├── .git_diff_name-only ├── .git_ls-tree_r_name-only_HEAD ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── questions-or-other-issues.md │ └── x-new-release.md └── workflows │ ├── pkgdown.glmmTMByaml │ └── pkgdown.yaml ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── CSEGriskfigure.R ├── CSEGtmufigure.R ├── MARSS-methods.R ├── MARSS.R ├── MARSSFisherI.r ├── MARSS_dfa.r ├── MARSS_marss.R ├── MARSS_marxss.R ├── MARSSaic.R ├── MARSSapplynames.R ├── MARSSboot.R ├── MARSScv.R ├── MARSSharveyobsFI.R ├── MARSShatyt.r ├── MARSShessian.R ├── MARSShessian_numerical.R ├── MARSSinfo.R ├── MARSSinits.R ├── MARSSinnovationsboot.R ├── MARSSkem.r ├── MARSSkemcheck.r ├── MARSSkf.r ├── MARSSkfas.r ├── MARSSkfss.R ├── MARSSoptim.r ├── MARSSparamCIs.R ├── MARSSresiduals.R ├── MARSSresiduals.tT.R ├── MARSSresiduals_tt.R ├── MARSSresiduals_tt1.R ├── MARSSsimulate.R ├── MARSSvectorizeparam.R ├── accuracy_marssMLE.R ├── autoplot_marssMLE.R ├── autoplot_marssPredict.R ├── autoplot_marssResiduals.R ├── checkMARSSInputs.r ├── checkModelList.r ├── coef_marssMLE.r ├── describe_marssMODEL.R ├── fitted_marssMLE.r ├── forecast_marssMLE.R ├── glance_marssMLE.R ├── is_marssMLE.r ├── is_marssMODEL.R ├── logLik_marssMLE.R ├── model_frame_marssMODEL.R ├── onLoad.R ├── plot_marssMLE.R ├── plot_marssPredict.R ├── plot_marssResiduals.R ├── predict_marssMLE.R ├── print_marssMLE.r ├── print_marssMODEL.R ├── print_marssPredict.R ├── progressBar.R ├── residuals_marssMLE.R ├── summary_marssMLE.R ├── summary_marssMODEL.R ├── sysdata.rda ├── tidy_marssMLE.R ├── toLatex_marssMODEL.R ├── tsSmooth_marssMLE.R └── utility_functions.R ├── Rplots.pdf ├── cran-comments.md ├── data ├── SalmonSurvCUI.rda ├── graywhales.rda ├── grouse.rda ├── harborSeal.rda ├── harborSealWA.rda ├── isleRoyal.rda ├── ivesDataByWeek.rda ├── ivesDataLP.rda ├── kestrel.rda ├── lakeWAplankton.rda ├── loggerhead.rda ├── loggerheadNoisy.rda ├── okanaganRedds.rda ├── prairiechicken.rda ├── redstart.rda ├── rockfish.rda └── wilddogs.rda ├── inst ├── CITATION ├── DEVELOPER_NOTES.html ├── DEVELOPER_NOTES.md ├── Makefile ├── derivations │ ├── EMDerivation.Rnw │ ├── EMDerivation.bib │ ├── EMDerivation.pdf │ ├── Makefile │ ├── Residuals-concordance.tex │ ├── Residuals.Rnw │ ├── Residuals.bbl │ ├── Residuals.log │ ├── Residuals.pdf │ ├── Residuals.synctex.gz │ ├── Residuals.tex │ ├── doc │ │ ├── EMDerivation.Rnw │ │ ├── EMDerivation.pdf │ │ ├── Residuals.Rnw │ │ └── Residuals.pdf │ ├── footmisc.sty │ └── hanging.sty ├── doc │ ├── Chapter_AnimalTracking.R │ ├── Chapter_CombiningTrendData.R │ ├── Chapter_Covariates.R │ ├── Chapter_DFA.R │ ├── Chapter_KFAS.R │ ├── Chapter_MARp.R │ ├── Chapter_MLR.R │ ├── Chapter_PVA.R │ ├── Chapter_SealPopStructure.R │ ├── Chapter_SealTrend.R │ ├── Chapter_SpeciesInteractions.R │ ├── Chapter_StructuralBreaks.R │ ├── Chapter_Structural_TS.R │ ├── Chapter_UnivariateDLM.R │ ├── Chapter_inits.R │ ├── EMDerivation.Rnw │ ├── EMDerivation.pdf │ ├── Learning_MARSS.Rmd │ ├── Learning_MARSS.html │ ├── Quick_Examples.R │ ├── Quick_Start.R │ ├── Quick_Start.Rmd │ ├── Quick_Start.html │ ├── Residuals.Rnw │ ├── Residuals.pdf │ ├── UserGuide.Rnw │ └── UserGuide.pdf ├── oldtex │ ├── MARSS_out.Rd │ ├── Residuals-PDF.Rmd │ ├── Residuals.Rmd │ ├── UserGuide.Rmd │ ├── XXMakefile │ ├── mathjax4.html │ └── nextsection.tex ├── testing-releases │ ├── build the package.txt │ ├── test-autoplot.Rmd │ ├── test-plot-kfas-kfss.Rmd │ ├── test-plot.Rmd │ ├── test-predict-plots.Rmd │ ├── test-resids-plots.Rmd │ └── versiontest.R └── userguide │ ├── LICENSE │ ├── Makefile │ ├── UserGuide.Rnw │ ├── \CS4--model_fits.RData │ ├── cbe.bst │ ├── chapter-debugging │ ├── debug_manual.R │ ├── debugger_template.Rnw │ ├── index.html │ ├── mathdefs.tex │ └── nextsection.tex │ ├── css │ ├── mathjax2.html │ ├── mathjax3.html │ └── mathjax4.html │ ├── doc │ ├── Chapter_AnimalTracking.R │ ├── Chapter_CombiningTrendData.R │ ├── Chapter_Covariates.R │ ├── Chapter_DFA.R │ ├── Chapter_KFAS.R │ ├── Chapter_MARp.R │ ├── Chapter_MLR.R │ ├── Chapter_PVA.R │ ├── Chapter_SealPopStructure.R │ ├── Chapter_SealTrend.R │ ├── Chapter_SpeciesInteractions.R │ ├── Chapter_StructuralBreaks.R │ ├── Chapter_Structural_TS.R │ ├── Chapter_UnivariateDLM.R │ ├── Chapter_inits.R │ ├── Quick_Examples.R │ └── UserGuide.pdf │ ├── figures │ ├── ARMAp--B.R │ ├── ARMAp--B.tex │ ├── ARMAp--Cs_000_required_libraries.R │ ├── ARMAp--Cs_000_required_libraries.tex │ ├── ARMAp--Cs_101_ar2-sim.R │ ├── ARMAp--Cs_101_ar2-sim.tex │ ├── ARMAp--Cs_102_ar2-model.R │ ├── ARMAp--Cs_102_ar2-model.tex │ ├── ARMAp--Cs_103_ar2-fit.R │ ├── ARMAp--Cs_103_ar2-fit.tex │ ├── ARMAp--Cs_104_ar2-fit.R │ ├── ARMAp--Cs_104_ar2-fit.tex │ ├── ARMAp--Cs_105_ar2-gappy.R │ ├── ARMAp--Cs_105_ar2-gappy.tex │ ├── ARMAp--Cs_106_ar2-gappy.R │ ├── ARMAp--Cs_106_ar2-gappy.tex │ ├── ARMAp--Cs_107_arima.R │ ├── ARMAp--Cs_107_arima.tex │ ├── ARMAp--Cs_108_non-stationary.R │ ├── ARMAp--Cs_108_non-stationary.tex │ ├── ARMAp--Cs_201_mar2-sim.R │ ├── ARMAp--Cs_201_mar2-sim.tex │ ├── ARMAp--Cs_202_mar2-sim.R │ ├── ARMAp--Cs_202_mar2-sim.tex │ ├── ARMAp--Cs_203_mar2-model.R │ ├── ARMAp--Cs_203_mar2-model.tex │ ├── ARMAp--Cs_204_mar2-fit.R │ ├── ARMAp--Cs_204_mar2-fit.tex │ ├── ARMAp--Cs_205_mar2-compare.R │ ├── ARMAp--Cs_205_mar2-compare.tex │ ├── ARMAp--Cs_206_compare-mars.R │ ├── ARMAp--Cs_206_compare-mars.tex │ ├── ARMAp--Cs_301_sim-ar3-data.R │ ├── ARMAp--Cs_301_sim-ar3-data.tex │ ├── ARMAp--Cs_302_set-up-ar3-model.R │ ├── ARMAp--Cs_302_set-up-ar3-model.tex │ ├── ARMAp--Cs_303_fit-ar3.R │ ├── ARMAp--Cs_303_fit-ar3.tex │ ├── ARMAp--Cs_304_fit-ar3.R │ ├── ARMAp--Cs_304_fit-ar3.tex │ ├── ARMAp--Cs_401_setseed5.R │ ├── ARMAp--Cs_401_setseed5.tex │ ├── ARMAp--Cs_402_fig-arss-model.R │ ├── ARMAp--Cs_402_fig-arss-model.tex │ ├── ARMAp--Cs_403_fig-arss-model.R │ ├── ARMAp--Cs_403_fig-arss-model.tex │ ├── ARMAp--Cs_404_fig-arss-model.R │ ├── ARMAp--Cs_404_fig-arss-model.tex │ ├── ARMAp--Cs_405_fit-arss2-model.R │ ├── ARMAp--Cs_405_fit-arss2-model.tex │ ├── ARMAp--Cs_406_fit-arss2-model.R │ ├── ARMAp--Cs_406_fit-arss2-model.tex │ ├── ARMAp--Cs_407_fit-arss2-model.R │ ├── ARMAp--Cs_407_fit-arss2-model.tex │ ├── ARMAp--Cs_408_fit-arss2-with-arima.R │ ├── ARMAp--Cs_408_fit-arss2-with-arima.tex │ ├── ARMAp--Cs_409_code-to-compare-arss-estimation.R │ ├── ARMAp--Cs_409_code-to-compare-arss-estimation.tex │ ├── ARMAp--Cs_410_marssperffig.R │ ├── ARMAp--Cs_410_marssperffig.pdf │ ├── ARMAp--Cs_410_marssperffig.tex │ ├── ARMAp--RUNFIRST.R │ ├── ARMAp--RUNFIRST.tex │ ├── ARMAp--Z.R │ ├── ARMAp--Z.tex │ ├── ARMAp--loadmarssperf.R │ ├── ARMAp--loadmarssperf.tex │ ├── ARMAp--reset.R │ ├── ARMAp--reset.tex │ ├── ARMAp--setseed.R │ ├── ARMAp--setseed.tex │ ├── ARMAp--setseed2.R │ ├── ARMAp--setseed2.tex │ ├── ARMAp--setseed3.R │ ├── ARMAp--setseed3.tex │ ├── ARMAp--setseed4.R │ ├── ARMAp--setseed4.tex │ ├── CAORWA.pdf │ ├── CS1--Cs1_Exercise1.R │ ├── CS1--Cs1_Exercise1.tex │ ├── CS1--Cs1_Exercise2.R │ ├── CS1--Cs1_Exercise2.tex │ ├── CS1--Cs1_Exercise3.R │ ├── CS1--Cs1_Exercise3.tex │ ├── CS1--Cs1_Exercise4.R │ ├── CS1--Cs1_Exercise4.tex │ ├── CS1--Cs1_Exercise5.R │ ├── CS1--Cs1_Exercise5.tex │ ├── CS1--Cs1_a_required_libraries.R │ ├── CS1--Cs1_a_required_libraries.tex │ ├── CS1--Ex2_results.R │ ├── CS1--Ex2_results.tex │ ├── CS1--Exercise3_figure.R │ ├── CS1--Exercise3_figure.pdf │ ├── CS1--Exercise3_figure.tex │ ├── CS1--RUNFIRST.R │ ├── CS1--RUNFIRST.tex │ ├── CS1--Reset.R │ ├── CS1--Reset.tex │ ├── CS1--Testing_Exercise5.R │ ├── CS1--Testing_Exercise5.tex │ ├── CS1--den91params.R │ ├── CS1--den91params.tex │ ├── CS1--dennisEsts.R │ ├── CS1--dennisEsts.tex │ ├── CS1--dennisregression.R │ ├── CS1--dennisregression.pdf │ ├── CS1--dennisregression.tex │ ├── CS1--fakeobsdata.R │ ├── CS1--fakeobsdata.tex │ ├── CS1--fakepopdata.R │ ├── CS1--fakepopdata.tex │ ├── CS1--figTMU.R │ ├── CS1--figTMU.pdf │ ├── CS1--figTMU.tex │ ├── CS1--fitKalmanEM1.R │ ├── CS1--fitKalmanEM1.tex │ ├── CS1--fitKalmanEM2.R │ ├── CS1--fitKalmanEM2.tex │ ├── CS1--initvals.R │ ├── CS1--initvals.tex │ ├── CS1--nineparams.R │ ├── CS1--nineparams.tex │ ├── CS1--noevalriskfigure.R │ ├── CS1--noevalriskfigure.tex │ ├── CS1--paramvals.R │ ├── CS1--paramvals.tex │ ├── CS1--plotkemstates.R │ ├── CS1--plotkemstates.pdf │ ├── CS1--plotkemstates.tex │ ├── CS1--probextcalc.R │ ├── CS1--probextcalc.tex │ ├── CS1--recode.data.as.transitions.R │ ├── CS1--recode.data.as.transitions.tex │ ├── CS1--riskfigure.R │ ├── CS1--riskfigure.pdf │ ├── CS1--riskfigure.tex │ ├── CS1--sim3x3.R │ ├── CS1--sim3x3.pdf │ ├── CS1--sim3x3.tex │ ├── CS2--024.R │ ├── CS2--024.tex │ ├── CS2--025.R │ ├── CS2--025.tex │ ├── CS2--026.R │ ├── CS2--026.tex │ ├── CS2--027.R │ ├── CS2--027.tex │ ├── CS2--Cs2-AIC2.R │ ├── CS2--Cs2-AIC2.tex │ ├── CS2--Cs2-analysis2obsvariance.R │ ├── CS2--Cs2-analysis2obsvariance.tex │ ├── CS2--Cs2-analysis3-UQ.R │ ├── CS2--Cs2-analysis3-UQ.tex │ ├── CS2--Cs2-analysis3-Z.R │ ├── CS2--Cs2-analysis3-Z.tex │ ├── CS2--Cs2-fig5.R │ ├── CS2--Cs2-fig5.pdf │ ├── CS2--Cs2-fig5.tex │ ├── CS2--Cs2-fitanalysis2.R │ ├── CS2--Cs2-fitanalysis2.tex │ ├── CS2--Cs2-readindata.R │ ├── CS2--Cs2-readindata.tex │ ├── CS2--Cs2-residuals-analysis3-fig6.R │ ├── CS2--Cs2-residuals-analysis3-fig6.pdf │ ├── CS2--Cs2-residuals-analysis3-fig6.tex │ ├── CS2--Cs2-setgroups.R │ ├── CS2--Cs2-setgroups.tex │ ├── CS2--Cs2-showdata.R │ ├── CS2--Cs2-showdata.tex │ ├── CS2--Cs2_Code1.R │ ├── CS2--Cs2_Code1.tex │ ├── CS2--Cs2_Code2.R │ ├── CS2--Cs2_Code2.tex │ ├── CS2--Cs2_Code3.R │ ├── CS2--Cs2_Code3.tex │ ├── CS2--Cs2_Code4.R │ ├── CS2--Cs2_Code4.tex │ ├── CS2--Cs2_Code5_7.R │ ├── CS2--Cs2_Code5_7.tex │ ├── CS2--RUNFIRST.R │ ├── CS2--RUNFIRST.tex │ ├── CS2--Reset.R │ ├── CS2--Reset.tex │ ├── CS2--fig1.R │ ├── CS2--fig1.pdf │ ├── CS2--fig1.tex │ ├── CS2--fig2.R │ ├── CS2--fig2.pdf │ ├── CS2--fig2.tex │ ├── CS2--funccallwithconstraints.R │ ├── CS2--funccallwithconstraints.tex │ ├── CS2--norun3.R │ ├── CS2--norun3.tex │ ├── CS2--noshow-listkem1.R │ ├── CS2--noshow-listkem1.tex │ ├── CS2--noshowlegend.R │ ├── CS2--noshowlegend.tex │ ├── CS2--setvarcov1.R │ ├── CS2--setvarcov1.tex │ ├── CS2--setwhichPop.R │ ├── CS2--setwhichPop.tex │ ├── CS3--Cs00_required_libraries.R │ ├── CS3--Cs00_required_libraries.tex │ ├── CS3--Cs01_set.up.data.R │ ├── CS3--Cs01_set.up.data.tex │ ├── CS3--Cs02_fig1.R │ ├── CS3--Cs02_fig1.pdf │ ├── CS3--Cs02_fig1.tex │ ├── CS3--Cs03_set.up.Z.models.R │ ├── CS3--Cs03_set.up.Z.models.tex │ ├── CS3--Cs04_Q.models.R │ ├── CS3--Cs04_Q.models.tex │ ├── CS3--Cs04a_other.models.R │ ├── CS3--Cs04a_other.models.tex │ ├── CS3--Cs05_run.the.models.R │ ├── CS3--Cs05_run.the.models.tex │ ├── CS3--Cs06_sort.results.R │ ├── CS3--Cs06_sort.results.tex │ ├── CS3--Cs07_add.delta.aicc.R │ ├── CS3--Cs07_add.delta.aicc.tex │ ├── CS3--Cs08_add.delta.aicc.R │ ├── CS3--Cs08_add.delta.aicc.tex │ ├── CS3--Cs09_aic.weight.R │ ├── CS3--Cs09_aic.weight.tex │ ├── CS3--Cs10_print.table.R │ ├── CS3--Cs10_print.table.tex │ ├── CS3--Cs11_fignorthsouth.R │ ├── CS3--Cs11_fignorthsouth.pdf │ ├── CS3--Cs11_fignorthsouth.tex │ ├── CS3--Cs12_new.Q.model.R │ ├── CS3--Cs12_new.Q.model.tex │ ├── CS3--Cs13_out.tab.2.R │ ├── CS3--Cs13_out.tab.2.tex │ ├── CS3--Cs14_out.tab.2.R │ ├── CS3--Cs14_out.tab.2.tex │ ├── CS3--Cs15_equalvarcov.weight.R │ ├── CS3--Cs15_equalvarcov.weight.tex │ ├── CS3--Cs16_Q.mat.R │ ├── CS3--Cs16_Q.mat.tex │ ├── CS3--Cs17_Q.diag.R │ ├── CS3--Cs17_Q.diag.tex │ ├── CS3--Cs18_Q.corr.R │ ├── CS3--Cs18_Q.corr.tex │ ├── CS3--Cs19_add.hood.canal.R │ ├── CS3--Cs19_add.hood.canal.tex │ ├── CS3--Cs20_hood.z.models.R │ ├── CS3--Cs20_hood.z.models.tex │ ├── CS3--Cs21_hood.uqr.models.R │ ├── CS3--Cs21_hood.uqr.models.tex │ ├── CS3--Cs22_hood-q3.R │ ├── CS3--Cs22_hood-q3.tex │ ├── CS3--Cs23_out.tab.hc.R │ ├── CS3--Cs23_out.tab.hc.tex │ ├── CS3--Cs24_sort.aicc.hc.R │ ├── CS3--Cs24_sort.aicc.hc.tex │ ├── CS3--Cs25_out.tab.2.R │ ├── CS3--Cs25_out.tab.2.tex │ ├── CS3--Q.model1.R │ ├── CS3--Q.model1.tex │ ├── CS3--Q.model2.R │ ├── CS3--Q.model2.tex │ ├── CS3--Q.model3.R │ ├── CS3--Q.model3.tex │ ├── CS3--RUNFIRST.R │ ├── CS3--RUNFIRST.tex │ ├── CS3--U.model14.R │ ├── CS3--U.model14.tex │ ├── CS3--Z.model.1.R │ ├── CS3--Z.model.1.tex │ ├── CS3--Z.model.R │ ├── CS3--Z.model.tex │ ├── CS3--kemcall.R │ ├── CS3--kemcall.tex │ ├── CS4--Cs00_required_libraries.R │ ├── CS4--Cs00_required_libraries.tex │ ├── CS4--Cs01_read_in_data.R │ ├── CS4--Cs01_read_in_data.tex │ ├── CS4--Cs02_transpose_data.R │ ├── CS4--Cs02_transpose_data.tex │ ├── CS4--Cs03_zscore.R │ ├── CS4--Cs03_zscore.tex │ ├── CS4--Cs03b_zscore.R │ ├── CS4--Cs03b_zscore.tex │ ├── CS4--Cs04_plotdata.R │ ├── CS4--Cs04_plotdata.pdf │ ├── CS4--Cs04_plotdata.tex │ ├── CS4--Cs05_setupZ.R │ ├── CS4--Cs05_setupZ.tex │ ├── CS4--Cs06_printZ.R │ ├── CS4--Cs06_printZ.tex │ ├── CS4--Cs07_setupQR.R │ ├── CS4--Cs07_setupQR.tex │ ├── CS4--Cs08_setupR.R │ ├── CS4--Cs08_setupR.tex │ ├── CS4--Cs09_printR.R │ ├── CS4--Cs09_printR.tex │ ├── CS4--Cs10_setupR_short.R │ ├── CS4--Cs10_setupR_short.tex │ ├── CS4--Cs11_setupU.R │ ├── CS4--Cs11_setupU.tex │ ├── CS4--Cs12_setupx0.R │ ├── CS4--Cs12_setupx0.tex │ ├── CS4--Cs13_define_model_list.R │ ├── CS4--Cs13_define_model_list.tex │ ├── CS4--Cs14_fit_data.R │ ├── CS4--Cs14_fit_data.tex │ ├── CS4--Cs15_plotfits.R │ ├── CS4--Cs15_plotfits.pdf │ ├── CS4--Cs15_plotfits.tex │ ├── CS4--Cs16_set_up_two_trends_echo.R │ ├── CS4--Cs16_set_up_two_trends_echo.tex │ ├── CS4--Cs17_compare_mods_2n3.R │ ├── CS4--Cs17_compare_mods_2n3.tex │ ├── CS4--Cs18_setupmanytrends_echo.R │ ├── CS4--Cs18_setupmanytrends_echo.tex │ ├── CS4--Cs19_makemodeltable.R │ ├── CS4--Cs19_makemodeltable.tex │ ├── CS4--Cs20_kem3_R_unconstrained.R │ ├── CS4--Cs20_kem3_R_unconstrained.tex │ ├── CS4--Cs21_varimax.R │ ├── CS4--Cs21_varimax.tex │ ├── CS4--Cs22_rotations.R │ ├── CS4--Cs22_rotations.tex │ ├── CS4--Cs22_rotations_cis.R │ ├── CS4--Cs22_rotations_cis.tex │ ├── CS4--Cs23_plotfacloadings.R │ ├── CS4--Cs23_plotfacloadings.pdf │ ├── CS4--Cs23_plotfacloadings.tex │ ├── CS4--Cs24_plottrends.R │ ├── CS4--Cs24_plottrends.pdf │ ├── CS4--Cs24_plottrends.tex │ ├── CS4--Cs25_func_get_DFA_fits.R │ ├── CS4--Cs25_func_get_DFA_fits.tex │ ├── CS4--Cs25b_get_DFA_fits.R │ ├── CS4--Cs25b_get_DFA_fits.tex │ ├── CS4--Cs25c_plotbestfits.R │ ├── CS4--Cs25c_plotbestfits.pdf │ ├── CS4--Cs25c_plotbestfits.tex │ ├── CS4--Cs25d_plotwithaugment.R │ ├── CS4--Cs25d_plotwithaugment.pdf │ ├── CS4--Cs25d_plotwithaugment.tex │ ├── CS4--Cs26_set-up-covar.R │ ├── CS4--Cs26_set-up-covar.tex │ ├── CS4--Cs27_fit_covar_echo.R │ ├── CS4--Cs27_fit_covar_echo.tex │ ├── CS4--Cs28_covar_AICs.R │ ├── CS4--Cs28_covar_AICs.tex │ ├── CS4--Cs29_plotbestcovarfits.R │ ├── CS4--Cs29_plotbestcovarfits.pdf │ ├── CS4--Cs29_plotbestcovarfits.tex │ ├── CS4--RUNFIRST.R │ ├── CS4--RUNFIRST.tex │ ├── CS4--Reset.R │ ├── CS4--Reset.tex │ ├── CS4--fit_covar.R │ ├── CS4--fit_covar.tex │ ├── CS4--fit_data_big_maxit.R │ ├── CS4--fit_data_big_maxit.tex │ ├── CS4--load_results_if_present.R │ ├── CS4--load_results_if_present.tex │ ├── CS4--makelatexofmodeltable.R │ ├── CS4--makelatexofmodeltable.tex │ ├── CS4--save_results.R │ ├── CS4--save_results.tex │ ├── CS4--set_up_two_trends_big_maxit.R │ ├── CS4--set_up_two_trends_big_maxit.tex │ ├── CS4--setupmanytrends_noecho.R │ ├── CS4--setupmanytrends_noecho.tex │ ├── CS5--Cs00_required_libraries.R │ ├── CS5--Cs00_required_libraries.tex │ ├── CS5--Cs01_data2.R │ ├── CS5--Cs01_data2.tex │ ├── CS5--Cs02_turtles2.R │ ├── CS5--Cs02_turtles2.tex │ ├── CS5--Cs03_data3.R │ ├── CS5--Cs03_data3.tex │ ├── CS5--Cs04_fig-code.R │ ├── CS5--Cs04_fig-code.tex │ ├── CS5--Cs05_badtagfig.R │ ├── CS5--Cs05_badtagfig.pdf │ ├── CS5--Cs05_badtagfig.tex │ ├── CS5--Cs06_setup2.R │ ├── CS5--Cs06_setup2.tex │ ├── CS5--Cs07_fitmodel.R │ ├── CS5--Cs07_fitmodel.tex │ ├── CS5--Cs08_code-to-plot.R │ ├── CS5--Cs08_code-to-plot.tex │ ├── CS5--Cs09_figbigmama.R │ ├── CS5--Cs09_figbigmama.pdf │ ├── CS5--Cs09_figbigmama.tex │ ├── CS5--Cs09b_GCDF.R │ ├── CS5--Cs09b_GCDF.tex │ ├── CS5--Cs10_distance.R │ ├── CS5--Cs10_distance.tex │ ├── CS5--Cs11_distance2.R │ ├── CS5--Cs11_distance2.tex │ ├── CS5--Cs13_disfig.R │ ├── CS5--Cs13_disfig.pdf │ ├── CS5--Cs13_disfig.tex │ ├── CS5--Cs14_disfig2.R │ ├── CS5--Cs14_disfig2.pdf │ ├── CS5--Cs14_disfig2.tex │ ├── CS5--Cs15_mean.miles.R │ ├── CS5--Cs15_mean.miles.tex │ ├── CS5--Cs16_turt-names.R │ ├── CS5--Cs16_turt-names.tex │ ├── CS5--Cs18_code.R │ ├── CS5--Cs18_code.tex │ ├── CS5--RUNFIRST.R │ ├── CS5--RUNFIRST.tex │ ├── CS5--Reset.R │ ├── CS5--Reset.tex │ ├── CS6--Cs00_required_packages.R │ ├── CS6--Cs00_required_packages.tex │ ├── CS6--Cs01_plotdata.R │ ├── CS6--Cs01_plotdata.pdf │ ├── CS6--Cs01_plotdata.tex │ ├── CS6--Cs02_mod-nile-0.R │ ├── CS6--Cs02_mod-nile-0.tex │ ├── CS6--Cs03_fit-data-0.R │ ├── CS6--Cs03_fit-data-0.tex │ ├── CS6--Cs04_mod-nile-1.R │ ├── CS6--Cs04_mod-nile-1.tex │ ├── CS6--Cs05_fit-data-1.R │ ├── CS6--Cs05_fit-data-1.tex │ ├── CS6--Cs06_mod-nile-2.R │ ├── CS6--Cs06_mod-nile-2.tex │ ├── CS6--Cs07_fit-data-2.R │ ├── CS6--Cs07_fit-data-2.tex │ ├── CS6--Cs08_plotfit.R │ ├── CS6--Cs08_plotfit.pdf │ ├── CS6--Cs08_plotfit.tex │ ├── CS6--Cs09_compute-resids.R │ ├── CS6--Cs09_compute-resids.tex │ ├── CS6--Cs10_plotoutliertests.R │ ├── CS6--Cs10_plotoutliertests.pdf │ ├── CS6--Cs10_plotoutliertests.tex │ ├── CS6--Cs11_plotresids.R │ ├── CS6--Cs11_plotresids.pdf │ ├── CS6--Cs11_plotresids.tex │ ├── CS6--RUNFIRST.R │ ├── CS6--RUNFIRST.tex │ ├── CS6--Reset.R │ ├── CS6--Reset.tex │ ├── CS6--fit-data-koop.R │ ├── CS6--fit-data-koop.tex │ ├── CS6--fit-mod-www.R │ ├── CS6--fit-mod-www.tex │ ├── CS6--fit-mod3.R │ ├── CS6--fit-mod3.tex │ ├── CS6--mod-nile-3.R │ ├── CS6--mod-nile-3.tex │ ├── CS6--plotslopetests-nile.R │ ├── CS6--plotslopetests-nile.pdf │ ├── CS6--plotslopetests-nile.tex │ ├── CS6--plotslopetests-www.R │ ├── CS6--plotslopetests-www.pdf │ ├── CS6--plotslopetests-www.tex │ ├── CS7--Cs01_load.wolf.data.R │ ├── CS7--Cs01_load.wolf.data.tex │ ├── CS7--Cs02_plotwolfmoosedata.R │ ├── CS7--Cs02_plotwolfmoosedata.pdf │ ├── CS7--Cs02_plotwolfmoosedata.tex │ ├── CS7--Cs03_z.score.wolf.data.R │ ├── CS7--Cs03_z.score.wolf.data.tex │ ├── CS7--Cs04_fit.model.R │ ├── CS7--Cs04_fit.model.tex │ ├── CS7--Cs05_fit.model.R0.R │ ├── CS7--Cs05_fit.model.R0.tex │ ├── CS7--Cs05_fit.model.tinitx1.R │ ├── CS7--Cs05_fit.model.tinitx1.tex │ ├── CS7--Cs06_print-wolf.B.R │ ├── CS7--Cs06_print-wolf.B.tex │ ├── CS7--Cs07_prep-cov-wolf-moose.R │ ├── CS7--Cs07_prep-cov-wolf-moose.tex │ ├── CS7--Cs08_cov.wolf.moose.model.R │ ├── CS7--Cs08_cov.wolf.moose.model.tex │ ├── CS7--Cs09_fit-cov-wolf-moose-model.R │ ├── CS7--Cs09_fit-cov-wolf-moose-model.tex │ ├── CS7--Cs10_figwolfcov.R │ ├── CS7--Cs10_figwolfcov.pdf │ ├── CS7--Cs10_figwolfcov.tex │ ├── CS7--Cs11_bad-data-2.R │ ├── CS7--Cs11_bad-data-2.tex │ ├── CS7--Cs12_load-plankton-data.R │ ├── CS7--Cs12_load-plankton-data.tex │ ├── CS7--Cs13_plot-plankton-data.R │ ├── CS7--Cs13_plot-plankton-data.pdf │ ├── CS7--Cs13_plot-plankton-data.tex │ ├── CS7--Cs14_set-up-plankton-model.R │ ├── CS7--Cs14_set-up-plankton-model.tex │ ├── CS7--Cs15_fit-plank-model-0.R │ ├── CS7--Cs15_fit-plank-model-0.tex │ ├── CS7--Cs16_print-B-0.R │ ├── CS7--Cs16_print-B-0.tex │ ├── CS7--Cs17_print-B-Ives.R │ ├── CS7--Cs17_print-B-Ives.tex │ ├── CS7--Cs18_test-rm-NAs.R │ ├── CS7--Cs18_test-rm-NAs.tex │ ├── CS7--Cs19_fit-plank-model-1.R │ ├── CS7--Cs19_fit-plank-model-1.tex │ ├── CS7--Cs20_print-B-1.R │ ├── CS7--Cs20_print-B-1.tex │ ├── CS7--Cs21_B-2.R │ ├── CS7--Cs21_B-2.tex │ ├── CS7--Cs22_fit-plank-model-2.R │ ├── CS7--Cs22_fit-plank-model-2.tex │ ├── CS7--Cs23_print-B-2.R │ ├── CS7--Cs23_print-B-2.tex │ ├── CS7--Cs24_fit-plank-model-3.R │ ├── CS7--Cs24_fit-plank-model-3.tex │ ├── CS7--Cs25_prep-covariates.R │ ├── CS7--Cs25_prep-covariates.tex │ ├── CS7--Cs26_add-covar-model-3.R │ ├── CS7--Cs26_add-covar-model-3.tex │ ├── CS7--Cs27_plank-model-4.R │ ├── CS7--Cs27_plank-model-4.tex │ ├── CS7--Cs28_print-C.R │ ├── CS7--Cs28_print-C.tex │ ├── CS7--Cs29_add-fish-to-data.R │ ├── CS7--Cs29_add-fish-to-data.tex │ ├── CS7--Cs30_B-covar.R │ ├── CS7--Cs30_B-covar.tex │ ├── CS7--Cs31_C-covar.R │ ├── CS7--Cs31_C-covar.tex │ ├── CS7--Cs32_R.covar.R │ ├── CS7--Cs32_R.covar.tex │ ├── CS7--Cs33_Q-covar.R │ ├── CS7--Cs33_Q-covar.tex │ ├── CS7--Cs34_fit-covar-model.R │ ├── CS7--Cs34_fit-covar-model.tex │ ├── CS7--Cs35_print-B.R │ ├── CS7--Cs35_print-B.tex │ ├── CS7--Cs36_logLik-variates.R │ ├── CS7--Cs36_logLik-variates.tex │ ├── CS7--Cs37_BQ.5.R │ ├── CS7--Cs37_BQ.5.tex │ ├── CS7--Cs38_max.eigen.R │ ├── CS7--Cs38_max.eigen.tex │ ├── CS7--Cs39_max.eig.kron.b.R │ ├── CS7--Cs39_max.eig.kron.b.tex │ ├── CS7--Cs40_Vinfty.R │ ├── CS7--Cs40_Vinfty.tex │ ├── CS7--Cs41_det.b.squared.R │ ├── CS7--Cs41_det.b.squared.tex │ ├── CS7--Cs42_det.b.scaled.R │ ├── CS7--Cs42_det.b.scaled.tex │ ├── CS7--Cs43_covar.sigma.Vinf.R │ ├── CS7--Cs43_covar.sigma.Vinf.tex │ ├── CS7--Cs44_worse.case.reactivity.R │ ├── CS7--Cs44_worse.case.reactivity.tex │ ├── CS7--RUNFIRST.R │ ├── CS7--RUNFIRST.tex │ ├── CS7--Reset.R │ ├── CS7--Reset.tex │ ├── CS7--bad.wolf.model.R │ ├── CS7--bad.wolf.model.tex │ ├── CS7--makemodeltable.R │ ├── CS7--makemodeltable.tex │ ├── CS8--Cs000_required_libraries.R │ ├── CS8--Cs000_required_libraries.tex │ ├── CS8--Cs001_readinredddata.R │ ├── CS8--Cs001_readinredddata.tex │ ├── CS8--Cs002_fig1.R │ ├── CS8--Cs002_fig1.pdf │ ├── CS8--Cs002_fig1.tex │ ├── CS8--Cs003_reddmodel1.R │ ├── CS8--Cs003_reddmodel1.tex │ ├── CS8--Cs004_reddmodel2.R │ ├── CS8--Cs004_reddmodel2.tex │ ├── CS8--Cs005_reddmodel3.R │ ├── CS8--Cs005_reddmodel3.tex │ ├── CS8--Cs005b_aic.R │ ├── CS8--Cs005b_aic.tex │ ├── CS8--Cs006_fig2.R │ ├── CS8--Cs006_fig2.pdf │ ├── CS8--Cs006_fig2.tex │ ├── CS8--Cs007_birddata.R │ ├── CS8--Cs007_birddata.tex │ ├── CS8--Cs008_plot-bird-data.R │ ├── CS8--Cs008_plot-bird-data.pdf │ ├── CS8--Cs008_plot-bird-data.tex │ ├── CS8--Cs009_fit-bird-model-1.R │ ├── CS8--Cs009_fit-bird-model-1.tex │ ├── CS8--Cs011_fit-bird-model-2.R │ ├── CS8--Cs011_fit-bird-model-2.tex │ ├── CS8--Cs013_fit-bird-model-3.R │ ├── CS8--Cs013_fit-bird-model-3.tex │ ├── CS8--Cs015_fit-bird-model-4.R │ ├── CS8--Cs015_fit-bird-model-4.tex │ ├── CS8--Cs016_aics.R │ ├── CS8--Cs016_aics.tex │ ├── CS8--Cs017_plot-bird-model-4-fits.R │ ├── CS8--Cs017_plot-bird-model-4-fits.pdf │ ├── CS8--Cs017_plot-bird-model-4-fits.tex │ ├── CS8--RUNFIRST.R │ ├── CS8--RUNFIRST.tex │ ├── CS8--Reset.R │ ├── CS8--Reset.tex │ ├── CS8--fig3.R │ ├── CS8--fig3.pdf │ ├── CS8--fig3.tex │ ├── CS8--fishmodel1.R │ ├── CS8--fishmodel1.tex │ ├── CS8--fishmodel2.R │ ├── CS8--fishmodel2.tex │ ├── CS8--fishmodel3.R │ ├── CS8--fishmodel3.tex │ ├── CS8--fit-rockfish1.R │ ├── CS8--fit-rockfish1.tex │ ├── CS8--fit-rockfish2.R │ ├── CS8--fit-rockfish2.tex │ ├── CS8--fitanalysis3.R │ ├── CS8--fitanalysis3.tex │ ├── CS8--getdat4.R │ ├── CS8--getdat4.tex │ ├── CS8--legend.R │ ├── CS8--legend.tex │ ├── CS8--rockfish1.R │ ├── CS8--rockfish1.pdf │ ├── CS8--rockfish1.tex │ ├── CS8--rockfish2.R │ ├── CS8--rockfish2.pdf │ ├── CS8--rockfish2.tex │ ├── CS8--set-up-rock-A.R │ ├── CS8--set-up-rock-A.tex │ ├── CS8--set-up-rockfish-data.R │ ├── CS8--set-up-rockfish-data.tex │ ├── CS8--setargs4.R │ ├── CS8--setargs4.tex │ ├── CS8--test-rock.R │ ├── CS8--test-rock.tex │ ├── CS8--testing.R │ ├── CS8--testing.tex │ ├── CSDLM--Cs_01_readindata.R │ ├── CSDLM--Cs_01_readindata.tex │ ├── CSDLM--Cs_02_zscore.R │ ├── CSDLM--Cs_02_zscore.tex │ ├── CSDLM--Cs_030_plotdata.R │ ├── CSDLM--Cs_030_plotdata.pdf │ ├── CSDLM--Cs_030_plotdata.tex │ ├── CSDLM--Cs_031_univDLMproc.R │ ├── CSDLM--Cs_031_univDLMproc.tex │ ├── CSDLM--Cs_04_univDLMobs.R │ ├── CSDLM--Cs_04_univDLMobs.tex │ ├── CSDLM--Cs_05_univDLM-list.R │ ├── CSDLM--Cs_05_univDLM-list.tex │ ├── CSDLM--Cs_06_univDLM-fit.R │ ├── CSDLM--Cs_06_univDLM-fit.tex │ ├── CSDLM--Cs_07_plotdlm1.R │ ├── CSDLM--Cs_07_plotdlm1.pdf │ ├── CSDLM--Cs_07_plotdlm1.tex │ ├── CSDLM--Cs_08_univDLM-fore-mean.R │ ├── CSDLM--Cs_08_univDLM-fore-mean.tex │ ├── CSDLM--Cs_09_univDLM-fore-Var.R │ ├── CSDLM--Cs_09_univDLM-fore-Var.tex │ ├── CSDLM--Cs_10_plot-dlm-Forecast-Logit.R │ ├── CSDLM--Cs_10_plot-dlm-Forecast-Logit.pdf │ ├── CSDLM--Cs_10_plot-dlm-Forecast-Logit.tex │ ├── CSDLM--Cs_11_plot-dlm-Forecast-Raw.R │ ├── CSDLM--Cs_11_plot-dlm-Forecast-Raw.pdf │ ├── CSDLM--Cs_11_plot-dlm-Forecast-Raw.tex │ ├── CSDLM--Cs_12_dlm-forecast-errors.R │ ├── CSDLM--Cs_12_dlm-forecast-errors.tex │ ├── CSDLM--Cs_13_plot-dlmQQ.R │ ├── CSDLM--Cs_13_plot-dlmQQ.pdf │ ├── CSDLM--Cs_13_plot-dlmQQ.tex │ ├── CSDLM--Cs_14_dlm-Innov-t-test.R │ ├── CSDLM--Cs_14_dlm-Innov-t-test.tex │ ├── CSDLM--Cs_15_plot-dlm-ACF.R │ ├── CSDLM--Cs_15_plot-dlm-ACF.pdf │ ├── CSDLM--Cs_15_plot-dlm-ACF.tex │ ├── CSDLM--RUNFIRST.R │ ├── CSDLM--RUNFIRST.tex │ ├── CSDLM--Reset.R │ ├── CSDLM--Reset.tex │ ├── CSDLM--dlm-QQplot.R │ ├── CSDLM--dlm-QQplot.tex │ ├── CSDLM--dlmACFplot.R │ ├── CSDLM--dlmACFplot.tex │ ├── Covar--Covar_sec0_required_libraries.R │ ├── Covar--Covar_sec0_required_libraries.tex │ ├── Covar--Covar_sec2_1_load-plankton-data.R │ ├── Covar--Covar_sec2_1_load-plankton-data.tex │ ├── Covar--Covar_sec2_2_z-score-covar-data.R │ ├── Covar--Covar_sec2_2_z-score-covar-data.tex │ ├── Covar--Covar_sec2_3_plot-dat.R │ ├── Covar--Covar_sec2_3_plot-dat.pdf │ ├── Covar--Covar_sec2_3_plot-dat.tex │ ├── Covar--Covar_sec3_1_covar-model-0.R │ ├── Covar--Covar_sec3_1_covar-model-0.tex │ ├── Covar--Covar_sec3_2_covar-model-0b.R │ ├── Covar--Covar_sec3_2_covar-model-0b.tex │ ├── Covar--Covar_sec4_1_covar-model-1.R │ ├── Covar--Covar_sec4_1_covar-model-1.tex │ ├── Covar--Covar_sec4_2_covar-model-1c.R │ ├── Covar--Covar_sec4_2_covar-model-1c.tex │ ├── Covar--Covar_sec5_1_covar-model-5.R │ ├── Covar--Covar_sec5_1_covar-model-5.tex │ ├── Covar--Covar_sec6_01_set-up-seasonal-dat.R │ ├── Covar--Covar_sec6_01_set-up-seasonal-dat.tex │ ├── Covar--Covar_sec6_02_set-up-month-factors.R │ ├── Covar--Covar_sec6_02_set-up-month-factors.tex │ ├── Covar--Covar_sec6_03_C-constrained.R │ ├── Covar--Covar_sec6_03_C-constrained.tex │ ├── Covar--Covar_sec6_04_C-constrained2.R │ ├── Covar--Covar_sec6_04_C-constrained2.tex │ ├── Covar--Covar_sec6_05_month-factor-marss-params.R │ ├── Covar--Covar_sec6_05_month-factor-marss-params.tex │ ├── Covar--Covar_sec6_06_fit-month-factor-with-MARSS.R │ ├── Covar--Covar_sec6_06_fit-month-factor-with-MARSS.tex │ ├── Covar--Covar_sec6_07_poly-month-factor.R │ ├── Covar--Covar_sec6_07_poly-month-factor.tex │ ├── Covar--Covar_sec6_08_seasonal-effect-poly.R │ ├── Covar--Covar_sec6_08_seasonal-effect-poly.tex │ ├── Covar--Covar_sec6_09_seasonal-fourier.R │ ├── Covar--Covar_sec6_09_seasonal-fourier.tex │ ├── Covar--Covar_sec6_10_seasonal-fourier-fit.R │ ├── Covar--Covar_sec6_10_seasonal-fourier-fit.tex │ ├── Covar--Covar_sec6_11_seasonal-effects-fourier.R │ ├── Covar--Covar_sec6_11_seasonal-effects-fourier.tex │ ├── Covar--Covar_sec6_12_plot-seas-effects.R │ ├── Covar--Covar_sec6_12_plot-seas-effects.pdf │ ├── Covar--Covar_sec6_12_plot-seas-effects.tex │ ├── Covar--Covar_sec6_13_show-aics.R │ ├── Covar--Covar_sec6_13_show-aics.tex │ ├── Covar--Covar_sec7_01_diag-code.R │ ├── Covar--Covar_sec7_01_diag-code.tex │ ├── Covar--Covar_sec7_02_plot-acf-1.R │ ├── Covar--Covar_sec7_02_plot-acf-1.pdf │ ├── Covar--Covar_sec7_02_plot-acf-1.tex │ ├── Covar--Covar_sec7_03_plot-acf-2.R │ ├── Covar--Covar_sec7_03_plot-acf-2.pdf │ ├── Covar--Covar_sec7_03_plot-acf-2.tex │ ├── Covar--Covar_sec7_04_plot-acf-2.R │ ├── Covar--Covar_sec7_04_plot-acf-2.pdf │ ├── Covar--Covar_sec7_04_plot-acf-2.tex │ ├── Covar--RUNFIRST.R │ ├── Covar--RUNFIRST.tex │ ├── Covar--get-LL-aug-2.R │ ├── Covar--get-LL-aug-2.tex │ ├── Covar--get-LL-aug.R │ ├── Covar--get-LL-aug.tex │ ├── Covar--reset.R │ ├── Covar--reset.tex │ ├── Fig1.jpg │ ├── KFAS--054.R │ ├── KFAS--054.tex │ ├── KFAS--Cs00_required-libraries.R │ ├── KFAS--Cs00_required-libraries.tex │ ├── KFAS--Cs101_fitting-models.R │ ├── KFAS--Cs101_fitting-models.tex │ ├── KFAS--Cs102_fitting-models.R │ ├── KFAS--Cs102_fitting-models.tex │ ├── KFAS--Cs103_fitting-models.R │ ├── KFAS--Cs103_fitting-models.tex │ ├── KFAS--Cs104_fitting-models.R │ ├── KFAS--Cs104_fitting-models.tex │ ├── KFAS--Cs105_fitting-models.R │ ├── KFAS--Cs105_fitting-models.tex │ ├── KFAS--Cs106_fitting-models.R │ ├── KFAS--Cs106_fitting-models.tex │ ├── KFAS--Cs107_fitting-models.R │ ├── KFAS--Cs107_fitting-models.tex │ ├── KFAS--Cs201_state-filtering.R │ ├── KFAS--Cs201_state-filtering.tex │ ├── KFAS--Cs202_state-filtering.R │ ├── KFAS--Cs202_state-filtering.tex │ ├── KFAS--Cs203_state-filtering.R │ ├── KFAS--Cs203_state-filtering.tex │ ├── KFAS--Cs204_state-filtering.R │ ├── KFAS--Cs204_state-filtering.tex │ ├── KFAS--Cs205_state-filtering.R │ ├── KFAS--Cs205_state-filtering.tex │ ├── KFAS--Cs206_state-filtering.R │ ├── KFAS--Cs206_state-filtering.tex │ ├── KFAS--Cs207_state-filtering.R │ ├── KFAS--Cs207_state-filtering.tex │ ├── KFAS--Cs208_state-filtering.R │ ├── KFAS--Cs208_state-filtering.tex │ ├── KFAS--Cs209_state-filtering.R │ ├── KFAS--Cs209_state-filtering.tex │ ├── KFAS--Cs301_obs-filtering.R │ ├── KFAS--Cs301_obs-filtering.tex │ ├── KFAS--Cs302_obs-filtering.R │ ├── KFAS--Cs302_obs-filtering.tex │ ├── KFAS--Cs304_obs-filtering.R │ ├── KFAS--Cs304_obs-filtering.tex │ ├── KFAS--Cs305_obs-filtering.R │ ├── KFAS--Cs305_obs-filtering.tex │ ├── KFAS--Cs306_obs-filtering.R │ ├── KFAS--Cs306_obs-filtering.tex │ ├── KFAS--Cs307_obs-filtering.R │ ├── KFAS--Cs307_obs-filtering.tex │ ├── KFAS--Cs308_obs-filtering.R │ ├── KFAS--Cs308_obs-filtering.tex │ ├── KFAS--Cs401_conf-int.R │ ├── KFAS--Cs401_conf-int.tex │ ├── KFAS--Cs402_conf-int.R │ ├── KFAS--Cs402_conf-int.tex │ ├── KFAS--Cs403_conf-int.R │ ├── KFAS--Cs403_conf-int.tex │ ├── KFAS--Cs404_conf-int.R │ ├── KFAS--Cs404_conf-int.tex │ ├── KFAS--Cs405_conf-int.R │ ├── KFAS--Cs405_conf-int.tex │ ├── KFAS--Cs406_conf-int.R │ ├── KFAS--Cs406_conf-int.tex │ ├── KFAS--Cs407_conf-int.R │ ├── KFAS--Cs407_conf-int.tex │ ├── KFAS--Cs408_conf-int.R │ ├── KFAS--Cs408_conf-int.tex │ ├── KFAS--Cs409_conf-int.R │ ├── KFAS--Cs409_conf-int.tex │ ├── KFAS--Cs410_conf-int.R │ ├── KFAS--Cs410_conf-int.tex │ ├── KFAS--Cs411_conf-int.R │ ├── KFAS--Cs411_conf-int.tex │ ├── KFAS--Cs412_conf-int.R │ ├── KFAS--Cs412_conf-int.tex │ ├── KFAS--Cs501_plotting.R │ ├── KFAS--Cs501_plotting.pdf │ ├── KFAS--Cs501_plotting.tex │ ├── KFAS--Cs501_residuals.R │ ├── KFAS--Cs501_residuals.tex │ ├── KFAS--Cs502_plotting.R │ ├── KFAS--Cs502_plotting.pdf │ ├── KFAS--Cs502_plotting.tex │ ├── KFAS--Cs502_residuals.R │ ├── KFAS--Cs502_residuals.tex │ ├── KFAS--Cs503_plotting.R │ ├── KFAS--Cs503_plotting.pdf │ ├── KFAS--Cs503_plotting.tex │ ├── KFAS--Cs503_residuals.R │ ├── KFAS--Cs503_residuals.tex │ ├── KFAS--Cs504_residuals.R │ ├── KFAS--Cs504_residuals.tex │ ├── KFAS--Cs505_residuals.R │ ├── KFAS--Cs505_residuals.tex │ ├── KFAS--Cs506_residuals.R │ ├── KFAS--Cs506_residuals.tex │ ├── KFAS--Cs507_residuals.R │ ├── KFAS--Cs507_residuals.tex │ ├── KFAS--Cs508_residuals.R │ ├── KFAS--Cs508_residuals.tex │ ├── KFAS--Cs509_residuals.R │ ├── KFAS--Cs509_residuals.tex │ ├── KFAS--Cs510_residuals.R │ ├── KFAS--Cs510_residuals.tex │ ├── KFAS--Cs601_missing-values.R │ ├── KFAS--Cs601_missing-values.tex │ ├── KFAS--Cs602_missing-values.R │ ├── KFAS--Cs602_missing-values.tex │ ├── KFAS--Cs603_missing-values.R │ ├── KFAS--Cs603_missing-values.tex │ ├── KFAS--Cs604_marss-mult-fig-2.R │ ├── KFAS--Cs604_marss-mult-fig-2.pdf │ ├── KFAS--Cs604_marss-mult-fig-2.tex │ ├── KFAS--Cs605_missing-values.R │ ├── KFAS--Cs605_missing-values.tex │ ├── KFAS--Cs606_missing-values.R │ ├── KFAS--Cs606_missing-values.pdf │ ├── KFAS--Cs606_missing-values.tex │ ├── KFAS--Cs701_globaltemp.R │ ├── KFAS--Cs701_globaltemp.pdf │ ├── KFAS--Cs701_globaltemp.tex │ ├── KFAS--Cs702_globaltemp.R │ ├── KFAS--Cs702_globaltemp.tex │ ├── KFAS--Cs703_globaltemp.R │ ├── KFAS--Cs703_globaltemp.tex │ ├── KFAS--Cs704_globaltemp.R │ ├── KFAS--Cs704_globaltemp.tex │ ├── KFAS--Cs705_globaltemp.R │ ├── KFAS--Cs705_globaltemp.pdf │ ├── KFAS--Cs705_globaltemp.tex │ ├── KFAS--Cs706_globaltemp.R │ ├── KFAS--Cs706_globaltemp.tex │ ├── KFAS--Cs707_globaltemp.R │ ├── KFAS--Cs707_globaltemp.pdf │ ├── KFAS--Cs707_globaltemp.tex │ ├── KFAS--Cs708_globaltemp.R │ ├── KFAS--Cs708_globaltemp.tex │ ├── KFAS--RUNFIRST.R │ ├── KFAS--RUNFIRST.tex │ ├── KFAS--reset.R │ ├── KFAS--reset.tex │ ├── MCI--Cs_mci_001.R │ ├── MCI--Cs_mci_001.tex │ ├── MCI--Cs_mci_002.R │ ├── MCI--Cs_mci_002.tex │ ├── MCI--Cs_mci_003.R │ ├── MCI--Cs_mci_003.tex │ ├── MCI--Cs_mci_004.R │ ├── MCI--Cs_mci_004.tex │ ├── MCI--Cs_mci_005.R │ ├── MCI--Cs_mci_005.tex │ ├── MCI--Cs_mci_006.R │ ├── MCI--Cs_mci_006.tex │ ├── MCI--Cs_mci_007.R │ ├── MCI--Cs_mci_007.tex │ ├── MCI--Cs_mci_008.R │ ├── MCI--Cs_mci_008.tex │ ├── MCI--Cs_mci_009.R │ ├── MCI--Cs_mci_009.tex │ ├── MCI--Cs_mci_010.R │ ├── MCI--Cs_mci_010.tex │ ├── MCI--Cs_mci_0101.R │ ├── MCI--Cs_mci_0101.tex │ ├── MCI--Cs_mci_011.R │ ├── MCI--Cs_mci_011.tex │ ├── MCI--Cs_mci_012.R │ ├── MCI--Cs_mci_012.tex │ ├── MCI--RUNFIRST.R │ ├── MCI--RUNFIRST.tex │ ├── MCI--reset.R │ ├── MCI--reset.tex │ ├── MLR--Cs_000_required_libraries.R │ ├── MLR--Cs_000_required_libraries.tex │ ├── MLR--Cs_001_example1_plot.R │ ├── MLR--Cs_001_example1_plot.pdf │ ├── MLR--Cs_001_example1_plot.tex │ ├── MLR--Cs_002_example1-data.R │ ├── MLR--Cs_002_example1-data.tex │ ├── MLR--Cs_003_example1-params.R │ ├── MLR--Cs_003_example1-params.tex │ ├── MLR--Cs_004_example1-params1.R │ ├── MLR--Cs_004_example1-params1.tex │ ├── MLR--Cs_005_example1-paramsR.R │ ├── MLR--Cs_005_example1-paramsR.tex │ ├── MLR--Cs_006_example1-paramsD.R │ ├── MLR--Cs_006_example1-paramsD.tex │ ├── MLR--Cs_007_example1-eVar.R │ ├── MLR--Cs_007_example1-eVar.tex │ ├── MLR--Cs_008_example1-marss.R │ ├── MLR--Cs_008_example1-marss.tex │ ├── MLR--Cs_009_example1-marss.R │ ├── MLR--Cs_009_example1-marss.tex │ ├── MLR--Cs_010_example1-lm.R │ ├── MLR--Cs_010_example1-lm.tex │ ├── MLR--Cs_011_example2-params.R │ ├── MLR--Cs_011_example2-params.tex │ ├── MLR--Cs_012_example2-marss.R │ ├── MLR--Cs_012_example2-marss.tex │ ├── MLR--Cs_013_example2-marss-with-inits.R │ ├── MLR--Cs_013_example2-marss-with-inits.tex │ ├── MLR--Cs_014_example2-gls.R │ ├── MLR--Cs_014_example2-gls.tex │ ├── MLR--Cs_014b_compare_marss_gls.R │ ├── MLR--Cs_014b_compare_marss_gls.tex │ ├── MLR--Cs_015_example2-plot.R │ ├── MLR--Cs_015_example2-plot.pdf │ ├── MLR--Cs_015_example2-plot.tex │ ├── MLR--Cs_016_full-model-list.R │ ├── MLR--Cs_016_full-model-list.tex │ ├── MLR--Cs_017_full-model-fit.R │ ├── MLR--Cs_017_full-model-fit.tex │ ├── MLR--Cs_018_full-em-ests.R │ ├── MLR--Cs_018_full-em-ests.tex │ ├── MLR--Cs_019_full-bfgs-ests.R │ ├── MLR--Cs_019_full-bfgs-ests.tex │ ├── MLR--Cs_020_full-lm-ests.R │ ├── MLR--Cs_020_full-lm-ests.tex │ ├── MLR--Cs_021_full-model-correrr.R │ ├── MLR--Cs_021_full-model-correrr.tex │ ├── MLR--Cs_022_full-correrr-fit-hide.R │ ├── MLR--Cs_022_full-correrr-fit-hide.tex │ ├── MLR--Cs_023_full-correrr-em-ests.R │ ├── MLR--Cs_023_full-correrr-em-ests.tex │ ├── MLR--Cs_024_full-correrr-bfgs-ests.R │ ├── MLR--Cs_024_full-correrr-bfgs-ests.tex │ ├── MLR--Cs_025_full-gls-ests.R │ ├── MLR--Cs_025_full-gls-ests.tex │ ├── MLR--Cs_026_loadsleep.R │ ├── MLR--Cs_026_loadsleep.tex │ ├── MLR--Cs_027_sleep-plot.R │ ├── MLR--Cs_027_sleep-plot.pdf │ ├── MLR--Cs_027_sleep-plot.tex │ ├── MLR--Cs_028_setupdata.R │ ├── MLR--Cs_028_setupdata.tex │ ├── MLR--Cs_029_sleepmod1.R │ ├── MLR--Cs_029_sleepmod1.tex │ ├── MLR--Cs_030_sleepmod1-lm.R │ ├── MLR--Cs_030_sleepmod1-lm.tex │ ├── MLR--Cs_031_sleepmod2.R │ ├── MLR--Cs_031_sleepmod2.tex │ ├── MLR--Cs_032_sleepmod2-lm.R │ ├── MLR--Cs_032_sleepmod2-lm.tex │ ├── MLR--Cs_033_sleepmod3.R │ ├── MLR--Cs_033_sleepmod3.tex │ ├── MLR--Cs_034_sleepmod4.R │ ├── MLR--Cs_034_sleepmod4.tex │ ├── MLR--Cs_035_sleepmod5.R │ ├── MLR--Cs_035_sleepmod5.tex │ ├── MLR--Cs_036_mod5-gls.R │ ├── MLR--Cs_036_mod5-gls.tex │ ├── MLR--Cs_037_makemodeltable.R │ ├── MLR--Cs_037_makemodeltable.tex │ ├── MLR--RUNFIRST.R │ ├── MLR--RUNFIRST.tex │ ├── MLR--reset.R │ ├── MLR--reset.tex │ ├── QE--Cs00_load_library.R │ ├── QE--Cs00_load_library.tex │ ├── QE--Cs01_model-gen-spec.R │ ├── QE--Cs01_model-gen-spec.tex │ ├── QE--Cs02_model-general.R │ ├── QE--Cs02_model-general.tex │ ├── QE--Cs03_enterdata.R │ ├── QE--Cs03_enterdata.tex │ ├── QE--Cs04_model-default.R │ ├── QE--Cs04_model-default.tex │ ├── QE--Cs05_B-setup.R │ ├── QE--Cs05_B-setup.tex │ ├── QE--Cs06_model-default-time.R │ ├── QE--Cs06_model-default-time.tex │ ├── QE--Cs07_model-bfgs.R │ ├── QE--Cs07_model-bfgs.tex │ ├── QE--Cs08_model-bfgs-time.R │ ├── QE--Cs08_model-bfgs-time.tex │ ├── QE--Cs09_model-bfgs2.R │ ├── QE--Cs09_model-bfgs2.tex │ ├── QE--Cs10_model-default.R │ ├── QE--Cs10_model-default.tex │ ├── QE--Cs11_model-corr1.R │ ├── QE--Cs11_model-corr1.tex │ ├── QE--Cs12_model-corr2.R │ ├── QE--Cs12_model-corr2.tex │ ├── QE--Cs13_model-u-NS.R │ ├── QE--Cs13_model-u-NS.tex │ ├── QE--Cs14_model-u-NS-fixR.R │ ├── QE--Cs14_model-u-NS-fixR.tex │ ├── QE--Cs15_model-pan1.R │ ├── QE--Cs15_model-pan1.tex │ ├── QE--Cs16_model-pan2.R │ ├── QE--Cs16_model-pan2.tex │ ├── QE--Cs17_model-two1.R │ ├── QE--Cs17_model-two1.tex │ ├── QE--Cs17_model-two2.R │ ├── QE--Cs17_model-two2.tex │ ├── QE--Cs18_model-time-varying.R │ ├── QE--Cs18_model-time-varying.tex │ ├── QE--Cs19_model-print.R │ ├── QE--Cs19_model-print.tex │ ├── QE--Cs19b_model-time-varying2.R │ ├── QE--Cs19b_model-time-varying2.tex │ ├── QE--Cs20_model-summary.R │ ├── QE--Cs20_model-summary.tex │ ├── QE--Cs23_model-print-R.R │ ├── QE--Cs23_model-print-R.tex │ ├── QE--Cs24_model-tidy-R.R │ ├── QE--Cs24_model-tidy-R.tex │ ├── QE--Cs25_CIs-hessian.R │ ├── QE--Cs25_CIs-hessian.tex │ ├── QE--Cs26_print-CIs.R │ ├── QE--Cs26_print-CIs.tex │ ├── QE--Cs27_CIs-pboot.R │ ├── QE--Cs27_CIs-pboot.tex │ ├── QE--Cs28_parvec.R │ ├── QE--Cs28_parvec.tex │ ├── QE--Cs29_tsSmooth.R │ ├── QE--Cs29_tsSmooth.tex │ ├── QE--Cs30_marsskf.R │ ├── QE--Cs30_marsskf.tex │ ├── QE--Cs31_like.kem.degen.R │ ├── QE--Cs31_like.kem.degen.tex │ ├── QE--Cs32_like.kem200.R │ ├── QE--Cs32_like.kem200.tex │ ├── QE--Cs33_like.kem.allow.degen.R │ ├── QE--Cs33_like.kem.allow.degen.tex │ ├── QE--Cs34_like.kem200.R │ ├── QE--Cs34_like.kem200.tex │ ├── QE--Cs35_boot.R │ ├── QE--Cs35_boot.tex │ ├── QE--Cs36_sim.R │ ├── QE--Cs36_sim.tex │ ├── QE--Cs37_sim-fit.R │ ├── QE--Cs37_sim-fit.tex │ ├── QE--Cs38_sim-like.R │ ├── QE--Cs38_sim-like.tex │ ├── QE--Cs39_AICb.R │ ├── QE--Cs39_AICb.tex │ ├── QE--RUNFIRST.R │ ├── QE--RUNFIRST.tex │ ├── QE--model.spec2.R │ ├── QE--model.spec2.tex │ ├── QE--reset.R │ ├── QE--reset.tex │ ├── STS--Cs00_required-libraries.R │ ├── STS--Cs00_required-libraries.tex │ ├── STS--Cs101_structTS-level.R │ ├── STS--Cs101_structTS-level.tex │ ├── STS--Cs102_structTS-level.R │ ├── STS--Cs102_structTS-level.tex │ ├── STS--Cs103_structTS-level.R │ ├── STS--Cs103_structTS-level.tex │ ├── STS--Cs104_structTS-level.R │ ├── STS--Cs104_structTS-level.pdf │ ├── STS--Cs104_structTS-level.tex │ ├── STS--Cs201_structTS-leveltrend.R │ ├── STS--Cs201_structTS-leveltrend.tex │ ├── STS--Cs202_structTS-leveltrend.R │ ├── STS--Cs202_structTS-leveltrend.tex │ ├── STS--Cs203_structTS-leveltrend.R │ ├── STS--Cs203_structTS-leveltrend.tex │ ├── STS--Cs204_structTS-leveltrend.R │ ├── STS--Cs204_structTS-leveltrend.tex │ ├── STS--Cs205_structTS-leveltrend.R │ ├── STS--Cs205_structTS-leveltrend.pdf │ ├── STS--Cs205_structTS-leveltrend.tex │ ├── STS--Cs301_structTS-bsm.R │ ├── STS--Cs301_structTS-bsm.tex │ ├── STS--Cs302_structTS-bsm.R │ ├── STS--Cs302_structTS-bsm.tex │ ├── STS--Cs303_structTS-bsm.R │ ├── STS--Cs303_structTS-bsm.tex │ ├── STS--Cs304_structTS-bsm.R │ ├── STS--Cs304_structTS-bsm.pdf │ ├── STS--Cs304_structTS-bsm.tex │ ├── STS--Cs401_forecast.R │ ├── STS--Cs401_forecast.tex │ ├── STS--Cs402_forecast.R │ ├── STS--Cs402_forecast.tex │ ├── STS--Cs403_forecast.R │ ├── STS--Cs403_forecast.tex │ ├── STS--Cs404_forecast.R │ ├── STS--Cs404_forecast.tex │ ├── STS--Cs405_forecast.R │ ├── STS--Cs405_forecast.pdf │ ├── STS--Cs405_forecast.tex │ ├── STS--Cs501_fitted.R │ ├── STS--Cs501_fitted.pdf │ ├── STS--Cs501_fitted.tex │ ├── STS--Cs502_fitted.R │ ├── STS--Cs502_fitted.tex │ ├── STS--Cs503_fitted.R │ ├── STS--Cs503_fitted.pdf │ ├── STS--Cs503_fitted.tex │ ├── STS--Cs504_fitted.R │ ├── STS--Cs504_fitted.pdf │ ├── STS--Cs504_fitted.tex │ ├── STS--Cs505_fitted.R │ ├── STS--Cs505_fitted.pdf │ ├── STS--Cs505_fitted.tex │ ├── STS--Cs601_residuals.R │ ├── STS--Cs601_residuals.tex │ ├── STS--Cs602_residuals.R │ ├── STS--Cs602_residuals.tex │ ├── STS--Cs603_residuals.R │ ├── STS--Cs603_residuals.pdf │ ├── STS--Cs603_residuals.tex │ ├── STS--Cs701_multivariate.R │ ├── STS--Cs701_multivariate.tex │ ├── STS--Cs702_multivariate.R │ ├── STS--Cs702_multivariate.pdf │ ├── STS--Cs702_multivariate.tex │ ├── STS--Cs703_multivariate.R │ ├── STS--Cs703_multivariate.tex │ ├── STS--Cs704_multivariate.R │ ├── STS--Cs704_multivariate.tex │ ├── STS--Cs705_multivariate.R │ ├── STS--Cs705_multivariate.tex │ ├── STS--Cs706_multivariate.R │ ├── STS--Cs706_multivariate.tex │ ├── STS--Cs707_multivariate.R │ ├── STS--Cs707_multivariate.pdf │ ├── STS--Cs707_multivariate.tex │ ├── STS--Cs708_multivariate.R │ ├── STS--Cs708_multivariate.pdf │ ├── STS--Cs708_multivariate.tex │ ├── STS--Cs709_multivariate.R │ ├── STS--Cs709_multivariate.tex │ ├── STS--Cs710_multivariate.R │ ├── STS--Cs710_multivariate.pdf │ ├── STS--Cs710_multivariate.tex │ ├── STS--Cs711_multivariate.R │ ├── STS--Cs711_multivariate.pdf │ ├── STS--Cs711_multivariate.tex │ ├── STS--Cs712_multivariate.R │ ├── STS--Cs712_multivariate.pdf │ ├── STS--Cs712_multivariate.tex │ ├── STS--Cs713_multivariate.R │ ├── STS--Cs713_multivariate.tex │ ├── STS--Cs714_multivariate.R │ ├── STS--Cs714_multivariate.pdf │ ├── STS--Cs714_multivariate.tex │ ├── STS--Cs715_multivariate.R │ ├── STS--Cs715_multivariate.pdf │ ├── STS--Cs715_multivariate.tex │ ├── STS--Cs716_multivariate.R │ ├── STS--Cs716_multivariate.tex │ ├── STS--Cs717_multivariate.R │ ├── STS--Cs717_multivariate.pdf │ ├── STS--Cs717_multivariate.tex │ ├── STS--Cs718_multivariate.R │ ├── STS--Cs718_multivariate.tex │ ├── STS--Cs719_multivariate.R │ ├── STS--Cs719_multivariate.tex │ ├── STS--Cs720_multivariate.R │ ├── STS--Cs720_multivariate.pdf │ ├── STS--Cs720_multivariate.tex │ ├── STS--RUNFIRST.R │ ├── STS--RUNFIRST.tex │ ├── STS--reset.R │ ├── STS--reset.tex │ └── tablesleepstudy.tex │ ├── footmisc.sty │ ├── hanging.sty │ ├── manual_files │ ├── AR2SS100.RData │ ├── CS4--model_fits.RData │ ├── Case_Study_1.Rnw │ ├── Case_Study_2.Rnw │ ├── Case_Study_3.Rnw │ ├── Case_Study_4.Rnw │ ├── Case_Study_5.Rnw │ ├── Case_Study_6.Rnw │ ├── Case_Study_7.Rnw │ ├── Case_Study_8.Rnw │ ├── Case_Study_dlm1.Rnw │ ├── Case_Study_mlr.Rnw │ ├── Chapter_Residuals.Rnw │ ├── Covariates.Rnw │ ├── Including_GH.Rnw │ ├── KFAS.Rnw │ ├── MARp.Rnw │ ├── Manual.Rnw │ ├── Quick_Examples.Rnw │ ├── Setting_Inits.Rnw │ └── Structural_TS.Rnw │ ├── svmono.cls │ ├── tables │ ├── tablefit.tex │ └── tableplank.tex │ └── tex │ ├── Algorithms.aux │ ├── Algorithms.tex │ ├── Directions.aux │ ├── Directions.tex │ ├── Functions.aux │ ├── Functions.tex │ ├── Introduction.aux │ ├── Introduction.tex │ ├── MARSS.aux │ ├── MARSS.tex │ ├── Manual.bib │ ├── ModelSpec.aux │ ├── ModelSpec.tex │ ├── SSreferences.aux │ ├── SSreferences.tex │ ├── dedic.aux │ ├── dedic.tex │ ├── headerfile.tex │ ├── mathdefs.tex │ ├── obj_structures.aux │ ├── obj_structures.tex │ ├── preface.aux │ ├── preface.tex │ ├── warnings.aux │ └── warnings.tex ├── man ├── CSEGriskfigure.Rd ├── CSEGtmufigure.Rd ├── MARSS-package.Rd ├── MARSS.Rd ├── MARSSFisherI.Rd ├── MARSS_dfa.Rd ├── MARSS_marss.Rd ├── MARSS_marxss.Rd ├── MARSS_vectorized.Rd ├── MARSSaic.Rd ├── MARSSapplynames.Rd ├── MARSSboot.Rd ├── MARSScv.Rd ├── MARSSfit.Rd ├── MARSSharveyobsFI.Rd ├── MARSShatyt.Rd ├── MARSShessian.Rd ├── MARSShessian_numerical.Rd ├── MARSSinfo.Rd ├── MARSSinits.Rd ├── MARSSinnovationsboot.Rd ├── MARSSkem.Rd ├── MARSSkemcheck.Rd ├── MARSSkf.Rd ├── MARSSoptim.Rd ├── MARSSparamCIs.Rd ├── MARSSresiduals.Rd ├── MARSSresiduals_tT.Rd ├── MARSSresiduals_tt1.Rd ├── MARSSresiduals_ttt.Rd ├── MARSSsimulate.Rd ├── MARSSvectorizeparam.Rd ├── SalmonSurvCUI.Rd ├── accuracy_marssMLE.Rd ├── allowed.Rd ├── as_marssMODEL.Rd ├── checkMARSSInputs.Rd ├── checkModelList.Rd ├── coef_marssMLE.Rd ├── datasets.Rd ├── describe_marssMODEL.Rd ├── fitted_marssMLE.Rd ├── forecast_marssMLE.Rd ├── glance_marssMLE.Rd ├── graywhales.Rd ├── harborSeal.Rd ├── is_marssMLE.Rd ├── is_marssMODEL.Rd ├── isleRoyal.Rd ├── ldiag.Rd ├── logLik_marssMLE.Rd ├── loggerhead.Rd ├── marssMLE-class.Rd ├── marssMODEL-class.Rd ├── marssPredict-class.Rd ├── marssResiduals-class.Rd ├── match_arg_exact.Rd ├── model_frame_marssMODEL.Rd ├── plankton.Rd ├── plot_marssMLE.Rd ├── plot_marssPredict.Rd ├── plot_marssResiduals.Rd ├── predict_help.Rd ├── predict_marssMLE.Rd ├── print_marssMLE.Rd ├── print_marssMODEL.Rd ├── print_marssPredict.Rd ├── residuals_marssMLE.Rd ├── stdInnov.Rd ├── summary_marssMLE.Rd ├── sysdata.Rd ├── tidy_marssMLE.Rd ├── toLatex_marssMLE.Rd ├── tsSmooth_marssMLE.Rd ├── utility_functions.Rd └── zscore.Rd ├── pkgdown ├── _pkgdown.yml ├── extra.js ├── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ └── favicon-32x32.png └── templates │ └── head.html └── vignettes ├── EMDerivation.Rnw ├── EMDerivation.bib ├── Learning_MARSS.Rmd ├── Quick_Start.Rmd ├── Residuals.Rnw ├── 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/inst/userguide/figures/ARMAp--B.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | [,1] [,2] [,3] [,4] 4 | [1,] "b1" 0 "b2" 0 5 | [2,] 0 "b1" 0 "b2" 6 | [3,] 1 0 0 0 7 | [4,] 0 1 0 0 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_000_required_libraries.