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Abundance Estimation Author Jeff Laake \u003C[jefflaake@gmail.com](jefflaake@gmail.com)>, Devin Johnson  \n\u003C[devin.johnson@noaa.gov](devin.johnson@noaa.gov)>, Paul Conn \u003C[paul.conn@noaa.gov](paul.conn@noaa.gov)>, example for simHMM  \nfrom Jay Rotella  \nMaintainer Jeff Laake \u003C[jefflaake@gmail.com](jefflaake@gmail.com)>  \nDescription Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival  \nestimation and POPAN structured Jolly-Seber models for abundance estimation.  \nThere are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.  \nDepends R (>= 3.5.0), lme4, methods, parallel  \nImports graphics, stats, utils, R2admb, truncnorm, coda, Matrix, numDeriv, expm, Rcpp (>= 0.9.13), TMB, optimx (>= 2013.8.6), data.table, knitr, kableExtra, bookdown  \nSuggests ggplot2 LinkingTo Rcpp  \nSystemRequirements ADMB version 11 \u003C[http://admb-project.org/](http://admb-project.org/)> for use.admb=TRUE; see readme.txt  \nLazyLoad yes VignetteBuilder knitr License GPL (>= 2) RoxygenNote 7.2.3 Encoding UTF-8 NeedsCompilation yes Repository CRAN  \nDate/Publication 2023-10-19 17:00:02 UTC  \nContents  \nbackward_prob ....................................... 3  \ncjs.accumulate ........................................ 4  \ncjs.hessian .......................................... 5  \ncjs.initial ........................................... 5  \ncjs.lnl ............................................ 6  \ncjs_admb .......................................... 8  \ncjs_delta ........................................... 11  \ncjs_gamma ......................................... 12  \ncjs_tmb ........................................... 12  \ncoef.crm ........................................... 15  \ncompute_matrices ...................................... 16  \ncompute_real ........................................ 16  \n[convert.link.to.real .....................................](convert.link.to.real ..................................... 18)[ 18](convert.link.to.real ..................................... 18)  \n[create.dm ..........................................](create.dm .......................................... 19)[ 19](create.dm .......................................... 19)  \n[create.dmdf .........................................](create.dmdf ......................................... 20)[ 20](create.dmdf ......................................... 20)  \n[create.fixed.matrix .....................................](create.fixed.matrix ..................................... 24)[ 24](create.fixed.matrix ..................................... 24)  \n[create.links .........................................](create.links ......................................... 25)[ 25](create.links ......................................... 25)  \n[crm .............................................](crm ............................................. 25)[ 25](crm ............................................. 25)  \n[crm.wrapper .........................................](crm.wrapper ......................................... 32)[ 32](crm.wrapper ......................................... 32)  \n[deriv_inverse.link ......................................](deriv_inverse.link ...................................... 34)[ 34](deriv_inverse.link ...................................... 34)  \n[dipper ............................................](dipper ............................................ 35)[ 35](dipper ............................................ 35)  \n[dmat_hsmm2hmm .....................................](dmat_hsmm2hmm ..................................... 36)[ 36](dmat_hsmm2hmm ..................................... 36)  \n[fix.parameters ........................................](f","cbCaifIx4eb7OBSG","https://ap.wps.com/l/cbCaifIx4eb7OBSG","pdf",351392,117,"English","# Functions and core model components\n## CJS and related computations\n## Multistate and link functions\n## Hidden Markov and simulation utilities","[{\"question\":\"What modeling approaches does the package support for capture-recapture data?\",\"answer\":\"It supports mixed-effects Cormack-Jolly-Seber (CJS), multistate models, and multivariate state structures, along with POPAN-structured Jolly-Seber models for abundance estimation.\"},{\"question\":\"How does the package handle hidden state dynamics?\",\"answer\":\"It includes Hidden Markov Model (HMM) implementations for CJS and multistate models, with options that incorporate state uncertainty.\"},{\"question\":\"What system requirements and dependencies are listed for using the package?\",\"answer\":\"It requires R (\\u003e= 3.5.0) and specifies dependencies and imports including tools such as TMB and Rcpp (\\u003e= 0.9.13), and can use ADMB 11 when enabled.\"}]","Mark-Recapture Analysis for Survival and Abundance Estimation | PDF",1792223242,295]