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marked  

Mark-Recapture Analysis for Survival and Abundance Estimation
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Download and install marked package within the R console
Install from CRAN:
install.packages("marked")

Install from Github:
library("remotes")
install_github("cran/marked")

Install by package version:
library("remotes")
install_version("marked", "1.2.8")



Attach the package and use:
library("marked")
Maintained by
Jeff Laake
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-01-25
Latest Update: 2023-10-19
Description:
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 estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.
How to cite:
Jeff Laake (2013). marked: Mark-Recapture Analysis for Survival and Abundance Estimation. R package version 1.2.8, https://cran.r-project.org/web/packages/marked. Accessed 05 Mar. 2026.
Previous versions and publish date:
1.0.9 (2013-01-25 08:24), 1.1.2 (2013-08-16 16:31), 1.1.3 (2013-11-23 06:48), 1.1.6 (2014-06-17 23:14), 1.1.8 (2015-03-17 00:07), 1.1.9 (2015-08-20 01:23), 1.1.10 (2015-08-20 19:24), 1.1.11 (2016-03-07 22:31), 1.1.13 (2016-12-06 18:27), 1.2.1 (2018-03-30 14:52), 1.2.6 (2019-12-09 07:40)
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Complete documentation for marked
Functions, R codes and Examples using the marked R package
Some associated functions: HMMLikelihood . Paradise_shelduck . Phi.mean . R_HMMLikelihood . backward_prob . cjs.accumulate . cjs.hessian . cjs.initial . cjs.lnl . cjs_admb . cjs_delta . cjs_gamma . cjs_tmb . coef.crm . compute_matrices . compute_real . convert.link.to.real . create.dm . create.dmdf . create.fixed.matrix . create.links . crm . crm.wrapper . deriv_inverse.link . dipper . dmat_hsmm2hmm . fix.parameters . function.wrapper . global_decode . hmmDemo . hsmm2hmm . initiate_pi . inverse.link . js.accumulate . js.hessian . js.lnl . js . local_decode . make.design.data . merge_design.covariates . mixed.model.admb . mscjs . mscjs_tmb . msld_tmb . mstrata . mvms_design_data . mvms_dmat . mvmscjs . mvmscjs_tmb . omega . predict.crm . print.crm . print.crmlist . probitCJS . proc.form . process.ch . process.data . resight.matrix . sealions . set.fixed . set.initial . set_mvms . set_scale . setup.model . setup.parameters . setup_admb . setup_tmb . simHMM . skagit . smsld_tmb . splitCH . tagloss . valid.parameters . 
Some associated R codes: admbutils.R . cjs.R . cjs.accumulate.R . cjs.initial.R . cjs_tmb.R . compute.real.R . create.dm.R . create.dmdf.R . crm.R . crm.wrapper.R . deriv.inverse.link.R . inverse.link.R . js.accumulate.R . js.hessian.R . make.design.data.R . marked-package.R . mvmscjs.R . mvmscjs_tmb.R . probitCJS.R . process.ch.R . process.data.R . set.fixed.R . setup.model.R . setup.parameters.R . splitCH.R . summary.fcts.R . utility.R . valid.parameters.R . zzz.R .  Full marked package functions and examples
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