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 2: Cs_000_required_libraries 3 | ################################################### 4 | library(MARSS) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_000_required_libraries.tex: -------------------------------------------------------------------------------- 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MARSS(sim.ar2[3:TT], model = model.list.2) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_104_ar2-fit.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 7: Cs_104_ar2-fit 3 | ################################################### 4 | print(cbind(true = true.2[2:4], estimates = coef(ar2, type = "vector"))) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_105_ar2-gappy.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | gappy.data <- sim.ar2[3:TT] 4 | gappy.data[floor(runif(TT / 2, 2, TT))] <- NA 5 | ar2.gappy <- MARSS(gappy.data, model = model.list.2, fun.kf="MARSSkfss") 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_107_arima.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 10: Cs_107_arima 3 | ################################################### 4 | arima(gappy.data, order = c(2, 0, 0), include.mean = FALSE) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_201_mar2-sim.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | TT <- 50 4 | true.2 <- c(r = 0, b1 = -1.5, b2 = -0.75, q = 1) 5 | temp1 <- arima.sim(n = TT, list(ar = true.2[c("b1", "b2")]), 6 | sd = sqrt(true.2["q"])) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_202_mar2-sim.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | temp2 <- arima.sim(n = TT, list(ar = true.2[c("b1", "b2")]), 4 | sd = sqrt(true.2["q"])) 5 | sim.mar2 <- rbind(temp1, temp2) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_204_mar2-fit.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 19: Cs_204_mar2-fit 3 | ################################################### 4 | mar2 <- MARSS(sim.mar2[, 2:TT], model = model.list.2m) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_204_mar2-fit.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mar2 <- MARSS(sim.mar2[, 2:TT], model = model.list.2m) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_206_compare-mars.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | true est.mar2 est.mar2a est.mar2b 4 | b1 -1.50 -1.4206301 -0.7209367 -1.3506409 5 | b2 -0.75 -0.7642604 -0.3954671 -0.6953739 6 | q 1.00 0.8986820 3.2098084 1.5552943 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_303_fit-ar3.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 25: Cs_303_fit-ar3 3 | ################################################### 4 | ar3 <- MARSS(sim.ar3[3:TT], model = model.list.3) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_303_fit-ar3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | ar3 <- MARSS(sim.ar3[3:TT], model = model.list.3) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_401_setseed5.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 27: Cs_401_setseed5 3 | ################################################### 4 | set.seed(14) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/ARMAp--Cs_401_setseed5.tex: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /inst/userguide/figures/CS1--Cs1_Exercise4.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | par(mfrow = c(1, 1)) 4 | CSEGtmufigure(N = 50, u = -0.05, s2p = 0.02) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS1--Cs1_a_required_libraries.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 2: Cs1_a_required_libraries 3 | ################################################### 4 | library(MARSS) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS1--Cs1_a_required_libraries.tex: -------------------------------------------------------------------------------- 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################################################### 2 | ### code chunk number 22: figTMU 3 | ################################################### 4 | par(mfrow = c(1, 1)) 5 | CSEGtmufigure(N = nYr, u = sim.u, s2p = sim.Q) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS1--figTMU.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS1--figTMU.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS1--figTMU.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS1--figTMU.tex -------------------------------------------------------------------------------- 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| \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--026.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 26: Case_Study_2.Rnw:578-579 (eval = FALSE) 3 | ################################################### 4 | ## R.model <- ldiag(c("boat", "boat", "plane", "plane", "plane")) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--026.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | R.model <- ldiag(c("boat", "boat", "plane", "plane", "plane")) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--027.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 27: Case_Study_2.Rnw:583-584 (eval = FALSE) 3 | ################################################### 4 | ## U.model <- matrix(c("puget sound", "puget sound", "hood canal"), 3, 1) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--027.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | U.model <- matrix(c("puget sound", "puget sound", "hood canal"), 3, 1) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-AIC2.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 15: Cs2-AIC2 3 | ################################################### 4 | c(kem1$AIC, kem2$AIC) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-AIC2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | c(kem1$AIC, kem2$AIC) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] 8.813447 -9.323982 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-analysis2obsvariance.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 12: Cs2-analysis2obsvariance 3 | ################################################### 4 | coef(kem1, type = "matrix")$R 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-analysis3-UQ.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 19: Cs2-analysis3-UQ (eval = FALSE) 3 | ################################################### 4 | ## U.model <- "equal" 5 | ## Q.model <- "diagonal and equal" 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-analysis3-UQ.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | U.model <- "equal" 4 | Q.model <- "diagonal and equal" 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-analysis3-Z.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Z.model <- matrix(c(1, 1, 0, 0, 0, 0, 0, 1, 1, 1), 5, 2) 4 | Z.model <- factor(c(1, 1, 2, 2, 2)) 5 | Z.model <- factor(c("N", "N", "S", "S", "S")) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-fig5.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 16: Cs2-fig5 3 | ################################################### 4 | plot(kem2, plot.type="model.resids.ytT") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-fig5.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS2--Cs2-fig5.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-fig5.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | plot type = model.resids.ytT 4 | \end{Soutput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-fitanalysis2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Z.model <- factor(c(1, 1, 1, 1, 1)) 4 | R.model <- "diagonal and unequal" 5 | kem2 <- MARSS(dat, model = list(Z = Z.model, R = R.model)) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-readindata.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | dat <- t(harborSealWA) # Transpose 4 | years <- dat[1, ] # [1,] means row 1 5 | n <- nrow(dat) - 1 6 | dat <- dat[2:nrow(dat), ] # no years 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-residuals-analysis3-fig6.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 21: Cs2-residuals-analysis3-fig6 3 | ################################################### 4 | plot(kem3, plot.type="model.resids.ytT", silent=TRUE) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-residuals-analysis3-fig6.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS2--Cs2-residuals-analysis3-fig6.pdf 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| \begin{Schunk} 2 | \begin{Sinput} 3 | R.model <- "diagonal and unequal" 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2-showdata.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 5: Cs2-showdata 3 | ################################################### 4 | print(harborSealWA[1:8, ], digits = 3) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Cs2_Code5_7.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS2--Cs2_Code5_7.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--RUNFIRST.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 1: RUNFIRST 3 | ################################################### 4 | library(MARSS) 5 | options(prompt = " ", continue = " ") 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--RUNFIRST.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS2--RUNFIRST.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--Reset.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 28: Reset 3 | ################################################### 4 | 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| ################################################### 2 | ### code chunk number 6: funccallwithconstraints (eval = FALSE) 3 | ################################################### 4 | ## kem1 <- MARSS(dat, model = list(Z = Z.model, R = R.model)) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--funccallwithconstraints.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem1 <- MARSS(dat, model = list(Z = Z.model, R = R.model)) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--norun3.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 23: norun3 (eval = FALSE) 3 | ################################################### 4 | ## Q.model <- "equalvarcov" 5 | ## Q.model <- matrix(c("q", "c", "c", "q"), 2, 2) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--norun3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Q.model <- "equalvarcov" 4 | Q.model <- matrix(c("q", "c", "c", "q"), 2, 2) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--noshow-listkem1.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 11: noshow-listkem1 (eval = FALSE) 3 | ################################################### 4 | ## names(kem1) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--noshow-listkem1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | names(kem1) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--noshowlegend.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS2--noshowlegend.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--setvarcov1.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 8: setvarcov1 3 | ################################################### 4 | R.model <- "diagonal and equal" 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--setvarcov1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | R.model <- "diagonal and equal" 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--setwhichPop.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 7: setwhichPop 3 | ################################################### 4 | Z.model <- factor(c(1, 1, 1, 1, 1)) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS2--setwhichPop.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Z.model <- factor(c(1, 1, 1, 1, 1)) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs00_required_libraries.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 2: Cs00_required_libraries 3 | ################################################### 4 | library(MARSS) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs00_required_libraries.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS3--Cs00_required_libraries.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs01_set.up.data.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | years <- harborSeal[, 1] # first col is years 4 | # leave off Hood Canal data for now 5 | sealData <- t(harborSeal[, c(2:7, 9:13)]) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs02_fig1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS3--Cs02_fig1.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs02_fig1.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS3--Cs02_fig1.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs04_Q.models.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 12: Cs04_Q.models 3 | ################################################### 4 | Q.models <- c("diagonal and equal", "diagonal and unequal") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs04_Q.models.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Q.models <- c("diagonal and equal", "diagonal and unequal") 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs06_sort.results.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 15: Cs06_sort.results 3 | ################################################### 4 | min.AICc <- order(out.tab$AICc) 5 | out.tab.1 <- out.tab[min.AICc, ] 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs06_sort.results.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | min.AICc <- order(out.tab$AICc) 4 | out.tab.1 <- out.tab[min.AICc, ] 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs07_add.delta.aicc.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 16: Cs07_add.delta.aicc 3 | ################################################### 4 | out.tab.1 <- cbind(out.tab.1, 5 | delta.AICc = out.tab.1$AICc - out.tab.1$AICc[1] 6 | ) 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs07_add.delta.aicc.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | out.tab.1 <- cbind(out.tab.1, 4 | delta.AICc = out.tab.1$AICc - out.tab.1$AICc[1] 5 | ) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs08_add.delta.aicc.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 17: Cs08_add.delta.aicc 3 | ################################################### 4 | out.tab.1 <- cbind(out.tab.1, 5 | rel.like = exp(-1 * out.tab.1$delta.AICc / 2) 6 | ) 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs08_add.delta.aicc.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | out.tab.1 <- cbind(out.tab.1, 4 | rel.like = exp(-1 * out.tab.1$delta.AICc / 2) 5 | ) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs09_aic.weight.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 18: Cs09_aic.weight 3 | ################################################### 4 | out.tab.1 <- cbind(out.tab.1, 5 | AIC.weight = out.tab.1$rel.like / sum(out.tab.1$rel.like) 6 | ) 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs09_aic.weight.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | out.tab.1 <- cbind(out.tab.1, 4 | AIC.weight = out.tab.1$rel.like / sum(out.tab.1$rel.like) 5 | ) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs11_fignorthsouth.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS3--Cs11_fignorthsouth.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs11_fignorthsouth.tex: -------------------------------------------------------------------------------- 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/inst/userguide/figures/CS3--Cs17_Q.diag.