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.Rbuildignore
.gitattributes
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/questions-or-other-issues.md
.github/ISSUE_TEMPLATE/x-new-release.md
.github/workflows/pkgdown.glmmTMByaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/CSEGriskfigure.R
R/CSEGtmufigure.R
R/MARSS-methods.R
R/MARSS.R
R/MARSSFisherI.r
R/MARSS_dfa.r
R/MARSS_marss.R
R/MARSS_marxss.R
R/MARSSaic.R
R/MARSSapplynames.R
R/MARSSboot.R
R/MARSScv.R
R/MARSSharveyobsFI.R
R/MARSShatyt.r
R/MARSShessian.R
R/MARSShessian_numerical.R
R/MARSSinfo.R
R/MARSSinits.R
R/MARSSinnovationsboot.R
R/MARSSkem.r
R/MARSSkemcheck.r
R/MARSSkf.r
R/MARSSkfas.r
R/MARSSkfss.R
R/MARSSoptim.r
R/MARSSparamCIs.R
R/MARSSresiduals.R
R/MARSSresiduals.tT.R
R/MARSSresiduals_tt.R
R/MARSSresiduals_tt1.R
R/MARSSsimulate.R
R/MARSSvectorizeparam.R
R/accuracy_marssMLE.R
R/autoplot_marssMLE.R
R/autoplot_marssPredict.R
R/autoplot_marssResiduals.R
R/checkMARSSInputs.r
R/checkModelList.r
R/coef_marssMLE.r
R/describe_marssMODEL.R
R/fitted_marssMLE.r
R/forecast_marssMLE.R
R/glance_marssMLE.R
R/is_marssMLE.r
R/is_marssMODEL.R
R/logLik_marssMLE.R
R/model_frame_marssMODEL.R
R/onLoad.R
R/plot_marssMLE.R
R/plot_marssPredict.R
R/plot_marssResiduals.R
R/predict_marssMLE.R
R/print_marssMLE.r
R/print_marssMODEL.R
R/print_marssPredict.R
R/progressBar.R
R/residuals_marssMLE.R
R/summary_marssMLE.R
R/summary_marssMODEL.R
R/sysdata.rda
R/tidy_marssMLE.R
R/toLatex_marssMODEL.R
R/tsSmooth_marssMLE.R
R/utility_functions.R
README.md
Rplots.pdf
_layouts/default.html
cran-comments.md
data/SalmonSurvCUI.rda
data/graywhales.rda
data/grouse.rda
data/harborSeal.rda
data/harborSealWA.rda
data/isleRoyal.rda
data/ivesDataByWeek.rda
data/ivesDataLP.rda
data/kestrel.rda
data/lakeWAplankton.rda
data/loggerhead.rda
data/loggerheadNoisy.rda
data/okanaganRedds.rda
data/prairiechicken.rda
data/redstart.rda
data/rockfish.rda
data/wilddogs.rda
favicon.ico
hexlogo.png
inst/CITATION
inst/DEVELOPER_NOTES.html
inst/DEVELOPER_NOTES.md
inst/Makefile
inst/WORDLIST
inst/derivations/EMDerivation.Rnw
inst/derivations/EMDerivation.bib
inst/derivations/EMDerivation.pdf
inst/derivations/Makefile
inst/derivations/Residuals-concordance.tex
inst/derivations/Residuals.Rnw
inst/derivations/Residuals.bbl
inst/derivations/Residuals.log
inst/derivations/Residuals.pdf
inst/derivations/Residuals.synctex.gz
inst/derivations/Residuals.tex
inst/derivations/doc/EMDerivation.Rnw
inst/derivations/doc/EMDerivation.pdf
inst/derivations/doc/Residuals.Rnw
inst/derivations/doc/Residuals.pdf
inst/derivations/footmisc.sty
inst/derivations/hanging.sty
inst/doc/Chapter_AnimalTracking.R
inst/doc/Chapter_CombiningTrendData.R
inst/doc/Chapter_Covariates.R
inst/doc/Chapter_DFA.R
inst/doc/Chapter_KFAS.R
inst/doc/Chapter_MARp.R
inst/doc/Chapter_MLR.R
inst/doc/Chapter_PVA.R
inst/doc/Chapter_SealPopStructure.R
inst/doc/Chapter_SealTrend.R
inst/doc/Chapter_SpeciesInteractions.R
inst/doc/Chapter_StructuralBreaks.R
inst/doc/Chapter_Structural_TS.R
inst/doc/Chapter_UnivariateDLM.R
inst/doc/Chapter_inits.R
inst/doc/EMDerivation.Rnw
inst/doc/EMDerivation.pdf
inst/doc/Quick_Examples.R
inst/doc/Residuals.Rnw
inst/doc/Residuals.pdf
inst/doc/UserGuide.pdf
inst/oldtex/MARSS_out.Rd
inst/oldtex/Residuals-PDF.Rmd
inst/oldtex/Residuals.Rmd
inst/oldtex/UserGuide.Rmd
inst/oldtex/XXMakefile
inst/oldtex/mathjax4.html
inst/oldtex/nextsection.tex
inst/testing-releases/build the package.txt
inst/testing-releases/test-autoplot.Rmd
inst/testing-releases/test-plot-kfas-kfss.Rmd
