├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── MD5 ├── NAMESPACE ├── NEWS.md ├── R ├── ELOS.R ├── LMAJ.R ├── MarkovTest.R ├── create.wData.omega.R ├── crprep.R ├── cuminc.R ├── cutLMms.R ├── datasets.R ├── etm2msdata.R ├── events.R ├── expand.covs.R ├── ggplot.Cuminc.R ├── ggplot.helpers.R ├── ggplot.msfit.R ├── ggplot.probtrans.R ├── imports.R ├── misc.R ├── msboot.R ├── msfit.R ├── msfit_subjects.R ├── msprep.R ├── mssample.R ├── paths.R ├── plot.Cuminc.R ├── plot.MarkovTest.R ├── plot.msfit.R ├── plot.msfit.subjects.R ├── plot.probtrans.R ├── plot.probtrans.subjects.R ├── print.Cuminc.R ├── print.MarkovTest.R ├── print.msdata.R ├── probtrans.R ├── probtrans_direct.R ├── probtrans_subjects.R ├── redrank.R ├── relsurv.haz_function.R ├── relsurv.match.ratetable.R ├── relsurv.msboot.relsurv.R ├── relsurv.msboot.relsurv.boot.R ├── relsurv.msfit.relsurv.R ├── relsurv.rformulate.R ├── relsurv.transMat.R ├── relsurv.varHaz.fixed.R ├── summary.Cuminc.R ├── summary.msfit.R ├── summary.probtrans.R ├── summary.probtrans.subjects.R ├── trans.R ├── transMat.R ├── transhelp.R ├── vis.mirror.pt.R ├── vis.multiple.pt.R └── xsect.R ├── README.md ├── _pkgdown.yml ├── data ├── aidssi.RData ├── aidssi2.RData ├── bmt.RData ├── ebmt1.RData ├── ebmt2.RData ├── ebmt3.RData ├── ebmt4.RData └── prothr.RData ├── docs ├── 404.html ├── articles │ ├── index.html │ ├── visuals_demo.html │ └── visuals_demo_files │ │ ├── accessible-code-block-0.0.1 │ │ └── empty-anchor.js │ │ ├── anchor-sections-1.0 │ │ ├── anchor-sections.css │ │ └── anchor-sections.js │ │ └── figure-html │ │ ├── mirror1-1.png │ │ ├── mirror2-1.png │ │ ├── msfitplot_base_1-1.png │ │ ├── msfitplot_base_2-1.png │ │ ├── msfitplot_confint1-1.png │ │ ├── msfitplot_confint2-1.png │ │ ├── msfitplot_customs-1.png │ │ ├── msfitplot_customs-2.png │ │ ├── msfitplot_ggplot2_1-1.png │ │ ├── msfitplot_ggplot_2-1.png │ │ ├── msfitplot_ggplot_2-2.png │ │ ├── plot.Cuminc1-1.png │ │ ├── plot.cuminc_x-1.png │ │ ├── plot.cuminc_x-2.png │ │ ├── plot_pt_filled1-1.png │ │ ├── plot_pt_filled2-1.png │ │ ├── plot_pt_filled3-1.png │ │ ├── plot_pt_filled4-1.png │ │ ├── plot_pt_separate1-1.png │ │ ├── plot_pt_separate2-1.png │ │ ├── plot_pt_single1-1.png │ │ ├── plot_pt_single2-1.png │ │ ├── plot_pt_single3-1.png │ │ ├── plot_pt_stacked-1.png │ │ ├── vis_multiple_plot-1.png │ │ └── vis_multiple_plot2-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── deps │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── docsearch.css ├── docsearch.js ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── EBMT-cause-of-death-data.html │ ├── EBMT-data.html │ ├── EBMT-platelet-recovery-data.html │ ├── EBMT-year-of-relapse-data.html │ ├── ELOS.html │ ├── LMAJ-1.png │ ├── LMAJ.html │ ├── Liver-cirrhosis-data.html │ ├── MarkovTest-1.png │ ├── MarkovTest-2.png │ ├── MarkovTest.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── absorbing.html │ ├── aidssi.html │ ├── aidssi2.html │ ├── bmt.html │ ├── crprep.default-1.png │ ├── crprep.default-2.png │ ├── crprep.default.html │ ├── crprep.html │ ├── cuminc.html │ ├── cutLMms.html │ ├── ebmt1.html │ ├── ebmt2.html │ ├── ebmt3.html │ ├── ebmt4.html │ ├── etm2msdata.html │ ├── events.html │ ├── expand.covs.default.html │ ├── expand.covs.html │ ├── expand.covs.msdata.html │ ├── haz_function.html │ ├── index.html │ ├── is.circular.html │ ├── modify_transMat.html │ ├── msboot.html │ ├── msboot.relsurv.boot.html │ ├── msboot.relsurv.html │ ├── msdata2etm.html │ ├── msfit.html │ ├── msfit.relsurv.html │ ├── msprep.html │ ├── mssample.html │ ├── mstate-package.html │ ├── mstate.html │ ├── optimal_weights_matrix.html │ ├── optimal_weights_multiple.html │ ├── paths.html │ ├── plot.Cuminc-1.png │ ├── plot.Cuminc-2.png │ ├── plot.Cuminc.html │ ├── plot.MarkovTest.html │ ├── plot.msfit-1.png │ ├── plot.msfit-2.png │ ├── plot.msfit-3.png │ ├── plot.msfit-4.png │ ├── plot.msfit.html │ ├── plot.probtrans-1.png │ ├── plot.probtrans-2.png │ ├── plot.probtrans-3.png │ ├── plot.probtrans-4.png │ ├── plot.probtrans.html │ ├── print.Cuminc.html │ ├── print.MarkovTest.html │ ├── print.msdata.html │ ├── print.summary.msfit.html │ ├── print.summary.probtrans.html │ ├── probtrans.html │ ├── prothr.html │ ├── redrank.html │ ├── summary.Cuminc.html │ ├── summary.msfit.html │ ├── summary.probtrans.html │ ├── to.trans2.html │ ├── tra2trans.html │ ├── trans.comprisk.html │ ├── trans.illdeath.html │ ├── trans2Q.html │ ├── trans2tra.html │ ├── transMat.html │ ├── transhelp.html │ ├── varHaz.fixed.html │ ├── vis.mirror.pt-1.png │ ├── vis.mirror.pt.html │ ├── vis.multiple.pt-1.png │ ├── vis.multiple.pt.html │ └── xsect.html ├── search.json └── sitemap.xml ├── inst ├── CITATION └── tinytest │ ├── test_msfit_subjects.R │ ├── test_mstate.R │ └── test_probtrans_subjects.R ├── man ├── Cuminc.Rd ├── EBMT-cause-of-death-data.Rd ├── EBMT-data.Rd ├── EBMT-platelet-recovery-data.Rd ├── EBMT-year-of-relapse-data.Rd ├── ELOS.Rd ├── LMAJ.Rd ├── 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