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 27: Cs17_Q.diag 3 | ################################################### 4 | diag(Q.unc) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs17_Q.diag.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | diag(Q.unc) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | nc is ps sc 7 | 0.009049512 0.007451479 0.004598690 0.005276587 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs19_add.hood.canal.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | sealData.hc <- rbind(sealData, harborSeal[, 8]) 4 | rownames(sealData.hc)[12] <- "Hood.Canal" 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Cs22_hood-q3.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 32: Cs22_hood-q3 3 | ################################################### 4 | Q.models$hood.independent 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Q.model1.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 7: Q.model1 3 | ################################################### 4 | Q.model <- matrix(list(0), 3, 3) 5 | diag(Q.model) <- c("q1", "q2", "q3") 6 | Q.model 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Q.model2.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 8: Q.model2 3 | ################################################### 4 | Q.model <- matrix(list(0), 3, 3) 5 | diag(Q.model) <- "q" 6 | Q.model 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Q.model3.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 21: Q.model3 3 | ################################################### 4 | #identical variances 5 | Q.model <- matrix("c", 3, 3) 6 | diag(Q.model) <- "q" 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Q.model3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | #identical variances 4 | Q.model <- matrix("c", 3, 3) 5 | diag(Q.model) <- "q" 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--RUNFIRST.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 1: RUNFIRST 3 | ################################################### 4 | library(MARSS) 5 | options(prompt=" ", continue=" ") 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--RUNFIRST.tex: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 5: Z.model.1 3 | ################################################### 4 | Z1 <- factor(c("wa.or", "wa.or", rep("ps", 4), 5 | "ca", "ca", "wa.or", "wa.or", "bc")) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--Z.model.1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Z1 <- factor(c("wa.or", "wa.or", rep("ps", 4), 4 | "ca", "ca", "wa.or", "wa.or", "bc")) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--kemcall.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 3: kemcall (eval = FALSE) 3 | ################################################### 4 | ## fit <- MARSS(sealData, model=list( 5 | ## Z = Z.model, Q = Q.model, ...)) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS3--kemcall.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | fit <- MARSS(sealData, model=list( 4 | Z = Z.model, Q = Q.model, ...)) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs00_required_libraries.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 2: Cs00_required_libraries 3 | ################################################### 4 | library(MARSS) 5 | library(xtable) 6 | 7 | 8 | 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-------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 6: Cs03b_zscore 3 | ################################################### 4 | dat.z <- zscore(dat.spp.1980) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs03b_zscore.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | dat.z <- zscore(dat.spp.1980) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs04_plotdata.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS4--Cs04_plotdata.pdf 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code chunk number 10: Cs07_setupQR 3 | ################################################### 4 | Q <- B <- diag(1, 3) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs07_setupQR.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Q <- B <- diag(1, 3) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs09_printR.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 12: Cs09_printR 3 | ################################################### 4 | print(R) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs10_setupR_short.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 13: Cs10_setupR_short 3 | ################################################### 4 | R <- "diagonal and unequal" 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs10_setupR_short.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | R <- "diagonal and unequal" 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs11_setupU.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 14: Cs11_setupU 3 | ################################################### 4 | x0 <- U <- matrix(0, nrow = 3, ncol = 1) 5 | A <- matrix(0, nrow = 6, ncol = 1) 6 | x0 <- U <- A <- "zero" 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs11_setupU.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | x0 <- U <- matrix(0, nrow = 3, ncol = 1) 4 | A <- matrix(0, nrow = 6, ncol = 1) 5 | x0 <- U <- A <- "zero" 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs12_setupx0.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 15: Cs12_setupx0 3 | ################################################### 4 | V0 <- diag(5, 3) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs12_setupx0.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | V0 <- diag(5, 3) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs13_define_model_list.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | dfa.model <- list( 4 | Z = Z, A = "zero", R = R, B = B, U = U, 5 | Q = Q, x0 = x0, V0 = V0 6 | ) 7 | cntl.list <- list(maxit = 50) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS4--Cs14_fit_data.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 17: Cs14_fit_data 3 | 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levels(loggerheadNoisy$turtle) 5 | turtles 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs03_data3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | turtlename <- "BigMama" 4 | theTurtle <- which(loggerheadNoisy$turtle == turtlename) 5 | dat <- loggerheadNoisy[theTurtle, 5:6] 6 | dat <- t(dat) # transpose 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs05_badtagfig.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS5--Cs05_badtagfig.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs05_badtagfig.tex: 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pred.lon[i - 1], pred.lon[i], 5 | pred.lat[i - 1], pred.lat[i] 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs13_disfig.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 15: Cs13_disfig 3 | ################################################### 4 | par(mfrow = c(1, 1)) 5 | hist(distance) # make a histogram of distance traveled per day 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs13_disfig.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS5--Cs13_disfig.pdf -------------------------------------------------------------------------------- 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################################################### 4 | levels(loggerheadNoisy$turtle) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs16_turt-names.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | levels(loggerheadNoisy$turtle) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] "BigMama" "Bruiser" "Humpty" "Isabelle" "Johanna" 7 | [6] "MaryLee" "TBA" "Yoto" 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS5--Cs18_code.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS5--Cs18_code.tex -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # load the datasets package 4 | library(datasets) 5 | data(Nile) # load the data 6 | plot(Nile, ylab = "Flow volume", xlab = "") 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs02_mod-nile-0.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod.nile.0 <- list( 4 | Z = matrix(1), A = matrix(0), R = matrix("r"), 5 | B = matrix(1), U = matrix(0), Q = matrix(0), 6 | x0 = matrix("a") 7 | ) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs04_mod-nile-1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod.nile.1 <- list( 4 | Z = matrix(1), A = matrix(0), R = matrix("r"), 5 | B = matrix(1), U = matrix("u"), Q = matrix(0), 6 | x0 = matrix("a") 7 | ) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs05_fit-data-1.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 7: Cs05_fit-data-1 3 | ################################################### 4 | kem.1 <- MARSS(dat, model = mod.nile.1, silent = TRUE) 5 | summary(kem.1) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs06_mod-nile-2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod.nile.2 <- list( 4 | Z = matrix(1), A = matrix(0), R = matrix("r"), 5 | B = matrix(1), U = matrix(0), Q = matrix("q"), 6 | x0 = matrix("pi") 7 | ) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs08_plotfit.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS6--Cs08_plotfit.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs08_plotfit.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS6--Cs08_plotfit.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--Cs10_plotoutliertests.pdf: -------------------------------------------------------------------------------- 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################################################### 2 | ### code chunk number 17: plotslopetests-nile 3 | ################################################### 4 | plot(WWWusage, xlab = "") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--plotslopetests-nile.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS6--plotslopetests-nile.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS6--plotslopetests-nile.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS6--plotslopetests-nile.tex -------------------------------------------------------------------------------- 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log(t(isleRoyal[yr1960to2011, c("Wolf", "Moose")])) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs02_plotwolfmoosedata.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS7--Cs02_plotwolfmoosedata.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs03_z.score.wolf.data.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # if missing values are in the data, they should be NAs 4 | z.royale.dat <- zscore(royale.dat) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs09_fit-cov-wolf-moose-model.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 11: Cs09_fit-cov-wolf-moose-model 3 | ################################################### 4 | kem.3 <- MARSS(z.royale.dat, model = royale.model.3) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs10_figwolfcov.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS7--Cs10_figwolfcov.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs10_figwolfcov.tex: -------------------------------------------------------------------------------- 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/inst/userguide/figures/CS7--Cs13_plot-plankton-data.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS7--Cs13_plot-plankton-data.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs15_fit-plank-model-0.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 18: Cs15_fit-plank-model-0 3 | ################################################### 4 | kem.plank.0 <- MARSS(d.plank.dat, model = plank.model.0) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs15_fit-plank-model-0.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.plank.0 <- MARSS(d.plank.dat, model = plank.model.0) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs17_print-B-Ives.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | LP SP D ND 4 | LP 0.48 -0.39 -- -- 5 | SP -- 0.25 -0.17 -0.11 6 | D -- -- 0.74 0.00 7 | ND -- 0.10 0.00 0.60 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs18_test-rm-NAs.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | test.dat <- d.plank.dat[, !is.na(d.plank.dat[1, ])] 4 | test <- MARSS(test.dat, model = plank.model.0) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs19_fit-plank-model-1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | plank.model.1 <- plank.model.0 4 | plank.model.1$Q <- "unconstrained" 5 | kem.plank.1 <- MARSS(d.plank.dat, model = plank.model.1) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs20_print-B-1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | LP SP D ND 4 | LP 0.4961 0.061 0.079 0.123 5 | SP -0.1833 0.896 0.067 0.011 6 | D 0.1180 0.350 0.638 0.370 7 | ND 0.0023 0.370 -0.122 0.810 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs22_fit-plank-model-2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # model 2 4 | plank.model.2 <- plank.model.1 5 | plank.model.2$B <- B.2 6 | kem.plank.2 <- MARSS(d.plank.dat, model = plank.model.2) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs23_print-B-2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | LP SP D ND 4 | LP 0.65 -0.33 -- -- 5 | SP -- 0.54 0.0016 -0.026 6 | D -- -- 0.8349 -- 7 | ND -- 0.13 -- 0.596 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs24_fit-plank-model-3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # model 3 4 | plank.model.3 <- plank.model.2 5 | plank.model.3$R <- diag(c(.04, .04, .16, .16)) 6 | kem.plank.3 <- MARSS(d.plank.dat, model = plank.model.3) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs26_add-covar-model-3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | plank.model.4 <- plank.model.3 4 | plank.model.4$C <- matrix(list("C11", "C21", 0, 0), 4, 1) 5 | plank.model.4$c <- d.phos 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs27_plank-model-4.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 30: Cs27_plank-model-4 3 | ################################################### 4 | kem.plank.4 <- MARSS(d.plank.dat, model = plank.model.4) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs27_plank-model-4.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.plank.4 <- MARSS(d.plank.dat, model = plank.model.4) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs28_print-C.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | [,1] 4 | LP 0.14 5 | SP 0.16 6 | D -- 7 | ND -- 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs31_C-covar.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 34: Cs31_C-covar 3 | ################################################### 4 | C <- matrix(list("C11", "C21", 0, 0, 0), 5, 1) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs31_C-covar.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | C <- matrix(list("C11", "C21", 0, 0, 0), 5, 1) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs32_R.covar.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 35: Cs32_R.covar 3 | ################################################### 4 | R <- matrix(list(0), 5, 5) 5 | diag(R) <- list(0.04, 0.04, 0.16, 0.16, 0.36) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs32_R.covar.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | R <- matrix(list(0), 5, 5) 4 | diag(R) <- list(0.04, 0.04, 0.16, 0.16, 0.36) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs35_print-B.