Files in bmcclintock/momentuHMM

Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

.Rbuildignore

.github/workflows/r.yml

DESCRIPTION

NAMESPACE

NEWS

R/AIC_momentuHMM.R R/AICweights.R R/CIbeta.R R/CIreal.R R/HMMfits.R R/MIfitHMM.R R/MIpool.R R/RcppExports.R R/allProbs.R R/checkInputs.R R/checkPar0.R R/circAngles.R R/crawlMerge.R R/crawlWrap.R R/crwData.R R/crwHierData.R R/crwHierSim.R R/crwSim.R R/distAngle.R R/exampleData.R R/expandPar.R R/fitHMM.R R/formatHierFormula.R R/formatHierHMM.R R/formatRecharge.R R/formatmiSum.R R/getCovNames.R R/getDM.R R/getPar.R R/getPar0.R R/getParDM.R R/getSplineDM.R R/getTrProbs.R R/getWorkBounds.R R/getXB.R R/get_fixParIndex.R R/get_inflation.R R/get_ncmean.R R/get_retrySD.R R/getboundInd.R R/is_formula.R R/logAlpha.R R/logBeta.R R/miHMM.R R/miSum.R R/mixtureProbs.R R/momentuHMM.R R/momentuHMMData.R R/momentuHMM_utils.R R/momentuHierHMM.R R/momentuHierHMMData.R R/moveData.R R/moveHMMwrap.R R/n2w.R R/nLogLike.R R/parDef.R R/plotPR.R R/plotSat.R R/plotSpatialCov.R R/plotStates.R R/plotStationary.R R/plot_crwData.R R/plot_miHMM.R R/plot_miSum.R R/plot_momentuHMM.R R/plot_momentuHMMData.R R/prepData.R R/printMessage.R R/print_miHMM.R R/print_miSum.R R/print_momentuHMM.R R/pseudoRes.R R/randomEffects.R R/rwrpcauchy.R R/setModelName.R R/setStateNames.R R/simData.R R/simHierData.R R/simObsData.R R/stateFormulas.R R/stateProbs.R R/stationary.R R/summary_momentuHMMData.R R/timeInStates.R R/turnAngle.R R/viterbi.R R/w2n.R README.md data-raw/exampleData.R

data/example.rda

data/forest.rda

data/miExample.rda

inst/CITATION

man/AIC.momentuHMM.Rd man/AICweights.Rd man/CIbeta.Rd man/CIreal.Rd man/HMMfits.Rd man/MIfitHMM.Rd man/MIpool.Rd man/XBloop_rcpp.Rd man/allProbs.Rd man/checkPar0.Rd man/circAngles.Rd man/crawlMerge.Rd man/crawlWrap.Rd man/crwData.Rd man/crwHierData.Rd man/crwHierSim.Rd man/crwSim.Rd man/dbern_rcpp.Rd man/dbeta_rcpp.Rd man/dcat_rcpp.Rd man/dexp_rcpp.Rd man/dgamma_rcpp.Rd man/distAngle.Rd man/dlnorm_rcpp.Rd man/dlogis_rcpp.Rd man/dmvnorm_rcpp.Rd man/dnbinom_rcpp.Rd man/dnorm_rcpp.Rd man/dpois_rcpp.Rd man/dt_rcpp.Rd man/dvm_rcpp.Rd man/dweibull_rcpp.Rd man/dwrpcauchy_rcpp.Rd man/exampleData.Rd man/expandPar.Rd man/fitHMM.Rd man/formatHierHMM.Rd man/getCovNames.Rd man/getDM_rcpp.Rd man/getPar.Rd man/getPar0.Rd man/getParDM.Rd man/getTrProbs.Rd man/is.HMMfits.Rd man/is.crwData.Rd man/is.crwHierData.Rd man/is.crwHierSim.Rd man/is.crwSim.Rd man/is.miHMM.Rd man/is.miSum.Rd man/is.momentuHMM.Rd man/is.momentuHMMData.Rd man/is.momentuHierHMM.Rd man/is.momentuHierHMMData.Rd man/logAlpha.Rd man/logBeta.Rd man/miHMM.Rd man/miSum.Rd man/mixtureProbs.Rd man/momentuHMM.Rd man/momentuHMMData.Rd man/momentuHierHMM.Rd man/momentuHierHMMData.Rd man/n2w.Rd man/nLogLike.Rd man/nLogLike_rcpp.Rd man/parDef.Rd man/plot.crwData.Rd man/plot.miHMM.Rd man/plot.miSum.Rd man/plot.momentuHMM.Rd man/plot.momentuHMMData.Rd man/plotPR.Rd man/plotSat.Rd man/plotSpatialCov.Rd man/plotStates.Rd man/plotStationary.Rd man/prepData.Rd man/print.miHMM.Rd man/print.miSum.Rd man/print.momentuHMM.Rd man/pseudoRes.Rd man/randomEffects.Rd man/setModelName.Rd man/setStateNames.Rd man/simData.Rd man/simObsData.Rd man/stateProbs.Rd man/stationary.Rd man/summary.momentuHMMData.Rd man/timeInStates.Rd man/trMatrix_rcpp.Rd man/turnAngle.Rd man/viterbi.Rd man/w2n.Rd

