Package: openCR 2.2.7

Murray Efford

openCR: Open Population Capture-Recapture

Non-spatial and spatial open-population capture-recapture analysis.

Authors:Murray Efford [aut, cre]

openCR_2.2.7.tar.gz
openCR_2.2.7.tar.gz(r-4.5-noble)openCR_2.2.7.tar.gz(r-4.4-noble)
openCR_2.2.7.tgz(r-4.4-emscripten)openCR_2.2.7.tgz(r-4.3-emscripten)
openCR.pdf |openCR.html✨
openCR/json (API)
NEWS

# Install 'openCR' in R:

install.packages('openCR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/murrayefford/opencr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

FebpossumCH - Orongorongo Valley Brushtail Possums
dipperCH - Dippers
fieldvoleCH - Kielder Field Voles
gonodontisCH - Gonodontis Moths
microtusCH - Patuxent Meadow Voles
microtusFCH - Patuxent Meadow Voles
microtusFMCH - Patuxent Meadow Voles
microtusMCH - Patuxent Meadow Voles
microtusRDCH - Patuxent Meadow Voles

3.44 score 1 stars 46 scripts 411 downloads 3 mentions 39 exports 35 dependencies

Last updated 7 days agofrom:0fefa235de. Checks:OK: 1 WARNING: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 24 2024
R-4.5-linux-x86_64	WARNING	Oct 24 2024

Exports:age.matrix bd.array classMembership cloned.fit cumMove dkernel expected.d extractFocal gkernel JS.counts JS.direct m.array make.kernel make.table matchscale moving.fit openCR.design openCR.esa openCR.fit openCR.pdot openCRlist par.openCR.fit pkernel primarysessions proportionInPolygon qkernel read.inp runsim.nonspatial runsim.RMark runsim.spatial secondarysessions sim.nonspatial squeeze strata strata<-stratify sumsims ucare.cjs unsqueeze

Dependencies:abind BH class classInt cli DBI e1071 glue KernSmooth lattice lifecycle magrittr MASS Matrix mgcv mvtnorm nlme plyr proxy raster Rcpp RcppEigen RcppNumerical RcppParallel rlang s2 secr sf sp stringi stringr terra units vctrs wk

openCR 2.2 - open population capture--recapture

Murray Efford

Rendered fromopenCR-vignette.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-10-23
Started: 2018-04-12

Citation

Readme and manuals

Help Manual

Help page	Topics
Open Population Capture-Recapture Models	openCR-package openCR
Session-specific Ages	age.matrix
Compare openCR Models	AIC.openCR AIC.openCRlist logLik.openCR
Class Membership Probability for Mixture Models	classMembership classMembership.openCR
Cloning to Evaluate Identifiability	cloned.fit
Array of Parameter Estimates	collate collate.openCR collate.openCRlist
Probability Distribution After Movement	cumMove proportionInPolygon
Derived Parameters From openCR Models	derived.openCR derived.openCRlist openCR.esa openCR.pdot
Dippers	dipperCH
Expected Distance Moved	expected.d
Kielder Field Voles	fieldvoleCH
Gonodontis Moths	gonodontisCH
Internal Functions	cyclic.fit PCH1 PCH1secr pradelloglik prwi prwisecr
Summarise Non-spatial Open-population Data	bd.array JS.counts m.array
Jolly-Seber Estimates	JS.direct
Plot Likelihood Surface	LLsurface LLsurface.openCR
Discrete Movement Kernel	make.kernel plot.kernel summary.kernel
Tabulate Estimates From Multiple Models	make.table
Create Default Design Data	makeNewData makeNewData.openCR
Match Kernel	matchscale
Patuxent Meadow Voles	microtusCH microtusFCH microtusFMCH microtusMCH microtusRDCH
Data Manipulation	primarysessions secondarysessions
Averaging of OpenCR Models Using Akaike's Information Criterion	modelAverage modelAverage.openCR modelAverage.openCRlist
List of Movement Models	Movement models
Moving Window Functions	extractFocal moving.fit
Defunct Functions in Package 'openCR'	openCR-defunct openCR.make.newdata plotKernel
Deprecated Functions in Package 'openCR'	openCR-deprecated
Design Data for Open population Models	openCR.design
Fit Open Population Capture-Recapture Model	openCR.fit
Bundle openCR Models	openCRlist [.openCRlist
Fit Multiple openCR Models	par.openCR.fit
Kernel Distribution Functions	dkernel gkernel pkernel qkernel
Plot Derived Estimates	plot.derivedopenCR
Plot Estimates	plot.openCR
Orongorongo Valley Brushtail Possums	FebpossumCH
openCR Model Predictions	predict.openCR predict.openCRlist
Print Method for Derived Estimates	print.derivedopenCR
Print or Summarise openCR Object	print.openCR summary.openCR
Import Data from RMark Input Format	read.inp
Reverse Primary Sessions	rev.capthist
Simulate Capture Histories	runsim.nonspatial runsim.RMark runsim.spatial sim.nonspatial sumsims
Unique Capture Histories	squeeze unsqueeze
Stratum names	strata strata<-
Stratify Capture-Recapture Data	stratify
Goodness-of-fit tests for the Cormack-Jolly-Seber model	ucare.cjs