{ "_id": "6a169b93acfb0bcc41d7e3a2", "Package": "openCR", "Type": "Package", "Title": "Open Population Capture-Recapture", "Version": "2.2.8", "Date": "2026-04-19", "Authors@R": "person(\"Murray\", \"Efford\", \nemail = \"murray.efford@otago.ac.nz\",\nrole = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0001-5231-5184\"))", "Description": "Non-spatial and spatial open-population capture-recapture\nanalysis.", "VignetteBuilder": "knitr", "License": "GPL (>=2)", "LazyData": "yes", "LazyDataCompression": "xz", "SystemRequirements": "GNU make", "URL": "https://www.otago.ac.nz/density/,\nhttps://github.com/MurrayEfford/openCR/", "BugReports": "https://github.com/MurrayEfford/openCR/issues/", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://murrayefford.r-universe.dev", "Date/Publication": "2026-05-27 03:25:15 UTC", "RemoteUrl": "https://github.com/MurrayEfford/openCR", "RemoteRef": "HEAD", "RemoteSha": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-27 07:07:35 UTC", "User": "root" }, "Author": "Murray Efford [aut, cre] (ORCID:\n)", "Maintainer": "Murray Efford ", "MD5sum": "bb2691558fd3bea18ce5b00004e1f88a", "_user": "murrayefford", "_type": "src", "_file": "openCR_2.2.8.tar.gz", "_fileid": "60cc9eb5d5c76f3e4c3236f9fba08b46cafe1ae2afe1c3eb90bb71aa326988e9", "_filesize": 2716885, "_sha256": "60cc9eb5d5c76f3e4c3236f9fba08b46cafe1ae2afe1c3eb90bb71aa326988e9", "_created": "2026-05-27T07:07:35.000Z", "_published": "2026-05-27T07:21:55.851Z", "_distro": "noble", "_jobs": [ { "job": 78025647378, "time": 320, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7234140063" }, { "job": 78025647476, "time": 362, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7234151228" }, { "job": 78025647469, "time": 363, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7234151046" }, { "job": 78025647564, "time": 311, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7234137563" }, { "job": 78025647552, "time": 191, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7234182444" }, { "job": 78025647416, "time": 695, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7234269716" }, { "job": 78025647418, "time": 238, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7234166928" }, { "job": 78025647538, "time": 397, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7234177322" }, { "job": 78024774691, "time": 383, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7234051345" }, { "job": 78025647443, "time": 196, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7234105652" }, { "job": 78025647391, "time": 388, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7234158323" }, { "job": 78025647399, "time": 368, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7234152805" }, { "job": 78025647421, "time": 441, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7234172676" } ], "_buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/MurrayEfford/openCR", "_commit": { "id": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "author": "MurrayEfford ", "committer": "MurrayEfford ", "message": "block MacOS check to dodge RMark problem\n", "time": 1779852315 }, "_maintainer": { "name": "Murray Efford", "email": "murray.efford@otago.ac.nz", "login": "murrayefford", "description": "", "uuid": 8920894, "orcid": "0000-0001-5231-5184" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "secr", "version": ">= 4.6.1", "role": "Depends" }, { "package": "BH", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "abind", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "nlme", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.14", "role": "Imports" }, { "package": "RcppParallel", "version": ">= 5.1.1", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "RMark", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "R2ucare", "role": "Suggests" }, { "package": "secrlinear", "role": "Suggests" } ], "_owner": "murrayefford", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 2 }, { "week": "2026-14", "n": 7 }, { "week": "2026-15", "n": 2 }, { "week": "2026-22", "n": 3 } ], "_tags": [], "_stars": 5, "_contributors": [ { "user": "murrayefford", "count": 161, "uuid": 8920894 } ], "_userbio": { "uuid": 8920894, "type": "user", "name": "MurrayEfford" }, "_downloads": { "count": 697, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/openCR" }, "_mentions": 3, "_devurl": "https://github.com/murrayefford/opencr", "_searchresults": 60, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/openCR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/murrayefford/opencr", "_realowner": "murrayefford", "_cranurl": true, "_releases": [ { "version": "1.1.1", "date": "2018-04-12" }, { "version": "1.1.2", "date": "2018-04-21" }, { "version": "1.2.0", "date": "2018-05-25" }, { "version": "1.3.0", "date": "2018-11-26" }, { "version": "1.3.1", "date": "2018-12-08" }, { "version": "1.3.2", "date": "2018-12-09" }, { "version": "1.3.4", "date": "2019-02-05" }, { "version": "1.3.5", "date": "2019-03-10" }, { "version": "1.4.0", "date": "2019-06-17" }, { "version": "1.4.1", "date": "2019-06-30" }, { "version": "1.4.4", "date": "2020-09-01" }, { "version": "1.5.0", "date": "2020-12-13" }, { "version": "2.0.1", "date": "2021-05-10" }, { "version": "2.0.2", "date": "2021-05-16" }, { "version": "2.1.0", "date": "2021-08-14" }, { "version": "2.2.0", "date": "2021-11-03" }, { "version": "2.2.1", "date": "2021-11-10" }, { "version": "2.2.2", "date": "2022-01-17" }, { "version": "2.2.4", "date": "2022-07-02" }, { "version": "2.2.5", "date": "2022-09-25" }, { "version": "2.2.6", "date": "2023-11-28" }, { "version": "2.2.7", "date": "2024-10-23" } ], "_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" ], "_datasets": [ { "name": "dipperCH", "title": "Dippers", "object": "dipper", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false }, { "name": "FebpossumCH", "title": "Orongorongo Valley Brushtail Possums", "object": "PPNpossums", "class": [ "capthist", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "fieldvoleCH", "title": "Kielder Field Voles", "object": "fieldvole", "class": [ "capthist", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "gonodontisCH", "title": "Gonodontis Moths", "object": "gonodontis", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false }, { "name": "microtusCH", "title": "Patuxent Meadow Voles", "object": "microtus", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false }, { "name": "microtusFCH", "title": "Patuxent Meadow Voles", "object": "microtus", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false }, { "name": "microtusFMCH", "title": "Patuxent Meadow Voles", "object": "microtus", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false }, { "name": "microtusMCH", "title": "Patuxent Meadow Voles", "object": "microtus", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false }, { "name": "microtusRDCH", "title": "Patuxent Meadow Voles", "object": "microtus", "class": [ "capthist" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "openCR-package", "title": "Open Population Capture-Recapture Models", "topics": [ "openCR-package", "openCR" ] }, { "page": "age.matrix", "title": "Session-specific Ages", "topics": [ "age.matrix" ] }, { "page": "AIC.openCR", "title": "Compare openCR Models", "topics": [ "AIC.openCR", "AIC.openCRlist", "logLik.openCR" ] }, { "page": "classMembership", "title": "Class Membership Probability for Mixture Models", "topics": [ "classMembership", "classMembership.openCR" ] }, { "page": "cloned.fit", "title": "Cloning to Evaluate Identifiability", "topics": [ "cloned.fit" ] }, { "page": "collate", "title": "Array of Parameter Estimates", "topics": [ "collate", "collate.openCR", "collate.openCRlist" ] }, { "page": "cumMove", "title": "Probability Distribution After Movement", "topics": [ "cumMove", "proportionInPolygon" ] }, { "page": "derived", "title": "Derived Parameters From openCR Models", "topics": [ "derived.openCR", "derived.openCRlist", "openCR.esa", "openCR.pdot" ] }, { "page": "dipper", "title": "Dippers", "topics": [ "dipperCH" ] }, { "page": "expected.d", "title": "Expected Distance Moved", "topics": [ "expected.d" ] }, { "page": "fieldvoleCH", "title": "Kielder Field Voles", "topics": [ "fieldvoleCH" ] }, { "page": "gonodontis", "title": "Gonodontis Moths", "topics": [ "gonodontisCH" ] }, { "page": "openCR-internal", "title": "Internal Functions", "topics": [ "cyclic.fit", "PCH1", "PCH1secr", "pradelloglik", "prwi", "prwisecr" ] }, { "page": "utility", "title": "Summarise Non-spatial Open-population Data", "topics": [ "bd.array", "JS.counts", "m.array" ] }, { "page": "JS.direct", "title": "Jolly-Seber Estimates", "topics": [ "JS.direct" ] }, { "page": "LLsurface", "title": "Plot Likelihood Surface", "topics": [ "LLsurface", "LLsurface.openCR" ] }, { "page": "kernel", "title": "Discrete Movement Kernel", "topics": [ "make.kernel", "plot.kernel", "summary.kernel" ] }, { "page": "make.table", "title": "Tabulate Estimates From Multiple Models", "topics": [ "make.table" ] }, { "page": "openCR.make.newdata", "title": "Create Default Design Data", "topics": [ "makeNewData", "makeNewData.openCR" ] }, { "page": "matchscale", "title": "Match Kernel", "topics": [ "matchscale" ] }, { "page": "microtus", "title": "Patuxent Meadow Voles", "topics": [ "microtusCH", "microtusFCH", "microtusFMCH", "microtusMCH", "microtusRDCH" ] }, { "page": "manip", "title": "Data Manipulation", "topics": [ "primarysessions", "secondarysessions" ] }, { "page": "modelAverage", "title": "Averaging of OpenCR Models Using Akaike's Information Criterion", "topics": [ "modelAverage", "modelAverage.openCR", "modelAverage.openCRlist" ] }, { "page": "movementmodels", "title": "List of Movement Models", "topics": [ "Movement models" ] }, { "page": "moving.fit", "title": "Moving Window Functions", "topics": [ "extractFocal", "moving.fit" ] }, { "page": "openCR-defunct", "title": "Defunct Functions in Package 'openCR'", "topics": [ "openCR-defunct", "openCR.make.newdata", "plotKernel" ] }, { "page": "openCR-deprecated", "title": "Deprecated Functions in Package 'openCR'", "topics": [ "openCR-deprecated" ] }, { "page": "openCR.design", "title": "Design Data for Open population Models", "topics": [ "openCR.design" ] }, { "page": "openCR.fit", "title": "Fit Open Population Capture-Recapture Model", "topics": [ "openCR.fit" ] }, { "page": "openCRlist", "title": "Bundle openCR Models", "topics": [ "openCRlist", "[.openCRlist" ] }, { "page": "par.openCR.fit", "title": "Fit Multiple openCR Models", "topics": [ "par.openCR.fit" ] }, { "page": "pkernel", "title": "Kernel Distribution Functions", "topics": [ "dkernel", "gkernel", "pkernel", "qkernel" ] }, { "page": "plot.derivedopenCR", "title": "Plot Derived Estimates", "topics": [ "plot.derivedopenCR" ] }, { "page": "plot.openCR", "title": "Plot Estimates", "topics": [ "plot.openCR" ] }, { "page": "PPNpossums", "title": "Orongorongo Valley Brushtail Possums", "topics": [ "FebpossumCH" ] }, { "page": "predict.openCR", "title": "openCR Model Predictions", "topics": [ "predict.openCR", "predict.openCRlist" ] }, { "page": "print.derivedopenCR", "title": "Print Method for Derived Estimates", "topics": [ "print.derivedopenCR" ] }, { "page": "print.openCR", "title": "Print or Summarise openCR Object", "topics": [ "print.openCR", "summary.openCR" ] }, { "page": "read.inp", "title": "Import Data from RMark Input Format", "topics": [ "read.inp" ] }, { "page": "rev.capthist", "title": "Reverse Primary Sessions", "topics": [ "rev.capthist" ] }, { "page": "simulate", "title": "Simulate Capture Histories", "topics": [ "runsim.nonspatial", "runsim.RMark", "runsim.spatial", "sim.nonspatial", "sumsims" ] }, { "page": "squeeze", "title": "Unique Capture Histories", "topics": [ "squeeze", "unsqueeze" ] }, { "page": "strata", "title": "Stratum names", "topics": [ "strata", "strata<-" ] }, { "page": "stratify", "title": "Stratify Capture-Recapture Data", "topics": [ "stratify" ] }, { "page": "ucare", "title": "Goodness-of-fit tests for the Cormack-Jolly-Seber model", "topics": [ "ucare.cjs" ] } ], "_readme": "https://github.com/MurrayEfford/openCR/raw/HEAD/README.md", "_rundeps": [ "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", "secrfunc", "sf", "sp", "stringi", "stringr", "terra", "units", "vctrs", "wk" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "openCR-vignette.Rmd", "filename": "openCR-vignette.html", "title": "openCR 2.2 - open population capture--recapture", "author": "Murray Efford", "engine": "knitr::rmarkdown", "headings": [ "Outline", "Model types", "Data", "Model specification and fitting", "Parameterization", "Features and limitations", "Dipper example", "A brief survey of open population capture--recapture models", "CJS vs JS", "Parameterization of recruitment in JSSA models", "Conditional (PLB) vs full likelihood JSSA", "Sufficient statistics vs capture histories", "Robust design", "Spatial vs nonspatial", "Home-range shifts between primary sessions", "Data structure and input", "Stratification", "Non-spatial openCR models", "Parameters and model types", "Non-spatial models using sufficient statistics", "Spatial