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Soutput} 3 | LP SP D ND 4 | LP 0.61 -0.465 -- -- 5 | SP -- 0.333 -0.019 -0.048 6 | D -- -- 0.896 -- 7 | ND -- 0.044 -- 0.675 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs36_logLik-variates.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 40: Cs36_logLik-variates 3 | ################################################### 4 | tmp <- kem.plank.5 5 | tmp$marss$data[5, ] <- NA 6 | LL.variates <- MARSSkf(tmp)$logLik 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs36_logLik-variates.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | tmp <- kem.plank.5 4 | tmp$marss$data[5, ] <- NA 5 | LL.variates <- MARSSkf(tmp)$logLik 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs37_BQ.5.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 41: Cs37_BQ.5 3 | ################################################### 4 | B <- coef(kem.plank.5, type = "matrix")$B[1:4, 1:4] 5 | Q <- coef(kem.plank.5, type = "matrix")$Q[1:4, 1:4] 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs37_BQ.5.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | B <- coef(kem.plank.5, type = "matrix")$B[1:4, 1:4] 4 | Q <- coef(kem.plank.5, type = "matrix")$Q[1:4, 1:4] 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs38_max.eigen.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 42: Cs38_max.eigen 3 | ################################################### 4 | max(eigen(B)$values) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs38_max.eigen.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | max(eigen(B)$values) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] 0.8964988 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs39_max.eig.kron.b.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 43: Cs39_max.eig.kron.b 3 | ################################################### 4 | max(eigen(kronecker(B, B))$values) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs39_max.eig.kron.b.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | max(eigen(kronecker(B, B))$values) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] 0.8037101 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs40_Vinfty.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | m <- nrow(B) 4 | vecV <- solve(diag(m * m) - kronecker(B, B)) %*% as.vector(Q) 5 | V_inf <- matrix(vecV, nrow = m, ncol = m) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs41_det.b.squared.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 45: Cs41_det.b.squared 3 | ################################################### 4 | abs(det(B))^2 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs41_det.b.squared.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | abs(det(B))^2 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] 0.01559078 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs42_det.b.scaled.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 46: Cs42_det.b.scaled 3 | ################################################### 4 | abs(det(B))^(2 / nrow(B)) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs42_det.b.scaled.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | abs(det(B))^(2 / nrow(B)) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] 0.3533596 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs43_covar.sigma.Vinf.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 47: Cs43_covar.sigma.Vinf 3 | ################################################### 4 | -sum(diag(Q)) / sum(diag(V_inf)) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs43_covar.sigma.Vinf.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | -sum(diag(Q)) / sum(diag(V_inf)) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] -0.346845 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs44_worse.case.reactivity.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 48: Cs44_worse.case.reactivity 3 | ################################################### 4 | max(eigen(t(B) %*% B)$values) - 1 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Cs44_worse.case.reactivity.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | max(eigen(t(B) %*% B)$values) - 1 4 | \end{Sinput} 5 | \begin{Soutput} 6 | [1] -0.1957795 7 | \end{Soutput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--RUNFIRST.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 1: RUNFIRST 3 | ################################################### 4 | library(MARSS) 5 | options(prompt = " ", continue = " ") 6 | library(xtable) 7 | tabledir <- "tables/" 8 | 9 | 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--RUNFIRST.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS7--RUNFIRST.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Reset.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 49: Reset 3 | ################################################### 4 | options(prompt = "> ", continue = "+ ") 5 | options(width = 120) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--Reset.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS7--Reset.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS7--makemodeltable.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS7--makemodeltable.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs000_required_libraries.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 2: Cs000_required_libraries 3 | ################################################### 4 | library(MARSS) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs000_required_libraries.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--Cs000_required_libraries.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs001_readinredddata.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 3: Cs001_readinredddata 3 | ################################################### 4 | head(okanaganRedds) 5 | logRedds <- log(t(okanaganRedds)[c("aerial", "ground"), ]) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs002_fig1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--Cs002_fig1.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs002_fig1.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--Cs002_fig1.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs003_reddmodel1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | model1 <- list() 4 | model1$R <- "diagonal and equal" 5 | model1$Z <- matrix(1, 2, 1) 6 | model1$A <- "scaling" 7 | kem1 <- MARSS(logRedds, model = model1) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs004_reddmodel2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | model2 <- model1 # model2 is based on model1 4 | model2$R <- "diagonal and unequal" 5 | kem2 <- MARSS(logRedds, model = model2) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs005b_aic.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 8: Cs005b_aic 3 | ################################################### 4 | c(mod1 = kem1$AICc, mod2 = kem2$AICc, mod3 = kem3$AICc) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs005b_aic.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | c(mod1 = kem1$AICc, mod2 = kem2$AICc, mod3 = kem3$AICc) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | mod1 mod2 mod3 7 | 133.9804 136.2164 174.1392 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs006_fig2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--Cs006_fig2.pdf 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\end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs016_aics.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 32: Cs016_aics 3 | ################################################### 4 | c(mod1 = kem.b1$AICc, mod2 = kem.b2$AICc, 5 | mod3 = kem.b3$AICc, mod4 = kem.b4$AICc) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Cs017_plot-bird-model-4-fits.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--Cs017_plot-bird-model-4-fits.pdf -------------------------------------------------------------------------------- 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", continue="+ ") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--Reset.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--Reset.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--fig3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--fig3.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--fig3.tex: -------------------------------------------------------------------------------- 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| -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--fit-rockfish2.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 14: fit-rockfish2 3 | ################################################### 4 | kem.rock2 <- MARSS(flatrecdat, model = list(A = A.model, Q = matrix(0.01))) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--fitanalysis3.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 25: fitanalysis3 3 | ################################################### 4 | model4 <- list(Z = Z4, Q = Q.model, R = R.model4, U = U.model) 5 | kem4 <- MARSS(t(dat4), model = model4) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--fitanalysis3.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | model4 <- list(Z = Z4, Q = Q.model, R = R.model4, U = U.model) 4 | kem4 <- MARSS(t(dat4), model = model4) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--rockfish1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--rockfish1.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--rockfish1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | graphics::matplot(rockfish[rec.years, 1], recdat, ylab = "", xlab = "Rec CPUE") 4 | title("Puget Sound Total Rockfish Recreational CPUE data") 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--rockfish2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--rockfish2.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--setargs4.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | n4 <- ncol(dat4) 4 | Z4 <- as.factor(rep(1, n4)) 5 | R.model4 <- matrix(list(0), n4, n4) 6 | diag(R.model4) <- list("1", "2", "2", "2", "2", "3", "4") 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--test-rock.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.rock3a <- MARSS(flatrecdat, model = list(A = A.model, tinitx = 0)) 4 | kem.rock3b <- MARSS(flatrecdat, model = list(A = A.model, tinitx = 1)) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CS8--testing.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CS8--testing.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_01_readindata.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | data(SalmonSurvCUI) 4 | years <- SalmonSurvCUI[, 1] 5 | TT <- length(years) 6 | # response data: logit(survival) 7 | dat <- matrix(SalmonSurvCUI[, 2], nrow = 1) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_02_zscore.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | CUI <- SalmonSurvCUI[, "CUI.apr"] 4 | CUI.z <- zscore(CUI) 5 | # number of state = # of regression params (slope(s) + intercept) 6 | m <- 1 + 1 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_030_plotdata.pdf: -------------------------------------------------------------------------------- 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\begin{Sinput} 3 | # forecast errors 4 | innov <- kf.out$Innov 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_13_plot-dlmQQ.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CSDLM--Cs_13_plot-dlmQQ.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_13_plot-dlmQQ.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CSDLM--Cs_13_plot-dlmQQ.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_14_dlm-Innov-t-test.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 17: Cs_14_dlm-Innov-t-test 3 | ################################################### 4 | # p-value for t-test of H0: E(innov) = 0 5 | t.test(t(innov), mu = 0)$p.value 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_14_dlm-Innov-t-test.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # p-value for t-test of H0: E(innov) = 0 4 | t.test(t(innov), mu = 0)$p.value 5 | \end{Sinput} 6 | \begin{Soutput} 7 | [1] 0.4840901 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Cs_15_plot-dlm-ACF.pdf: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 20: Reset 3 | ################################################### 4 | options(prompt = "> ", continue = "+ ") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--Reset.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/CSDLM--Reset.tex -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--dlm-QQplot.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # Q-Q plot of innovations 4 | qqnorm(t(innov), main = "", pch = 16, col = "blue") 5 | # add y=x line for easier interpretation 6 | qqline(t(innov)) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--dlmACFplot.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 18: dlmACFplot (eval = FALSE) 3 | ################################################### 4 | ## # plot ACF of innovations 5 | ## acf(t(innov), lag.max = 10) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/CSDLM--dlmACFplot.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # plot ACF of innovations 4 | acf(t(innov), lag.max = 10) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- 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| 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/Covar--get-LL-aug.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | y.aug <- rbind(data, covariates) 4 | fit.aug <- MARSS(y.aug, model = model.aug) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/Covar--reset.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 30: reset 3 | ################################################### 4 | options(prompt = "> ", continue = " +", width = 120) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/Covar--reset.tex: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod.nile <- list( 4 | Z = matrix(1), A = matrix(0), R = matrix("r"), 5 | B = matrix(1), U = matrix(0), Q = matrix("q"), 6 | tinitx = 1 7 | ) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs201_state-filtering.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | fit_kfas <- fit_kfas_stoch 4 | fit_marss <- fit_em_stoch 5 | fit_marss$par$Q[1, 1] <- fit_kfas$model$Q 6 | fit_marss$par$R[1, 1] <- fit_kfas$model$H 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs202_state-filtering.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kf_kfas <- KFS(fit_kfas$model, 4 | filtering = "state", 5 | smoothing = "state", simplify = FALSE 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs203_state-filtering.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 12: Cs203_state-filtering 3 | ################################################### 4 | kf_marss <- MARSSkfss(fit_marss) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs203_state-filtering.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kf_marss <- MARSSkfss(fit_marss) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs204_state-filtering.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 13: Cs204_state-filtering 3 | ################################################### 4 | names(kf_kfas) 5 | names(kf_marss) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs204_state-filtering.