{ "_id": "6a2a60e47b7a29ca6003e7a8", "Package": "marked", "Version": "1.3.1", "Date": "2025-04-02", "Title": "Mark-Recapture Analysis for Survival and Abundance Estimation", "Author": "Jeff Laake , Devin Johnson\n, Paul Conn ,\nexample for simHMM from Jay Rotella", "Maintainer": "Jeff Laake ", "Description": "Functions for fitting various models to capture-recapture\ndata including mixed-effects Cormack-Jolly-Seber(CJS) and\nmultistate models and the multi-variate state model structure\nfor survival estimation and POPAN structured Jolly-Seber models\nfor abundance estimation. There are also Hidden Markov model\n(HMM) implementations of CJS and multistate models with and\nwithout state uncertainty and a simulation capability for HMM\nmodels.", "SystemRequirements": "ADMB version 11 for\nuse.admb=TRUE; see readme.txt", "LazyLoad": "yes", "VignetteBuilder": "knitr", "License": "GPL (>=2)", "RoxygenNote": "7.3.1", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev", "Repository": "https://dsjohnson.r-universe.dev", "Date/Publication": "2026-04-12 22:45:58 UTC", "RemoteUrl": "https://github.com/jlaake/marked", "RemoteRef": "devel", "RemoteSha": "fe6e80628d940824a6a0c492c40bc603b5200c5d", "RemoteSubdir": "marked", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-11 07:09:04 UTC", "User": "root" }, "MD5sum": "836bd31e56a0fefdbb6e7d41964b90bb", "_user": "dsjohnson", "_type": "src", "_file": "marked_1.3.1.tar.gz", "_fileid": 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"setup_admb", "setup_tmb", "setup.model", "setup.parameters", "simHMM", "smsld_tmb", "splitCH", "ums_dmat", "ums2_dmat" ], "_datasets": [ { "name": "dipper", "title": "Dipper capture-recapture data", "object": "dipper", "file": "dipper.rda", "class": [ "data.frame" ], "fields": [ "ch", "sex" ], "rows": 294, "table": true, "tojson": true }, { "name": "mstrata", "title": "Multistrata example data", "object": "mstrata", "file": "mstrata.rda", "class": [ "data.frame" ], "fields": [ "ch", "freq" ], "rows": 255, "table": true, "tojson": true }, { "name": "ps", "title": "Mulstistate Live-Dead Paradise Shelduck Data", "object": "Paradise_shelduck", "file": "Paradise_shelduck.rda", "class": [ "data.frame" ], "fields": [ "ch", "freq", "sex" ], "rows": 1704, "table": true, "tojson": true }, { "name": "sealions", "title": "Multivariate State example data", "object": "sealions", "file": "sealions.rda", "class": [ "data.frame" ], "fields": [ "ch", "sex", "weight" ], "rows": 485, "table": true, 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"js", "title": "Fitting function for Jolly-Seber model using Schwarz-Arnason POPAN formulation", "topics": [ "js" ] }, { "page": "js.accumulate", "title": "Accumulates common capture history values", "topics": [ "js.accumulate" ] }, { "page": "js.hessian", "title": "Compute variance-covariance matrix for fitted JS model", "topics": [ "js.hessian" ] }, { "page": "js.lnl", "title": "Likelihood function for Jolly-Seber model using Schwarz-Arnason POPAN formulation", "topics": [ "js.lnl" ] }, { "page": "local_decode", "title": "Local decoding of HMM", "topics": [ "local_decode" ] }, { "page": "make.design.data", "title": "Create design dataframes for crm", "topics": [ "make.design.data" ] }, { "page": "merge_design.covariates", "title": "Merge time (occasion) and/or group specific covariates into design data", "topics": [ "merge.design.covariates", "merge_design.covariates" ] }, { "page": "mixed.model.admb", "title": "Mixed effect model contstruction", "topics": [ "mixed.model", 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uncertainty models", "topics": [ "mvmscjs_tmb" ] }, { "page": "omega", "title": "Compute 1 to k-step transition proportions", "topics": [ "omega" ] }, { "page": "Paradise_shelduck", "title": "Mulstistate Live-Dead Paradise Shelduck Data", "topics": [ "Paradise_shelduck", "ps" ] }, { "page": "Phi.mean", "title": "Various utility parameter summary functions", "topics": [ "p.boxplot", "p.mean", "Phi.boxplot", "Phi.mean" ] }, { "page": "predict.crm", "title": "Compute estimates of real parameters", "topics": [ "predict.crm" ] }, { "page": "print.crm", "title": "Print model results", "topics": [ "print.crm" ] }, { "page": "print.crmlist", "title": "Print model table from model list", "topics": [ "print.crmlist" ] }, { "page": "probitCJS", "title": "Perform MCMC analysis of a CJS model", "topics": [ "probitCJS" ] }, { "page": "proc.form", "title": "Mixed effect model formula parser Parses a mixed effect model in the lme4 structure of ~fixed +(re1|g1) +...+(ren|gn)", "topics": [ "proc.form" ] 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