openCR models", "Model formulae", "Built-in predictors", "User-provided covariates", "More on modelling", "Closed populations", "Finite mixtures", "Age", "Sampling intervals", "Custom design data", "Transience", "Factor coding", "Mean of a parameter across levels of a factor", "Movement models", "Movement kernels", "Zero-inflated kernels", "User-defined kernel", "Sparse kernels", "Edge effects", "Plotting and summary", "Warnings", "Settlement models", "Derived parameters", "Simulating open-population data", "Troubleshooting", "Nonidentifiability", "Failure of numerical maximization", "Starting values", "Boundary estimates", "Alternative algorithms", "Step into infeasible parameter space", "Number of iterations", "Factor coding", "Speed", "Extras", "Sampling variance warning", "Example datasets", "Testing assumptions", "Limitations of openCR", "Differences from secr", "Relationship to other software", "References", "Appendix 1. Code for figures." ], "created": "2021-11-14 07:51:36", "modified": "2024-05-23 08:12:57", "commits": 16 } ], "_score": 6.2552725051033065, "_indexed": true, "_nocasepkg": "opencr", "_universes": [ "murrayefford" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2.8", "date": "2026-05-27T07:11:03.000Z", "distro": "noble", "arch": "aarch64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "10b5e509cf24c5e5ff6c0512fd2fef42ca3f8f460120335e0a140903db484ab0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.7.0", "os": "linux", "version": "2.2.8", "date": "2026-05-27T07:11:13.000Z", "distro": "noble", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "f01b66abadcdacdc2772a6d35754ffe63871d07176e0b8922851bf7933f8345a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.6.0", "os": "linux", "version": "2.2.8", "date": "2026-05-27T07:11:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "11c8efc593ac28429b798a4c3ae1a189a5c243b1ce525f5d315a3ff77ad5617b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.6.0", "os": "linux", "version": "2.2.8", "date": "2026-05-27T07:11:30.000Z", "distro": "noble", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "f6615871de4430c392627bb3b4f43dd9581200b66d9a3b205abfbe4cc093252a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.5.3", "os": "mac", "version": "2.2.8", "date": "2026-05-27T07:14:58.000Z", "arch": "aarch64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "5bc67401166ce9e9b24680bfac8f85cd02d79393d83b172532784a145d8d07f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.5.3", "os": "mac", "version": "2.2.8", "date": "2026-05-27T07:14:56.000Z", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "385083ef42e9f1a2e3f3fc9d375a2979198fe1769c4623572f4db38440ccdee9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.6.0", "os": "mac", "version": "2.2.8", "date": "2026-05-27T07:13:42.000Z", "arch": "aarch64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "ecd5730abff383cb01b0be87558de99b998b822b9ab48f283d101395b5d139b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.6.0", "os": "mac", "version": "2.2.8", "date": "2026-05-27T07:12:29.000Z", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "dca255843e8adc754fa104530c48ea75977d3595db86c522ffdbeb5f51a81c16", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.6.0", "os": "wasm", "version": "2.2.8", "date": "2026-05-27T07:11:27.000Z", "arch": "emscripten", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "953b7ec55b4d9f3376f2fc187c443416afb897da720f134ddacaabc50a287b58", "status": "success", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.7.0", "os": "win", "version": "2.2.8", "date": "2026-05-27T07:10:36.000Z", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "cc2bc5bcfecd090ece08bff38dc51e22110e9bc49f694b0670fd991c9aeb6fc7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.5.3", "os": "win", "version": "2.2.8", "date": "2026-05-27T07:10:10.000Z", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "3a92a6055d6cbe61604421ac8ca180b6f921a939756591ce89ab94adb21c2940", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" }, { "r": "4.6.0", "os": "win", "version": "2.2.8", "date": "2026-05-27T07:10:34.000Z", "arch": "x86_64", "commit": "556ceafc083e4bfdcf346548c1e7e813a9e9c4b7", "fileid": "532f0a4f2b2581547e7995db8d36e71431523c9b21c7772d69a2face444ecf55", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/murrayefford/actions/runs/26496151798" } ] }