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | names(kf_kfas) 4 | names(kf_marss) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs205_state-filtering.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 14: Cs205_state-filtering 3 | ################################################### 4 | n <- 5 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs205_state-filtering.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/KFAS--Cs205_state-filtering.tex -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs207_state-filtering.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 16: Cs207_state-filtering 3 | ################################################### 4 | cbind(kf_kfas$alphahat[1:n], kf_marss$xtT[1:n]) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs301_obs-filtering.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kf_kfas <- KFS(fit_kfas$model, 4 | filtering = "signal", 5 | smoothing = "signal", simplify = FALSE 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs302_obs-filtering.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 20: Cs302_obs-filtering 3 | ################################################### 4 | kf_marss <- MARSSkf(fit_marss) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs302_obs-filtering.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kf_marss <- MARSSkf(fit_marss) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs304_obs-filtering.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 21: Cs304_obs-filtering 3 | ################################################### 4 | n <- 10 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs304_obs-filtering.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/KFAS--Cs304_obs-filtering.tex 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-------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs406_conf-int.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | pred_marss2 <- predict(fit_marss, 4 | type = "ytT", 5 | interval = "prediction", level = 0.95 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs408_conf-int.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 33: Cs408_conf-int 3 | ################################################### 4 | conf_marss1_t1 <- fitted(fit_marss, type = "ytt1", interval = "confidence") 5 | head(conf_marss1_t1) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs411_conf-int.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 36: Cs411_conf-int 3 | ################################################### 4 | pred_marss1_t1 <- fitted(fit_marss, type = "ytt1", interval = "prediction") 5 | head(pred_marss1_t1) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs412_conf-int.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | pred_marss2_t1 <- predict(fit_marss, 4 | type = "ytt1", 5 | interval = "prediction", level = 0.95 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs501_plotting.pdf: 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/inst/userguide/figures/KFAS--Cs502_plotting.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | plot.type <- ifelse(packageVersion("MARSS") < '3.11.4', "model.ytT", "fitted.ytT") 4 | plot(fit_marss, plot.type = plot.type, pi.int = TRUE) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs503_plotting.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/KFAS--Cs503_plotting.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--Cs604_marss-mult-fig-2.pdf: -------------------------------------------------------------------------------- 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################################################### 2 | ### code chunk number 67: reset 3 | ################################################### 4 | options(prompt = "> ", continue = " +", width = 120) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/KFAS--reset.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/KFAS--reset.tex -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_004.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 5: Cs_mci_004 3 | ################################################### 4 | coef(kem, what = "par") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_004.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | coef(kem, what = "par") 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_005.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 6: Cs_mci_005 3 | ################################################### 4 | out <- coef(kem, what = "par") 5 | out$D 6 | out$Q 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_007.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 8: Cs_mci_007 3 | ################################################### 4 | inits <- list(Q = matrix(c(1, 0.5, 0.7), 3, 1)) 5 | kem <- MARSS(dat, model = model.list, inits = inits) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_007.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | inits <- list(Q = matrix(c(1, 0.5, 0.7), 3, 1)) 4 | kem <- MARSS(dat, model = model.list, inits = inits) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_008.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | inits <- list(Q = matrix(c(1, 0.5, 0.7), 3, 1), D = 1) 4 | kem <- MARSS(dat, model = model.list, inits = inits) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_009.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 10: Cs_mci_009 3 | ################################################### 4 | inits <- list(D = coef(kem, what = "par")$D) 5 | kem <- MARSS(dat, model = model.list, inits = inits) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_009.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | inits <- list(D = coef(kem, what = "par")$D) 4 | kem <- MARSS(dat, model = model.list, inits = inits) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_010.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # create the par list from the output 4 | inits <- coef(kem, what = "par") 5 | bfgs <- MARSS(dat, model = model.list, inits = inits, method = "BFGS") 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_0101.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | # create the par list from the output 4 | bfgs <- MARSS(dat, model = model.list, inits = kem, method = "BFGS") 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MCI--Cs_mci_011.tex: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 4: Cs_002_example1-data 3 | ################################################### 4 | data(longley) 5 | Employed <- matrix(longley$Employed, nrow = 1) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_002_example1-data.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | data(longley) 4 | Employed <- matrix(longley$Employed, nrow = 1) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_003_example1-params.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 5: Cs_003_example1-params 3 | ################################################### 4 | longley.model <- list() 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_003_example1-params.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | longley.model <- list() 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_005_example1-paramsR.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 7: Cs_005_example1-paramsR 3 | ################################################### 4 | longley.model$R <- matrix("r") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_005_example1-paramsR.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | longley.model$R <- matrix("r") 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_006_example1-paramsD.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | longley.model$A <- matrix("intercept") 4 | longley.model$D <- matrix(c("GNP", "Pop"), nrow = 1) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_007_example1-eVar.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 9: Cs_007_example1-eVar 3 | ################################################### 4 | longley.model$d <- rbind(longley$GNP, longley$Population) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_007_example1-eVar.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | longley.model$d <- rbind(longley$GNP, longley$Population) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_008_example1-marss.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 10: Cs_008_example1-marss 3 | ################################################### 4 | mod1 <- MARSS(Employed, model = longley.model) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_008_example1-marss.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod1 <- MARSS(Employed, model = longley.model) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_009_example1-marss.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 11: Cs_009_example1-marss 3 | ################################################### 4 | coef(mod1, type = "vector") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_009_example1-marss.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | coef(mod1, type = "vector") 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_010_example1-lm.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 12: Cs_010_example1-lm 3 | ################################################### 4 | mod1.lm <- lm(Employed ~ GNP + Population, data = longley) 5 | coef(mod1.lm) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_011_example2-params.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | longley.ar1 <- longley.model 4 | longley.ar1$B <- matrix("b") 5 | longley.ar1$Q <- matrix("q") 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_012_example2-marss.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 14: Cs_012_example2-marss 3 | ################################################### 4 | mod2 <- MARSS(Employed, model = longley.ar1) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_012_example2-marss.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod2 <- MARSS(Employed, model = longley.ar1) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_014b_compare_marss_gls.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 17: Cs_014b_compare_marss_gls 3 | ################################################### 4 | rbind(MARSS = ests.marss, GLS = ests.gls) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_015_example2-plot.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 18: Cs_015_example2-plot 3 | ################################################### 4 | pairs(longley) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_015_example2-plot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--Cs_015_example2-plot.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_015_example2-plot.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--Cs_015_example2-plot.tex -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_017_full-model-fit.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod3.em <- MARSS(Employed, model = longley.model) 4 | mod3.bfgs <- MARSS(Employed, model = longley.model, method = "BFGS") 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_019_full-bfgs-ests.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 22: Cs_019_full-bfgs-ests 3 | ################################################### 4 | c(coef(mod3.bfgs, type = "vector")[par.names], logLik = mod3.bfgs$logLik) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_021_full-model-correrr.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | longley.correrr.model <- longley.model 4 | longley.correrr.model$B <- matrix("b") 5 | longley.correrr.model$Q <- matrix("q") 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_023_full-correrr-em-ests.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 26: Cs_023_full-correrr-em-ests 3 | ################################################### 4 | c(coef(mod4.em, type = "vector")["B.b"], logLik = mod4.em$logLik) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_023_full-correrr-em-ests.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | c(coef(mod4.em, type = "vector")["B.b"], logLik = mod4.em$logLik) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | B.b logLik 7 | -0.7737465 4.5374546 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_024_full-correrr-bfgs-ests.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | c(coef(mod4.bfgs, type = "vector")["B.b"], logLik = mod4.bfgs$logLik) 4 | \end{Sinput} 5 | \begin{Soutput} 6 | B.b logLik 7 | 0.8368899 0.9066497 8 | \end{Soutput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_026_loadsleep.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 29: Cs_026_loadsleep 3 | ################################################### 4 | data(sleepstudy, package = "lme4") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_026_loadsleep.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | data(sleepstudy, package = "lme4") 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_027_sleep-plot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--Cs_027_sleep-plot.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_027_sleep-plot.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--Cs_027_sleep-plot.tex -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_030_sleepmod1-lm.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 33: Cs_030_sleepmod1-lm 3 | ################################################### 4 | sleep.lm1 <- lm(Reaction ~ -1 + Subject + Days, data = sleepstudy) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_030_sleepmod1-lm.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | sleep.lm1 <- lm(Reaction ~ -1 + Subject + Days, data = sleepstudy) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_032_sleepmod2-lm.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 35: Cs_032_sleepmod2-lm 3 | ################################################### 4 | sleep.lm2 <- lm(Reaction ~ 0 + Subject + Days:Subject, data = sleepstudy) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_032_sleepmod2-lm.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | sleep.lm2 <- lm(Reaction ~ 0 + Subject + Days:Subject, data = sleepstudy) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_036_mod5-gls.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | sleep.mod5.gls <- gls(Reaction ~ 0 + Subject + Days:Subject, 4 | data = sleepstudy, 5 | correlation = corAR1(form = ~ 1 | Subject), method = "ML" 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--Cs_037_makemodeltable.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--Cs_037_makemodeltable.tex -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--RUNFIRST.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 1: RUNFIRST 3 | ################################################### 4 | tabledir <- "figures/" 5 | options(prompt = " ", continue = " ", width = 60) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--RUNFIRST.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--RUNFIRST.tex -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--reset.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 41: reset 3 | ################################################### 4 | options(prompt = "> ", continue = " +", width = 120) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/MLR--reset.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/MLR--reset.tex -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs00_load_library.