Package: markedTMB 0.3.0

Jeff Laake

markedTMB: Mark-Recapture Analysis for Survival Estimation

Functions for fitting various models to capture-recapture data including mixed-effects multistate models, multi-variate state models and multistate live and dead recovery structure for survival estimation. All models are implemented with TMB.

Authors:Jeff Laake <[email protected]>

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NEWS

# Install 'markedTMB' in R:
install.packages('markedTMB', repos = c('https://dsjohnson.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jlaake/markedtmb/issues

Datasets:
  • dipper - Dipper capture-recapture data
  • mstrata - Multistrata example data
  • ps - Mulstistate Live-Dead Paradise Shelduck Data
  • sealions - Multivariate State example data
  • skagit - An example of the Mulstistrata (multi-state) model in which states are routes taken by migrating fish.

On CRAN:

1.70 score 1 stars 1 scripts 52 exports 63 dependencies

Last updated 3 months agofrom:519dd14104 (on master). Checks:OK: 1 WARNING: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-win-x86_64WARNINGNov 04 2024
R-4.5-linux-x86_64WARNINGNov 04 2024
R-4.4-win-x86_64WARNINGNov 04 2024
R-4.4-mac-x86_64WARNINGNov 04 2024
R-4.4-mac-aarch64WARNINGNov 04 2024
R-4.3-win-x86_64WARNINGNov 04 2024
R-4.3-mac-x86_64WARNINGNov 04 2024
R-4.3-mac-aarch64WARNINGNov 04 2024

Exports:abundance_estimateabundance_estimate_bsaccumulate_databackward_probboot_pred_statescjs_deltacollapseCHcompute_matricescompute_realcreate.model.listcrmcrm.wrappercrmlist_fromfilesdmat_hsmm2hmmfix.parametersfunction.wrapperfx.aicfx.par.countglobal_decodehsmm2hmminitiate_piload_libload.modellocal_decodemake.design.datamcmc_modemerge_design.covariatesmodel.tablemscjs_tmbmsjs_tmbmsjsu_tmbmsld_tmbmvms_design_datamvmscjs_deltamvmscjs_tmbnaive.survivalomegap.boxplotp.meanPhi.boxplotPhi.meanprocess.chprocess.datarerun_crmresight.matrixset_mvmssetup_tmbsetup.modelsetup.parameterssmsld_tmbsplitCHValues

Dependencies:base64encbookdownbootbslibcachemclicodacolorspacecpp11data.tabledigestevaluateexpmfarverfastmapfontawesomefsgluehighrhtmltoolsjquerylibjsonlitekableExtraknitrlabelinglatticelifecyclelme4magrittrMASSMatrixmemoisemimeminqamunsellmvtnormnlmenloptrnumDerivoptimxpracmaR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrstudioapisassscalesstringistringrsvglitesystemfontstinytexTMBtruncnormvctrsviridisLitexfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Computes backward probabilitiesbackward_prob
Parametric bootstrap of state predictionsboot_pred_states
HMM Initial state distribution functionscjs_delta mvmscjs_delta
Accumulates common capture history valuescjs.accumulate
Extract coefficientscoef.crm
Compute HMM matricescompute_matrices
Compute estimates of real parameterscompute_real
Convert link values to real parametersconvert.link.to.real
Creates a design matrix for a parametercreate.dm create.dml
Creates a dataframe with all the design data for a particular parameter in a crm modelcreate.dmdf
Create parameters with fixed matrixcreate.fixed.matrix
Creates a 0/1 vector for real parameters with sin linkcreate.links
Capture-recapture model fitting functioncrm
Automation of model runscreate.model.list crm.wrapper crmlist_fromfiles load.model model.table rerun_crm
Derivatives of inverse of link function (internal use)deriv.inverse.link deriv_inverse.link
Dipper capture-recapture datadipper
Create expanded state-dependent observation matrix for HMM from HSMMdmat_hsmm2hmm
Fixing real parameters in crm modelsfix.parameters
Utility extract functionsfunction.wrapper fx.aic fx.par.count
Global decoding of HMMglobal_decode
Compute transition matrix for HMM from HSMMhsmm2hmm
Setup fixed values for pi in design datainitiate_pi
Inverse link functions (internal use)inverse.link
Load library for TMB modelload_lib
Local decoding of HMMlocal_decode
Create design dataframes for crmmake.design.data
Merge time (occasion) and/or group specific covariates into design datamerge.design.covariates merge_design.covariates
Mixed effect model contstructionmixed.model mixed.model.admb mixed.model.dat reindex
Fitting function for Multistate CJS models with TMBmscjs_tmb
Fitting function for Multistate JS models with TMBmsjs_tmb
Fitting function for Multistate JS models with state uncertainty via TMBmsjsu_tmb
Fitting function for Multistate CJS live-dead models with TMBmsld_tmb
Multistrata example datamstrata
Multivariate Multistate (mvms) Design Datamvms_design_data
TMB version: Fitting function for Multivariate Multistate CJS with uncertainty modelsmvmscjs_tmb
Compute 1 to k-step transition proportionsomega
Mulstistate Live-Dead Paradise Shelduck DataParadise_shelduck ps
Various utility parameter summary functionsp.boxplot p.mean Phi.boxplot Phi.mean
Compute estimates of real parameterspredict.crm
Print model resultsprint.crm
Print model table from model listprint.crmlist
Mixed effect model formula parser Parses a mixed effect model in the lme4 structure of ~fixed +(re1|g1) +...+(ren|gn)proc.form
Process release-recapture history dataprocess.ch
Process encounter history dataframe for MARK analysisaccumulate_data process.data
Various utility functionsmcmc_mode naive.survival resight.matrix
Multivariate State example datasealions
Multivariate Multistate (mvms) Specificationset_mvms
Set fixed real parameter values in ddlset.fixed
Set initial valuesset.initial
Scaling functionsscale.dm scale.par set.scale unscale.par
TMB setupsetup_tmb
Defines model specific parameters (internal use)setup.model setupHMM
Setup parameter structure specific to model (internal use)setup.parameters
An example of the Mulstistrata (multi-state) model in which states are routes taken by migrating fish.skagit
Fitting function for Multistate CJS live-dead models with TMBsmsld_tmb
Split/collapse capture historiescollapseCH splitCH
Determine validity of parameters for a model (internal use)valid.parameters
Summarize statistic values across parametric bootstraps of state predictionsValues