inst/testing-releases/test-plot.Rmd
inst/testing-releases/test-predict-plots.Rmd
inst/testing-releases/test-resids-plots.Rmd
inst/testing-releases/versiontest.R
inst/userguide/LICENSE
inst/userguide/Makefile
inst/userguide/README.md
inst/userguide/UserGuide.Rnw
"inst/userguide/\\CS4--model_fits.RData"
inst/userguide/cbe.bst
inst/userguide/chapter-debugging/debug_manual.R
inst/userguide/chapter-debugging/debugger_template.Rnw
inst/userguide/chapter-debugging/index.html
inst/userguide/chapter-debugging/mathdefs.tex
inst/userguide/chapter-debugging/nextsection.tex
inst/userguide/css/mathjax2.html
inst/userguide/css/mathjax3.html
inst/userguide/css/mathjax4.html
inst/userguide/doc/Chapter_AnimalTracking.R
inst/userguide/doc/Chapter_CombiningTrendData.R
inst/userguide/doc/Chapter_Covariates.R
inst/userguide/doc/Chapter_DFA.R
inst/userguide/doc/Chapter_KFAS.R
inst/userguide/doc/Chapter_MARp.R
inst/userguide/doc/Chapter_MLR.R
inst/userguide/doc/Chapter_PVA.R
inst/userguide/doc/Chapter_SealPopStructure.R
inst/userguide/doc/Chapter_SealTrend.R
inst/userguide/doc/Chapter_SpeciesInteractions.R
inst/userguide/doc/Chapter_StructuralBreaks.R
inst/userguide/doc/Chapter_Structural_TS.R
inst/userguide/doc/Chapter_UnivariateDLM.R
inst/userguide/doc/Chapter_inits.R
inst/userguide/doc/Quick_Examples.R
inst/userguide/doc/UserGuide.pdf
inst/userguide/figures/ARMAp--B.R
inst/userguide/figures/ARMAp--B.tex
inst/userguide/figures/ARMAp--Cs_000_required_libraries.R
inst/userguide/figures/ARMAp--Cs_000_required_libraries.tex
inst/userguide/figures/ARMAp--Cs_101_ar2-sim.R
inst/userguide/figures/ARMAp--Cs_101_ar2-sim.tex
inst/userguide/figures/ARMAp--Cs_102_ar2-model.R
inst/userguide/figures/ARMAp--Cs_102_ar2-model.tex
inst/userguide/figures/ARMAp--Cs_103_ar2-fit.R
inst/userguide/figures/ARMAp--Cs_103_ar2-fit.tex
inst/userguide/figures/ARMAp--Cs_104_ar2-fit.R
inst/userguide/figures/ARMAp--Cs_104_ar2-fit.tex
inst/userguide/figures/ARMAp--Cs_105_ar2-gappy.R
inst/userguide/figures/ARMAp--Cs_105_ar2-gappy.tex
inst/userguide/figures/ARMAp--Cs_106_ar2-gappy.R
inst/userguide/figures/ARMAp--Cs_106_ar2-gappy.tex
inst/userguide/figures/ARMAp--Cs_107_arima.R
inst/userguide/figures/ARMAp--Cs_107_arima.tex
inst/userguide/figures/ARMAp--Cs_108_non-stationary.R
inst/userguide/figures/ARMAp--Cs_108_non-stationary.tex
inst/userguide/figures/ARMAp--Cs_201_mar2-sim.R
inst/userguide/figures/ARMAp--Cs_201_mar2-sim.tex
inst/userguide/figures/ARMAp--Cs_202_mar2-sim.R
inst/userguide/figures/ARMAp--Cs_202_mar2-sim.tex
inst/userguide/figures/ARMAp--Cs_203_mar2-model.R
inst/userguide/figures/ARMAp--Cs_203_mar2-model.tex
inst/userguide/figures/ARMAp--Cs_204_mar2-fit.R
inst/userguide/figures/ARMAp--Cs_204_mar2-fit.tex
inst/userguide/figures/ARMAp--Cs_205_mar2-compare.R
inst/userguide/figures/ARMAp--Cs_205_mar2-compare.tex
inst/userguide/figures/ARMAp--Cs_206_compare-mars.R
inst/userguide/figures/ARMAp--Cs_206_compare-mars.tex
inst/userguide/figures/ARMAp--Cs_301_sim-ar3-data.R
inst/userguide/figures/ARMAp--Cs_301_sim-ar3-data.tex
inst/userguide/figures/ARMAp--Cs_302_set-up-ar3-model.R
inst/userguide/figures/ARMAp--Cs_302_set-up-ar3-model.tex
inst/userguide/figures/ARMAp--Cs_303_fit-ar3.R
inst/userguide/figures/ARMAp--Cs_303_fit-ar3.tex
inst/userguide/figures/ARMAp--Cs_304_fit-ar3.R
inst/userguide/figures/ARMAp--Cs_304_fit-ar3.tex
inst/userguide/figures/ARMAp--Cs_401_setseed5.R
inst/userguide/figures/ARMAp--Cs_401_setseed5.tex
inst/userguide/figures/ARMAp--Cs_402_fig-arss-model.R
inst/userguide/figures/ARMAp--Cs_402_fig-arss-model.tex