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 2: Cs00_load_library 3 | ################################################### 4 | library(MARSS) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs00_load_library.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/QE--Cs00_load_library.tex -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs02_model-general.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 4: Cs02_model-general (eval = FALSE) 3 | ################################################### 4 | ## kem <- MARSS(dat, model = model.gen) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs02_model-general.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem <- MARSS(dat, model = model.gen) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs03_enterdata.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 5: Cs03_enterdata 3 | ################################################### 4 | dat <- t(harborSealWA) 5 | dat <- dat[2:nrow(dat), ] # remove the year row 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs03_enterdata.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | dat <- t(harborSealWA) 4 | dat <- dat[2:nrow(dat), ] # remove the year row 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs04_model-default.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 6: Cs04_model-default 3 | ################################################### 4 | kem <- MARSS(dat) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs06_model-default-time.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 8: Cs06_model-default-time 3 | ################################################### 4 | kem.time <- system.time(MARSS(dat, silent = TRUE)) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs06_model-default-time.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/QE--Cs06_model-default-time.tex -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs07_model-bfgs.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 9: Cs07_model-bfgs 3 | ################################################### 4 | bfgs <- MARSS(dat, method = "BFGS") 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs08_model-bfgs-time.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 10: Cs08_model-bfgs-time 3 | ################################################### 4 | bfgs.time <- system.time(MARSS(dat, silent = TRUE, method = "BFGS")) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs08_model-bfgs-time.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/QE--Cs08_model-bfgs-time.tex -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs09_model-bfgs2.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 11: Cs09_model-bfgs2 3 | ################################################### 4 | bfgs2 <- MARSS(dat, method = "BFGS", inits = kem$par) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs09_model-bfgs2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | bfgs2 <- MARSS(dat, method = "BFGS", inits = kem$par) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs10_model-default.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 12: Cs10_model-default (eval = FALSE) 3 | ################################################### 4 | ## kem.strange <- MARSS(dat, model = list(tinitx = 1)) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs10_model-default.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.strange <- MARSS(dat, model = list(tinitx = 1)) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs11_model-corr1.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 13: Cs11_model-corr1 3 | ################################################### 4 | kem <- MARSS(dat, model = list(Q = "unconstrained")) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs11_model-corr1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem <- MARSS(dat, model = list(Q = "unconstrained")) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs12_model-corr2.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 14: Cs12_model-corr2 3 | ################################################### 4 | kem <- MARSS(dat, model = list(Q = "equalvarcov")) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs12_model-corr2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem <- MARSS(dat, model = list(Q = "equalvarcov")) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs13_model-u-NS.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | regions <- list("N", "N", "N", "S", "S") 4 | U <- matrix(regions, 5, 1) 5 | Q <- matrix(list(0), 5, 5) 6 | diag(Q) <- regions 7 | kem <- MARSS(dat, model = list(U = U, Q = Q)) 8 | \end{Sinput} 9 | \end{Schunk} 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs15_model-pan1.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 17: Cs15_model-pan1 3 | ################################################### 4 | Z <- factor(c(1, 1, 1, 1, 1)) 5 | kem <- MARSS(dat, model = list(Z = Z)) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs17_model-two1.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Z <- factor(c("N", "N", "N", "S", "S")) 4 | Q <- "diagonal and equal" 5 | U <- "equal" 6 | kem <- MARSS(dat, model = list(Z = Z, Q = Q, U = U)) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs17_model-two2.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 21: Cs17_model-two2 3 | ################################################### 4 | kem <- MARSS(dat, model = list(Z = Z, Q = Q, U = U, A="zero")) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs17_model-two2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem <- MARSS(dat, model = list(Z = Z, Q = Q, U = U, A="zero")) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs19_model-print.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 24: Cs19_model-print 3 | ################################################### 4 | print(kem) 5 | print(kem$model) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs19_model-print.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | print(kem) 4 | print(kem$model) 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs20_model-summary.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 25: Cs20_model-summary 3 | ################################################### 4 | summary(kem$model) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs20_model-summary.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | summary(kem$model) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs23_model-print-R.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 26: Cs23_model-print-R 3 | ################################################### 4 | x <- print(kem, what = "states", silent = TRUE) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs23_model-print-R.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | x <- print(kem, what = "states", silent = TRUE) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs24_model-tidy-R.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 27: Cs24_model-tidy-R 3 | ################################################### 4 | tidy(kem) 5 | glance(kem) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs25_CIs-hessian.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 28: Cs25_CIs-hessian 3 | ################################################### 4 | kem.with.hess.CIs <- MARSSparamCIs(kem) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs25_CIs-hessian.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.with.hess.CIs <- MARSSparamCIs(kem) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs26_print-CIs.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 29: Cs26_print-CIs 3 | ################################################### 4 | print(kem.with.hess.CIs) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs27_CIs-pboot.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 30: Cs27_CIs-pboot 3 | ################################################### 4 | kem.w.boot.CIs <- MARSSparamCIs(kem, method = "parametric", nboot = 10) 5 | print(kem.w.boot.CIs) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs28_parvec.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 31: Cs28_parvec 3 | ################################################### 4 | parvec <- coef(kem, type = "vector") 5 | parvec 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs29_tsSmooth.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 32: Cs29_tsSmooth 3 | ################################################### 4 | df <- tsSmooth(kem) 5 | head(df) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs32_like.kem200.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.degen2 <- MARSS(dat.short, control = list( 4 | maxit = 1000, 5 | allow.degen = FALSE 6 | ), silent = 2) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs33_like.kem.allow.degen.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 36: Cs33_like.kem.allow.degen 3 | ################################################### 4 | kem.short <- MARSS(dat.short) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs35_boot.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 38: Cs35_boot 3 | ################################################### 4 | boot.params <- MARSSboot(kem, 5 | nboot = 20, output = "parameters", sim = "parametric" 6 | )$boot.params 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs36_sim.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 39: Cs36_sim 3 | ################################################### 4 | sim.data <- MARSSsimulate(kem, nsim = 2, tSteps = 100)$sim.data 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs36_sim.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | sim.data <- MARSSsimulate(kem, nsim = 2, tSteps = 100)$sim.data 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs37_sim-fit.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 40: Cs37_sim-fit 3 | ################################################### 4 | kem.sim.1 <- MARSS(sim.data[, , 1]) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs37_sim-fit.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.sim.1 <- MARSS(sim.data[, , 1]) 4 | \end{Sinput} 5 | \end{Schunk} 6 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs38_sim-like.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 41: Cs38_sim-like 3 | ################################################### 4 | kem.sim.2 <- kem.sim.1 5 | kem.sim.2$model$data <- sim.data[, , 2] 6 | MARSSkf(kem.sim.2)$logLik 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--Cs38_sim-like.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | kem.sim.2 <- kem.sim.1 4 | kem.sim.2$model$data <- sim.data[, , 2] 5 | MARSSkf(kem.sim.2)$logLik 6 | \end{Sinput} 7 | \begin{Soutput} 8 | [1] -244.1662 9 | \end{Soutput} 10 | \end{Schunk} 11 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--RUNFIRST.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 1: RUNFIRST 3 | ################################################### 4 | library(MARSS) 5 | options(prompt = " ", continue = " ", width = 60) 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--RUNFIRST.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/QE--RUNFIRST.tex -------------------------------------------------------------------------------- /inst/userguide/figures/QE--model.spec2.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | U <- matrix(list("-0.1+1*u","0.1+1*u"),2,1) 4 | Q <- matrix(list("q11",0,0,0.01),2,2) 5 | Z <- matrix(list("1*z1+-1*z2",0,"z2",0,0,"2*z1","z1",0,"z3","1+z3"),5,2) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--reset.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 43: reset 3 | ################################################### 4 | options(prompt = "> ", continue = " +", width = 120) 5 | 6 | 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/QE--reset.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/QE--reset.tex -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs00_required-libraries.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | library(MARSS) 4 | library(tidyr) 5 | library(ggplot2) 6 | library(forecast) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs101_structTS-level.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | y <- window(treering, start = 0, end = 20) 4 | fit1 <- StructTS(y, type = "level") 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs104_structTS-level.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/STS--Cs104_structTS-level.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs104_structTS-level.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/STS--Cs104_structTS-level.tex -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs201_structTS-leveltrend.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | y <- log10(forecast:::subset.ts(UKgas, quarter = 2)) 4 | fit1 <- StructTS(y, type = "trend") 5 | \end{Sinput} 6 | \end{Schunk} 7 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs205_structTS-leveltrend.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/STS--Cs205_structTS-leveltrend.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs205_structTS-leveltrend.tex: -------------------------------------------------------------------------------- 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17: Cs402_forecast 3 | ################################################### 4 | fr1 <- predict(fit1, n.ahead = 5) 5 | fr1 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs403_forecast.R: -------------------------------------------------------------------------------- 1 | ################################################### 2 | ### code chunk number 18: Cs403_forecast 3 | ################################################### 4 | fr2 <- predict(fit2, n.ahead = 5, interval = "prediction") 5 | fr2 6 | 7 | 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs405_forecast.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/STS--Cs405_forecast.pdf 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MARSSkfss(fit2)$xtt 5 | fitted3 <- ts(t(fitted3[1:3, ])) 6 | plot(fitted3) 7 | 8 | 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs504_fitted.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atsa-es/MARSS/a12ffb7d479968c524d71bc95b90e526cdee0440/inst/userguide/figures/STS--Cs504_fitted.pdf -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs504_fitted.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | fitted3 <- MARSSkfss(fit2)$xtt 4 | fitted3 <- ts(t(fitted3[1:3, ])) 5 | plot(fitted3) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs505_fitted.pdf: 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"diagonal and equal" 7 | ) 8 | 9 | 10 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs704_multivariate.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | mod.list.y <- list( 4 | A = "zero", 5 | R = "diagonal and equal" 6 | ) 7 | \end{Sinput} 8 | \end{Schunk} 9 | -------------------------------------------------------------------------------- /inst/userguide/figures/STS--Cs705_multivariate.tex: -------------------------------------------------------------------------------- 1 | \begin{Schunk} 2 | \begin{Sinput} 3 | Z <- matrix(c(1, 0), 1, 2, byrow = TRUE) 4 | mod.list <- c(mod.list.x, mod.list.y, list(Z = Z)) 5 | fitu <- MARSS(ym[1, ], model = mod.list, method = "BFGS", inits = list(x0 = 0)) 6 | \end{Sinput} 7 | \end{Schunk} 8 | -------------------------------------------------------------------------------- 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