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

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.


News

multimark 2.1.0 2019-04-21

CHANGES

  • clusterSetRNGStream now used for reproducible parallel processing

  • added error trap to processdataSCR if Enc.Mat includes non-zero encounters on inactive traps

  • NAMESPACE now generated using roxygen2

BUG FIXES

  • when using processdataSCR to generate a study area, the number of grid cells are now automatically adjusted to ensure cells are square

multimark 2.0.1 2017-06-30

NEW FEATURES

  • Added bobcatSCR example data for spatial capture-recapture analysis using multimarkClosedSCR

BUG FIXES

  • Typo corrections in help files

multimark 2.0.0 2016-05-23

NEW FEATURES

  • Added spatial capture-recapture model of Royle et al. (2009) using a semi-complete data likelihood (King et al. 2016)

  • Added tiger example data for spatial capture-recapture analysis using markClosedSCR

  • Increased capacity for handling hundreds of sampling occasions

multimark 1.3.2 2015-12-18

BUG FIXES

  • Allow delta_B = 0 (i.e. 1 - (delta_1 + delta_2) = 0) in 'simdataCJS()' and 'simdataClosed();

multimark 1.3.1 2015-10-20

CHANGES

  • Updated citations for 'multimark'

BUG FIXES

  • Typo corrections in help files

multimark 1.3.0 2015-07-27

NEW FEATURES

  • 'markClosed()' and 'markCJS()' wrappers facilitate conventional'' capture-recapture analysis with a single mark type; Bayesian multimodel inference using 'multimodelClosed()' and 'multimodelCJS()' can also be implemented with output from theseconventional'' models

CHANGES

  • 'mms' no longer an argument for 'multimodelClosed()' or 'multimodelCJS()'; these data are now returned with individual model output for additional error checking

  • CJS latent variable 'z' now denoted as 'q'

BUG FIXES

  • Fixed bug in 'multimarkClosed()' when all encounter histories are known

multimark 1.2.0 2015-06-23

NEW FEATURES

  • Beta prior for 'psi' parameter can now be user specified in 'multimarkCJS()' and 'multimarkClosed()' using 'a0psi' and 'b0psi' arguments

  • burn-in and thinning interval can now be user specified in 'multimodelCJS()' and 'multimodelClosed()' using 'mburnin' and 'mthin' arguments

CHANGES

  • Minor bug fixes in updates for 'psi', 'sigma2_zp', and 'sigma2_zphi' in 'multimarkCJS()'

  • developed using R version 3.2.1 (2015-06-18); 'multimark' now requires R >=3.2.1 for compatibility with changes to base function 'nchar()'

multimark 1.1.4 2015-04-29

NEW FEATURES

  • parallel processing now used in 'multimodelCJS()' and 'multimodelClosed()' for >1 chains

CHANGES

  • parallel processing now only used with >1 chains in 'multimarkCJS()' and 'multimarkClosed()'

  • modified chain progress printing for 'multimarkCJS()', 'multimarkClosed()', 'multimodelCJS()' and 'multimodelClosed()'

  • temporal trend (Time) predictors centered around zero

  • updated package citation

  • modification to documentation to avoid overflow on pdf

  • developed using R version 3.2.0 (2015-04-16)

multimark 1.1.3 2015-04-16

Initial CRAN posting

Reference manual

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install.packages("multimark")

2.1.2 by Brett T. McClintock, 9 months ago


Browse source code at https://github.com/cran/multimark


Authors: 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)


Documentation:   PDF Manual  


GPL-2 license


Imports parallel, Matrix, coda, statmod, RMark, Brobdingnag, mvtnorm, graphics, methods, stats, utils, prodlim, sp, raster

Suggests testthat


See at CRAN