Open Population Capture-Recapture

Functions for non-spatial and spatial open-population capture-recapture analysis.


News

version 1.3.5 (2019-03-10)

New features and changed behaviour o none

Other o correct one line in vignette latex code \vec

Bugs fixed o none

version 1.3.4 (2019-02-05)

Bugs fixed o bad keyword in classMembership.Rd

Other o removed unnecessary pdf from inst/doc

version 1.3.3 (2019-02-04)

New features and changed behaviour o enabled detector-level covariates o summary method compatible with secr 3.2.0 (moves)

Bugs fixed o openCR.make.newdata() and dependent methods (print, predict, summary etc.) failed with learned responses (~b etc.)

version 1.3.2 (2018-12-09)

New features and changed behaviour o none

Other o conditional use of R2ucare in Examples, vignette

version 1.3.1 (2018-12-08)

New features and changed behaviour o sumsims accepts simulated fits with method = "none"

Other o R2ucare now in Suggests not Imports, with tweak to ucare.cjs()

version 1.3.0 (2018-11-26)

New features and changed behaviour o canned predictors for learned responses (b, bk etc.) redefined and extended o AIC method acquires argument n to override the default effective sample size o openCR.fit() no longer computes 'posterior' component for mixture models o classMembership method for finite mixture models ('posterior' component removed) o specifying native R routines for the likelihood forces ncores = 1 o print and AIC methods for summary.openCR o openCR.fit() acquires argument dframe0 for pesky custom models with learned response o par.openCR.fit() default trace = FALSE o rev method for reversing primary sessions of capthist objects

Bugs fixed o varying usage unreliable with 'multi' detector type in some circumstances o summary method for openCR objects: erroneous counts in capthist component (ignored freq) o finite mixture model posterior class membership crashed openCR.fit() for spatial models o finite mixture models failed for 'multi' detector type

Other o help page for openCR.design corrected

version 1.2.1 (2018-10-31)

New features and changed behaviour o runsim.spatial() acquires intervals argument o summary method for openCR objects o sumsims() accepts output from summary.openCR o sumsims() acquires argument 'true' and adds summaries of bias, coverage etc. o CJSp1 = TRUE details argument respected by openCR.design etc.

Bugs fixed o sumsims() failed with parameters superN and superD o derived method for openCR objects: erroneous f and lambda for some models when intervals not 1.0 o print.derivedopenCR did not apply Dscale to session-specific D

Other o changed default starting value for superD o tweaks to print method for derivedopenCR class o not published on CRAN

version 1.2.0 (2018-05-25)

New features and changed behaviour o multithreaded execution of some functions (up to 4x speed gain) o openCR.fit() types 'secrCL' and 'secrD' emulate closed-population analyses of 'secr' o openCR.fit() trace may be a positive integer (frequency of reporting) o ucare.cjs() wrapper for R2ucare test functions o moving.fit() and extractFocal() functions for moving window of sessions o m.array() reports releases on final session (last.session = TRUE) o openCR.fit() details ignoreusage option o runsim.spatial() and runsim.nonspatial() ncores argument defaults to NULL for multithreading o cyclic.fit() exposed as internal function but not exported o derived() method for openCR objects acquires arguments newdata and all.levels

Bugs fixed o usage of count detectors not properly accounted for (noted by Richard Glennie) o fixedbeta clashed with start argument (some options) o session covariates not matched correctly with robust design sessions o LLonly reported x -1 o details$hessian = FALSE failed

Other o Links to RcppParallel o Additional check for nonidentifiable parameters in print.openCR()

version 1.1.2 (2018-04-16)

New features and changed behaviour o none

Other o tweaks to C++ code for CRAN (fabs -> abs) o check for availability of RMark o better failure criterion in bd.array() o http changed to https where possible

version 1.1.1 (2018-04-11)

New features and changed behaviour o movement kernel exposed o bd.array() probability of (b,d) o improved simulation functions o start may be named numeric vector

Other o first CRAN submission o consolidates CJS and JSSA C code (e.g. prwisecrcpp) o timevaryingcov<- disabled until next release secr

version 1.0.2 (2018-03-26)

New features and changed behaviour o movement kernel unsuppressed

version 1.0.1 (2018-03-25)

New features and changed behaviour o movement kernel [temporarily suppressed] o plotKernel() o movementmodel argument replaces staticHR o experimental timevarying individual covariates

version 1.0.0 (2018-03-11)

Known bugs o CI of predicted b[1]

Other o renumbered 1.0.0 (previously unreleased 2.2.3)

Reference manual

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install.packages("openCR")

1.4.0 by Murray Efford, 12 days ago


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


Authors: Murray Efford [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports utils, MASS, nlme, parallel, stats, Rcpp, stringr, plyr, abind, methods, RcppParallel

Depends on secr

Suggests knitr, RMark, rgdal, R2ucare

Linking to Rcpp, RcppParallel

System requirements: GNU make


Imported by secrdesign.


See at CRAN