multimark: Capture-Mark-Recapture Analysis using Multiple Non-Invasive Marks

Share:

Traditional and spatial capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo. Addressing deficiencies in currently available software, 'multimark' also provides a user-friendly interface for performing Bayesian multimodel inference using non-spatial or spatial capture-recapture data consisting of a single conventional mark or multiple non-invasive marks.

Author
Brett T. McClintock [aut, cre], Acho Arnold [ctb, cph] (C original matrix library, https://github.com/najela/matrix.h), Barry Brown [ctb] (Fortran original ranlib library), James Lovato [ctb] (Fortran original ranlib library), John Burkardt [ctb] (C original ranlib library, http://people.sc.fsu.edu/~jburkardt/c_src/ranlib), Cleve Moler [ctb] (C original linpack library, http://www.kkant.net/geist/ranlib/), Arjun Gopalaswamy [ctb] (modified snippets of R package SPACECAP code)
Date of publication
2016-09-02 12:17:15
Maintainer
Brett T. McClintock <brett.mcclintock@noaa.gov>
License
GPL-2
Version
2.0.0

View on CRAN

Man pages

bobcat
Bobcat data
getdensityClosedSCR
Calculate population density estimates
getprobsCJS
Calculate posterior capture and survival probabilities
getprobsClosed
Calculate posterior capture and recapture probabilities
getprobsClosedSCR
Calculate posterior capture and recapture probabilities
markCJS
Fit open population survival models for "traditional"...
markClosed
Fit closed population abundance models for "traditional"...
markClosedSCR
Fit spatial population abundance models for "traditional"...
multimarkCJS
Fit open population survival models for...
multimarkClosed
Fit closed population abundance models for...
multimarkClosedSCR
Fit spatially-explicit population abundance models for...
multimarkSCRsetup-class
Class '"multimarkSCRsetup"'
multimarksetup-class
Class '"multimarksetup"'
multimodelCJS
Multimodel inference for 'multimark' open population survival...
multimodelClosed
Multimodel inference for 'multimark' closed population...
multimodelClosedSCR
Multimodel inference for 'multimark' spatial population...
plotSpatialData
Plot spatial capture-mark-recapture data
processdata
Generate model inputs for fitting 'multimark' models
processdataSCR
Generate model inputs for fitting spatial 'multimark' models
simdataCJS
Simulate open population capture-mark-recapture data arising...
simdataClosed
Simulate closed population capture-mark-recapture data...
simdataClosedSCR
Simulate spatially-explicit capture-mark-recapture data from...
tiger
Tiger data

Files in this package

multimark
multimark/inst
multimark/inst/CITATION
multimark/src
multimark/src/matrix.c
multimark/src/ranlib.c
multimark/src/ProbitCJS.c
multimark/src/Closed.c
multimark/src/ClosedSCR.c
multimark/src/ranlib.h
multimark/src/matrix.h
multimark/NAMESPACE
multimark/NEWS
multimark/data
multimark/data/bobcat.RData
multimark/data/tiger.RData
multimark/R
multimark/R/Closed.R
multimark/R/multimark_functions.R
multimark/R/CJS.R
multimark/R/ClosedSCR.R
multimark/MD5
multimark/DESCRIPTION
multimark/man
multimark/man/processdataSCR.Rd
multimark/man/multimodelClosedSCR.Rd
multimark/man/plotSpatialData.Rd
multimark/man/tiger.Rd
multimark/man/getprobsClosedSCR.Rd
multimark/man/multimarkClosed.Rd
multimark/man/multimarkSCRsetup-class.Rd
multimark/man/multimodelClosed.Rd
multimark/man/multimodelCJS.Rd
multimark/man/simdataClosed.Rd
multimark/man/processdata.Rd
multimark/man/getprobsCJS.Rd
multimark/man/markClosedSCR.Rd
multimark/man/getdensityClosedSCR.Rd
multimark/man/multimarkCJS.Rd
multimark/man/bobcat.Rd
multimark/man/simdataClosedSCR.Rd
multimark/man/markCJS.Rd
multimark/man/simdataCJS.Rd
multimark/man/markClosed.Rd
multimark/man/multimarkClosedSCR.Rd
multimark/man/multimarksetup-class.Rd
multimark/man/getprobsClosed.Rd