manuscript/adjcalc.sty

manuscript/adjustbox.sty

manuscript/coastUTM.RData

manuscript/elephantExample.R

manuscript/elephant_plotSat.png

manuscript/greySealData_TPM.RData

manuscript/greySealExample_TPM.R manuscript/harbourSealExample.R

manuscript/master.bib

manuscript/mee.bst

manuscript/momentuHMM_manuscript.Rnw

manuscript/momentuHMM_manuscript.tex

manuscript/momentuHMM_manuscript_MEE.Rnw

manuscript/momentuHMM_manuscript_MEE.tex

manuscript/momentuHMM_manuscript_MEE_final.Rnw

manuscript/momentuHMM_manuscript_MEE_rev1.Rnw

manuscript/nfsData.RData

manuscript/nfsExample.R manuscript/plot_elephantResults001.pdf manuscript/plot_elephantResults002.pdf manuscript/plot_elephantResults009.pdf manuscript/plot_elephantResults010.pdf manuscript/plot_elephantResults012.pdf manuscript/plot_elephantResults013.pdf manuscript/plot_elephantResults015.pdf manuscript/plot_elephantResults016.pdf manuscript/plot_elephantResults017.pdf

manuscript/plot_greySealResults1.png

manuscript/plot_greySealResults2.png

manuscript/plot_nfsResults.pdf manuscript/plot_turtleResults001.pdf manuscript/plot_turtleResults002.pdf manuscript/plot_turtleResults004.pdf manuscript/plot_turtleResults2.pdf

manuscript/sesData.csv

manuscript/sesExample.R

manuscript/turtleData.RData

manuscript/turtleExample.R manuscript/vignette_examples.R

manuscript/vignette_inputs.RData

manuscript/workflow.pdf

manuscript/workflow.pptx

manuscript/workflow_simData.pdf

manuscript/workflow_simData.pptx

manuscript/workflow_simData_rev1.pdf

manuscript/workflow_simData_rev1.pptx

src/.DS_Store

src/Makevars

src/RcppExports.cpp

src/XBloop.cpp

src/combine.h

src/densities.h

src/getDM.cpp

src/momentuHMM_init.c

src/nLogLike.cpp

src/trMatrix.cpp

tests/testthat.R tests/testthat/extraExamples.R

tests/testthat/extraExamples.RData

tests/testthat/test_CIbeta.R tests/testthat/test_CIreal.R tests/testthat/test_MIfitHMM.R tests/testthat/test_allProbs.R tests/testthat/test_crawlWrap.R tests/testthat/test_densities.R tests/testthat/test_doFuture.R tests/testthat/test_extraDistr.R tests/testthat/test_extraExamples.R tests/testthat/test_fitHMM.R tests/testthat/test_getDM.R tests/testthat/test_logAlpha.R tests/testthat/test_momentuHMM.R tests/testthat/test_momentuHMMData.R tests/testthat/test_moveData.R tests/testthat/test_n2w.R tests/testthat/test_nLogLike.R tests/testthat/test_parDef.R tests/testthat/test_plotSat.R tests/testthat/test_plot_momentuHMM.R tests/testthat/test_plot_momentuHMMData.R tests/testthat/test_prepData.R tests/testthat/test_simData.R tests/testthat/test_stateProbs.R tests/testthat/test_trMatrix_rcpp.R tests/testthat/test_turnAngle.R tests/testthat/test_viterbi.R tests/testthat/test_w2n.R

