GitHub with

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

Value

A list of results, possibly nested by the grouping variable by. The verbose form includes both the overall result of each test and its breakdown into components (‘details’).

References

Burnham, K. P., Anderson, D. R., White, G. C., Brownie, C. and Pollock, K. H. (1987) Design and Analysis Methods for Fish Survival Experiments Based on Release-Recapture. American Fisheries Society Monograph 5. Bethesda, Maryland, USA.

Choquet, R., Lebreton, J.-D., Gimenez, O., Reboulet, A.-M. and Pradel, R. (2009) U-CARE: Utilities for performing goodness of fit tests and manipulating CApture-REcapture data. Ecography 32, 1071–1074.

Gimenez, O., Lebreton, J.-D., Choquet, R. and 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.

Gimenez, O., Lebreton, J.-D., Choquet, R. and Pradel, R. (2022) R2ucare: Goodness-of-Fit Tests for Capture-Recapture Models. R package version 1.0.2. https://github.com/oliviergimenez/R2ucare/

Lebreton, J.-D., Burnham, K. P., Clobert, J., and Anderson, D. R. (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological Monographs 62, 67–118.

Pradel, R., Gimenez O. and Lebreton, J.-D. (2005) Principles and interest of GOF tests for multistate capture–recapture models. Animal Biodiversity and Conservation 28, 189–204.

See Also

m.array

Examples

if (requireNamespace("R2ucare"))
    ucare.cjs(dipperCH, verbose = FALSE, by = 'sex')

openCR documentation built on Sept. 25, 2022, 5:06 p.m.