Files in chjackson/msm
Multi-State Markov and Hidden Markov Models in Continuous Time

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
ChangeLog
DESCRIPTION
NAMESPACE
NEWS.md R/MatrixExp.R R/boot.R R/constants.R R/datasets_doc.R R/deltamethod.R R/draic.R R/efpt.R R/hmm-dists.R R/hmm.R R/hmodel2list.R R/internals_doc.R R/medists.R R/msm-package.R R/msm.R R/mstate.R R/olddata.R R/optim.R R/outputs.R R/pearson.R R/pexp.R R/phase.R R/plot.R R/ppass.R R/prevalence.R R/print.R R/qgeneric.R R/scoreresid.R R/simul.R R/summary.R R/tidy.R R/tnorm.R R/totlos.R R/utils.R R/viterbi.R README.md
TODO
_pkgdown.yml
codecov.yml
data/bos3.rda
data/bos4.rda
data/msmdata.rda
docs/404.html
docs/authors.html
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/bootstrap-5.3.1/font.css
docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff
docs/deps/bootstrap-5.3.1/fonts/1adeadb2fe618c5ed46221f15e12b9c8.woff
docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgo6ew.woff
docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgoKfw7w.woff
docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff
docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff
docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff
docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff
docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff
docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff
docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff
docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff
docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff
docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff
docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff
docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff
docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff
docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff
docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff
docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff
docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff
docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Me5g.woff
docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Mu4mxM.woff
docs/deps/bootstrap-5.3.1/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff
docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxsAXC-s.woff
docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxswWA.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVeww.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USSwiPHw.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USeww.woff
docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHjx4wWA.woff
docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHvxo.woff
docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff
docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff
docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff
docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff
docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff
docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff
docs/deps/bootstrap-5.3.1/fonts/a98f7a7574819ba83bec6279a2cecd95.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff
docs/deps/bootstrap-5.3.1/fonts/q5uGsou0JOdh94bfvQlr.woff
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/index.html
docs/link.svg
docs/msmcourse/404.html
docs/msmcourse/advanced.html
docs/msmcourse/cjackson_bordeaux2020.pdf
docs/msmcourse/covariates.html
docs/msmcourse/index.html
docs/msmcourse/libs/anchor-sections-1.0.1/anchor-sections.css
docs/msmcourse/libs/anchor-sections-1.0.1/anchor-sections.js
docs/msmcourse/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
docs/msmcourse/libs/gitbook-2.6.7/css/plugin-bookdown.css
docs/msmcourse/libs/gitbook-2.6.7/css/plugin-clipboard.css
docs/msmcourse/libs/gitbook-2.6.7/css/plugin-fontsettings.css
docs/msmcourse/libs/gitbook-2.6.7/css/plugin-highlight.css
docs/msmcourse/libs/gitbook-2.6.7/css/plugin-search.css
docs/msmcourse/libs/gitbook-2.6.7/css/plugin-table.css
docs/msmcourse/libs/gitbook-2.6.7/css/style.css
docs/msmcourse/libs/gitbook-2.6.7/js/app.min.js
docs/msmcourse/libs/gitbook-2.6.7/js/clipboard.min.js
docs/msmcourse/libs/gitbook-2.6.7/js/jquery.highlight.js
docs/msmcourse/libs/gitbook-2.6.7/js/lunr.js
docs/msmcourse/libs/gitbook-2.6.7/js/plugin-bookdown.js
docs/msmcourse/libs/gitbook-2.6.7/js/plugin-clipboard.js
docs/msmcourse/libs/gitbook-2.6.7/js/plugin-fontsettings.js
docs/msmcourse/libs/gitbook-2.6.7/js/plugin-search.js
docs/msmcourse/libs/gitbook-2.6.7/js/plugin-sharing.js
docs/msmcourse/libs/header-attrs-2.10/header-attrs.js
docs/msmcourse/libs/jquery-3.6.0/jquery-3.6.0.min.js
docs/msmcourse/msmbasic.html
docs/msmcourse/msmcourse_files/figure-html/cav-model-1.png
docs/msmcourse/msmcourse_files/figure-html/psor-model-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-12-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-2-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-3-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-31-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-32-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-35-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-36-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-37-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-38-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-39-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-4-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-41-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-5-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-56-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-56-2.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-58-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-58-2.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-6-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-62-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-64-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-76-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-77-1.png
docs/msmcourse/msmcourse_files/figure-html/unnamed-chunk-78-1.png
docs/msmcourse/outputs.html
docs/msmcourse/reference-keys.txt
docs/msmcourse/search_index.json
docs/msmcourse/style.css
docs/msmcourse/theory.html
docs/msmcourse/timedep.html
docs/msmcourse_src/01-intro.Rmd docs/msmcourse_src/02-msm-basic.Rmd docs/msmcourse_src/03-outputs.Rmd docs/msmcourse_src/04-covariates.Rmd docs/msmcourse_src/05-timedep.Rmd docs/msmcourse_src/06-advanced.Rmd docs/msmcourse_src/README.md
docs/msmcourse_src/_bookdown.yml
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/__packages