vignettes/Atlantic_cod_data_set.RData

vignettes/adjcalc.sty

vignettes/adjustbox.sty

vignettes/caracaraExample.RData

vignettes/coastUTM.RData

vignettes/codDist.pdf vignettes/codStates.pdf

vignettes/elephant_plotSat.png

vignettes/examples/buffaloExample.R vignettes/examples/caracaraExample.R vignettes/examples/codExample.R vignettes/examples/elephantExample.R vignettes/examples/garterSnakeExample.R vignettes/examples/greySealExample.R vignettes/examples/groupExample.R vignettes/examples/harborPorpoiseExample.R vignettes/examples/harbourSealExample.R vignettes/examples/hornSharkExample.R vignettes/examples/landConstraintExample.R vignettes/examples/nfsExample.R vignettes/examples/northernFulmarExample.R vignettes/examples/pilotWhaleExample.R vignettes/examples/sesExample.R vignettes/examples/turtleExample.R vignettes/examples/turtleExample_rw_mvnorm2.R vignettes/garterSnakeDist.pdf vignettes/garterSnakeStates.pdf

vignettes/greySealData.RData

vignettes/harborPorpoiseDist.pdf vignettes/harborPorpoiseStates.pdf

vignettes/horn_shark_data_set.RData

vignettes/master.bib

vignettes/mee.bst

vignettes/momentuHMM.Rnw

vignettes/momentuHMM.pdf

vignettes/momentuHMM.pdf.asis

vignettes/momentuHMM.tex

vignettes/nfsData.RData

vignettes/pilotWhaleData.RData

vignettes/plot_buffaloExample011.pdf vignettes/plot_buffaloResults.pdf vignettes/plot_buffaloStates.pdf vignettes/plot_codExample001.pdf vignettes/plot_codExample002.pdf vignettes/plot_codStationary001.pdf vignettes/plot_codStationary002.pdf vignettes/plot_codStationary003.pdf vignettes/plot_elephantResults001.pdf vignettes/plot_elephantResults002.pdf vignettes/plot_elephantResults009.pdf vignettes/plot_elephantResults010.pdf vignettes/plot_elephantResults012.pdf vignettes/plot_elephantResults013.pdf vignettes/plot_elephantResults015.pdf vignettes/plot_elephantResults016.pdf vignettes/plot_elephantResults017.pdf vignettes/plot_garterSnakePR.pdf vignettes/plot_greySealResults002.pdf vignettes/plot_greySealResults006.pdf vignettes/plot_greySealResults009.pdf vignettes/plot_greySealResults013.pdf

vignettes/plot_greySealResults1.png

vignettes/plot_greySealResults2.png

vignettes/plot_groupExample001.pdf vignettes/plot_groupExampleCentroid001.pdf vignettes/plot_groupExampleResults007.pdf vignettes/plot_groupExampleResults008.pdf vignettes/plot_harborPorpoiseStates001.pdf vignettes/plot_harborPorpoiseStates002.pdf

vignettes/plot_harbourSeal.png

vignettes/plot_harbourSealResults020.pdf

vignettes/plot_landConstraintExample.png

vignettes/plot_nfsResults.pdf

vignettes/plot_northernFulmarExample.png

vignettes/plot_sesResults001.pdf vignettes/plot_sesResults003.pdf vignettes/plot_sesResults007.pdf vignettes/plot_sesResults009.pdf

vignettes/plot_sesResults2.png

vignettes/plot_turtleResults001.pdf vignettes/plot_turtleResults002.pdf vignettes/plot_turtleResults004.pdf vignettes/plot_turtleResults2.pdf

vignettes/script.sh

vignettes/sesData.csv

vignettes/sharkDist.pdf vignettes/sharkStates.pdf

vignettes/trimclip.sty

vignettes/turtleData.RData

vignettes/vignetteResults/codExample.RData

vignettes/vignetteResults/garterSnakeExample.RData

vignettes/vignetteResults/harborPorpoiseExample.RData

vignettes/vignetteResults/hornSharkExample.RData

vignettes/vignetteResults/pilotWhaleExample.RData

vignettes/vignette_inputs.R

vignettes/vignette_inputs.RData

bmcclintock/momentuHMM documentation built on Oct. 26, 2022, 1 a.m.