{ "_id": "6a103080acfb0bcc41c95767", "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": "2026-05-12 09:30:53 UTC", "User": "root" }, "MD5sum": "569b0c3d46be68519ab7249091a901af", "_user": "dsjohnson", "_type": "src", "_file": "marked_1.3.1.tar.gz", "_fileid": 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"cjs.hessian", "title": "Compute variance-covariance matrix for fitted CJS model", "topics": [ "cjs.hessian" ] }, { "page": "cjs.initial", "title": "Computes starting values for CJS p and Phi parameters", "topics": [ "cjs.initial" ] }, { "page": "cjs.lnl", "title": "Likelihood function for Cormack-Jolly-Seber model", "topics": [ "cjs.lnl" ] }, { "page": "coef.crm", "title": "Extract coefficients", "topics": [ "coef.crm" ] }, { "page": "compute_matrices", "title": "Compute HMM matrices", "topics": [ "compute_matrices" ] }, { "page": "compute_real", "title": "Compute estimates of real parameters", "topics": [ "compute_real" ] }, { "page": "convert.link.to.real", "title": "Convert link values to real parameters", "topics": [ "convert.link.to.real" ] }, { "page": "create.dm", "title": "Creates a design matrix for a parameter", "topics": [ "create.dm", "create.dml" ] }, { "page": "create.dmdf", "title": "Creates a dataframe with all the design data for a particular parameter in a crm model", "topics": [ "create.dmdf" ] }, { "page": "create.fixed.matrix", "title": "Create parameters with fixed matrix", "topics": [ "create.fixed.matrix" ] }, { "page": "create.links", "title": "Creates a 0/1 vector for real parameters with sin link", "topics": [ "create.links" ] }, { "page": "crm", "title": "Capture-recapture model fitting function", "topics": [ "crm" ] }, { "page": "crm.wrapper", "title": "Automation of model runs", "topics": [ "create.model.list", "crm.wrapper", "crmlist_fromfiles", "load.model", "model.table", "rerun_crm" ] }, { "page": "deriv_inverse.link", "title": "Derivatives of inverse of link function (internal use)", "topics": [ "deriv.inverse.link", "deriv_inverse.link" ] }, { "page": "dipper", "title": "Dipper capture-recapture data", "topics": [ "dipper" ] }, { "page": "dmat_hsmm2hmm", "title": "Create expanded state-dependent observation matrix for HMM from HSMM", "topics": [ "dmat_hsmm2hmm" ] }, { "page": "fix.parameters", "title": "Fixing real parameters in crm models", "topics": [ "fix.parameters" ] }, { "page": "function.wrapper", "title": "Utility extract functions", "topics": [ "function.wrapper", "fx.aic", "fx.par.count" ] }, { "page": "global_decode", "title": "Global decoding of HMM", "topics": [ "global_decode" ] }, { "page": "hmmDemo", "title": "HMM computation demo functions", "topics": [ "hmmDemo" ] }, { "page": "HMMLikelihood", "title": "Hidden Markov Model likelihood functions", "topics": [ "hmm.lnl", "HMMLikelihood", "reals" ] }, { "page": "hsmm2hmm", "title": "Compute transition matrix for HMM from HSMM", "topics": [ "hsmm2hmm" ] }, { "page": "initiate_pi", "title": "Setup fixed values for pi in design data", "topics": [ "initiate_pi" ] }, { "page": "inverse.link", "title": "Inverse link functions (internal use)", "topics": [ "inverse.link" ] }, { "page": "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", "mixed.model.admb", "mixed.model.dat", "reindex" ] }, { "page": "mscjs", "title": "Fitting function for Multistate CJS models", "topics": [ "mscjs" ] }, { "page": "mscjs_tmb", "title": "Fitting function for Multistate CJS models with TMB", "topics": [ "mscjs_tmb" ] }, { "page": "msld_tmb", "title": "Fitting function for Multistate CJS live-dead models with TMB", "topics": [ "msld_tmb" ] }, { "page": "mstrata", "title": "Multistrata example data", "topics": [ "mstrata" ] }, { "page": "mvms_design_data", "title": "Multivariate Multistate (mvms) Design Data", "topics": [ "mvms_design_data" ] }, { "page": "mvms_dmat", "title": "HMM Observation Probability matrix functions", "topics": [ "cjs_dmat", "ms_dmat", "mvms_dmat", "ums2_dmat", "ums_dmat" ] }, { "page": "mvmscjs", "title": "Fitting function for Multivariate Multistate CJS with uncertainty models", "topics": [ "mvmscjs" ] }, { "page": "mvmscjs_tmb", "title": "TMB version: Fitting function for Multivariate Multistate CJS with 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" ] }, { "page": "process.ch", "title": "Process release-recapture history data", "topics": [ "process.ch" ] }, { "page": "process.data", "title": "Process encounter history dataframe for MARK analysis", "topics": [ "accumulate_data", "process.data" ] }, { "page": "R_HMMLikelihood", "title": "Hidden Markov Model Functions", "topics": [ "loglikelihood", "R_HMMLikelihood" ] }, { "page": "resight.matrix", "title": "Various utility functions", "topics": [ "mcmc_mode", "naive.survival", "resight.matrix" ] }, { "page": "sealions", "title": "Multivariate State example data", "topics": [ "sealions" ] }, { "page": "set_mvms", "title": "Multivariate Multistate (mvms) Specification", "topics": [ "set_mvms" ] }, { "page": "set_scale", "title": "Scaling functions", "topics": [ "scale_dm", "scale_par", "set_scale", "unscale_par" ] }, { "page": "set.fixed", "title": "Set fixed real parameter values in ddl", "topics": [ "set.fixed" ] }, { "page": "set.initial", "title": "Set initial values", "topics": [ "set.initial" ] }, { "page": "setup_admb", "title": "ADMB setup", "topics": [ "setup_admb" ] }, { "page": "setup_tmb", "title": "TMB setup", "topics": [ "setup_tmb" ] }, { "page": "setup.model", "title": "Defines model specific parameters (internal use)", "topics": [ "setup.model", "setupHMM" ] }, { "page": "setup.parameters", "title": "Setup parameter structure specific to model (internal use)", "topics": [ "setup.parameters" ] }, { "page": "simHMM", "title": "Simulates data from Hidden Markov Model", "topics": [ "simHMM" ] }, { "page": "skagit", "title": "An example of the Mulstistrata (multi-state) model in which states are routes taken by migrating fish.", "topics": [ "skagit" ] }, { "page": "smsld_tmb", "title": "Fitting function for Multistate CJS live-dead models with TMB", "topics": [ "smsld_tmb" ] }, { "page": "splitCH", "title": "Split/collapse capture histories", "topics": [ "collapseCH", "splitCH" ] }, { "page": "tagloss", "title": "Tag loss example", "topics": [ "tagloss" ] }, { "page": "valid.parameters", "title": "Determine validity of parameters for a model (internal use)", "topics": [ "valid.parameters" ] } ], 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