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marked: an R package for maximum likelihood and M arkov C hain M onte C arlo analysis of capture–recapture data
Author(s) -
Laake Jeff L.,
Johnson Devin S.,
Conn Paul B.
Publication year - 2013
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12065
Subject(s) - covariate , maximum likelihood , statistics , data set , r package , mathematics , set (abstract data type) , combinatorics , computer science , programming language
Summary We describe an open‐source r package, marked, for analysis of mark–recapture data to estimate survival and animal abundance. Currently, marked is capable of fitting C ormack– J olly– S eber ( CJS ) and J olly– S eber models with maximum likelihood estimation ( MLE ) and CJS models with B ayesian M arkov C hain M onte C arlo methods. The CJS models can be fitted with MLE using optimization code in R or with A utomatic D ifferentiation M odel B uilder. The latter allows incorporation of random effects. Some package features include: (i) individual‐specific time intervals between sampling occasions, (ii) generation of optimization starting values from generalized linear model approximations and (iii) prediction of demographic parameters associated with unique combinations of individual and time‐specific covariates. We demonstrate marked with a commonly analysed E uropean dipper ( Cinclus cinclus ) data set. The package will be most useful to ecologists with large mark–recapture data sets and many individual covariates.