inst/userguide/figures/ARMAp--Cs_403_fig-arss-model.R
inst/userguide/figures/ARMAp--Cs_403_fig-arss-model.tex
inst/userguide/figures/ARMAp--Cs_404_fig-arss-model.R
inst/userguide/figures/ARMAp--Cs_404_fig-arss-model.tex
inst/userguide/figures/ARMAp--Cs_405_fit-arss2-model.R
inst/userguide/figures/ARMAp--Cs_405_fit-arss2-model.tex
inst/userguide/figures/ARMAp--Cs_406_fit-arss2-model.R
inst/userguide/figures/ARMAp--Cs_406_fit-arss2-model.tex
inst/userguide/figures/ARMAp--Cs_407_fit-arss2-model.R
inst/userguide/figures/ARMAp--Cs_407_fit-arss2-model.tex
inst/userguide/figures/ARMAp--Cs_408_fit-arss2-with-arima.R
inst/userguide/figures/ARMAp--Cs_408_fit-arss2-with-arima.tex
inst/userguide/figures/ARMAp--Cs_409_code-to-compare-arss-estimation.R
inst/userguide/figures/ARMAp--Cs_409_code-to-compare-arss-estimation.tex
inst/userguide/figures/ARMAp--Cs_410_marssperffig.R
inst/userguide/figures/ARMAp--Cs_410_marssperffig.pdf
inst/userguide/figures/ARMAp--Cs_410_marssperffig.tex
inst/userguide/figures/ARMAp--RUNFIRST.R
inst/userguide/figures/ARMAp--RUNFIRST.tex
inst/userguide/figures/ARMAp--Z.R
inst/userguide/figures/ARMAp--Z.tex
inst/userguide/figures/ARMAp--loadmarssperf.R
inst/userguide/figures/ARMAp--loadmarssperf.tex
inst/userguide/figures/ARMAp--reset.R
inst/userguide/figures/ARMAp--reset.tex
inst/userguide/figures/ARMAp--setseed.R
inst/userguide/figures/ARMAp--setseed.tex
inst/userguide/figures/ARMAp--setseed2.R
inst/userguide/figures/ARMAp--setseed2.tex
inst/userguide/figures/ARMAp--setseed3.R
inst/userguide/figures/ARMAp--setseed3.tex
inst/userguide/figures/ARMAp--setseed4.R
inst/userguide/figures/ARMAp--setseed4.tex
inst/userguide/figures/CAORWA.pdf
inst/userguide/figures/CS1--Cs1_Exercise1.R
inst/userguide/figures/CS1--Cs1_Exercise1.tex
inst/userguide/figures/CS1--Cs1_Exercise2.R
inst/userguide/figures/CS1--Cs1_Exercise2.tex
inst/userguide/figures/CS1--Cs1_Exercise3.R
inst/userguide/figures/CS1--Cs1_Exercise3.tex
inst/userguide/figures/CS1--Cs1_Exercise4.R
inst/userguide/figures/CS1--Cs1_Exercise4.tex
inst/userguide/figures/CS1--Cs1_Exercise5.R
inst/userguide/figures/CS1--Cs1_Exercise5.tex
inst/userguide/figures/CS1--Cs1_a_required_libraries.R
inst/userguide/figures/CS1--Cs1_a_required_libraries.tex
inst/userguide/figures/CS1--Ex2_results.R
inst/userguide/figures/CS1--Ex2_results.tex
inst/userguide/figures/CS1--Exercise3_figure.R
inst/userguide/figures/CS1--Exercise3_figure.pdf
inst/userguide/figures/CS1--Exercise3_figure.tex
inst/userguide/figures/CS1--RUNFIRST.R
inst/userguide/figures/CS1--RUNFIRST.tex
inst/userguide/figures/CS1--Reset.R
inst/userguide/figures/CS1--Reset.tex
inst/userguide/figures/CS1--Testing_Exercise5.R
inst/userguide/figures/CS1--Testing_Exercise5.tex
inst/userguide/figures/CS1--den91params.R
inst/userguide/figures/CS1--den91params.tex
inst/userguide/figures/CS1--dennisEsts.R
inst/userguide/figures/CS1--dennisEsts.tex
inst/userguide/figures/CS1--dennisregression.R
inst/userguide/figures/CS1--dennisregression.pdf
inst/userguide/figures/CS1--dennisregression.tex
inst/userguide/figures/CS1--fakeobsdata.R
inst/userguide/figures/CS1--fakeobsdata.tex
inst/userguide/figures/CS1--fakepopdata.R
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inst/userguide/figures/CS1--figTMU.R
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inst/userguide/figures/KFAS--Cs406_conf-int.R
inst/userguide/figures/KFAS--Cs406_conf-int.tex
inst/userguide/figures/KFAS--Cs407_conf-int.R
inst/userguide/figures/KFAS--Cs407_conf-int.tex
inst/userguide/figures/KFAS--Cs408_conf-int.R