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-51_73d4d60fbfd83985ab89926e4ed003d7.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-51_73d4d60fbfd83985ab89926e4ed003d7.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-51_73d4d60fbfd83985ab89926e4ed003d7.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-52_9a739d3d8d1047b1c965c55308c70888.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-52_9a739d3d8d1047b1c965c55308c70888.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-52_9a739d3d8d1047b1c965c55308c70888.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-57_eb63e2b28e0c0660941b11e71b2229f2.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-57_eb63e2b28e0c0660941b11e71b2229f2.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-57_eb63e2b28e0c0660941b11e71b2229f2.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-72_4085963235f7caab4f92b2276cd967b7.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-72_4085963235f7caab4f92b2276cd967b7.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-72_4085963235f7caab4f92b2276cd967b7.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-73_e826c3f7a9cde043b933da722124a94f.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-73_e826c3f7a9cde043b933da722124a94f.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-73_e826c3f7a9cde043b933da722124a94f.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-74_6668bc20a16a73897d49f65b2f00f642.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-74_6668bc20a16a73897d49f65b2f00f642.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-74_6668bc20a16a73897d49f65b2f00f642.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-75_c2a52b6552256a67c5dde4886433e170.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-75_c2a52b6552256a67c5dde4886433e170.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-75_c2a52b6552256a67c5dde4886433e170.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-76_000c0a710b1a40112c681fcc1a795aca.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-76_000c0a710b1a40112c681fcc1a795aca.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/html/unnamed-chunk-76_000c0a710b1a40112c681fcc1a795aca.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/__packages
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-51_4f49aaa48fd8c0280810c8df5d0af592.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-51_4f49aaa48fd8c0280810c8df5d0af592.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-51_4f49aaa48fd8c0280810c8df5d0af592.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-52_51615918b75202fc40ad3c5d4836774b.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-52_51615918b75202fc40ad3c5d4836774b.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-52_51615918b75202fc40ad3c5d4836774b.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-57_6c8a7d6a13d5153d44904d249782493a.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-57_6c8a7d6a13d5153d44904d249782493a.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-57_6c8a7d6a13d5153d44904d249782493a.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-72_5c9cab8321d1c671d0926a27af297430.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-72_5c9cab8321d1c671d0926a27af297430.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-72_5c9cab8321d1c671d0926a27af297430.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-73_eccb6fd315c0336cc89f9fbd907c9d7e.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-73_eccb6fd315c0336cc89f9fbd907c9d7e.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-73_eccb6fd315c0336cc89f9fbd907c9d7e.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-74_51fd0a9bd53fd30952eb142c2986f763.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-74_51fd0a9bd53fd30952eb142c2986f763.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-74_51fd0a9bd53fd30952eb142c2986f763.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-75_191cbee06a7adf0a714f8321e67401fc.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-75_191cbee06a7adf0a714f8321e67401fc.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-75_191cbee06a7adf0a714f8321e67401fc.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-76_72b958022fb39d46fd7803f892163a0c.RData
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-76_72b958022fb39d46fd7803f892163a0c.rdb
docs/msmcourse_src/_bookdown_files/msmcourse_cache/latex/unnamed-chunk-76_72b958022fb39d46fd7803f892163a0c.rdx
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/cav-model-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/cav-model-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/psor-model-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/psor-model-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-12-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-12-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-2-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-2-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-3-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-32-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-37-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-38-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-4-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-4-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-41-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-41-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-5-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-5-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-58-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-58-2.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-6-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-6-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-64-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-64-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-77-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-77-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-78-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-html/unnamed-chunk-78-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/cav-model-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/psor-model-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-12-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-2-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-3-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-32-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-37-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-38-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-4-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-4-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-41-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-41-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-5-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-5-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-58-1.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-58-2.pdf docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-6-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-6-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-64-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-64-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-77-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-77-1.png
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-78-1.pdf
docs/msmcourse_src/_bookdown_files/msmcourse_files/figure-latex/unnamed-chunk-78-1.png
docs/msmcourse_src/_output.yml
docs/msmcourse_src/figure/unnamed-chunk-1-1.pdf
docs/msmcourse_src/figure/unnamed-chunk-1-1.png
docs/msmcourse_src/figure/unnamed-chunk-3-1.pdf
docs/msmcourse_src/figure/unnamed-chunk-3-1.png
docs/msmcourse_src/figure/unnamed-chunk-34-1.pdf
docs/msmcourse_src/figure/unnamed-chunk-34-1.png
docs/msmcourse_src/figure/unnamed-chunk-4-1.pdf
docs/msmcourse_src/figure/unnamed-chunk-4-1.png
docs/msmcourse_src/figure/unnamed-chunk-5-1.pdf
docs/msmcourse_src/figure/unnamed-chunk-5-1.png
docs/msmcourse_src/index.Rmd
docs/msmcourse_src/packages.bib
docs/msmcourse_src/preamble.tex
docs/msmcourse_src/style.css
docs/msmcourse_src/toc.css
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/MatrixExp.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/aneur.html
docs/reference/boot.msm.html
docs/reference/bos.html
docs/reference/cav.html
docs/reference/cmodel.object.html
docs/reference/coef.msm.html
docs/reference/crudeinits.msm.html
docs/reference/deltamethod.html
docs/reference/draic.msm.html
docs/reference/ecmodel.object.html
docs/reference/efpt.msm.html
docs/reference/ematrix.msm.html
docs/reference/emodel.object.html
docs/reference/fev.html
docs/reference/hazard.msm.html
docs/reference/hmm-dists.html
docs/reference/hmmMV.html
docs/reference/hmodel.object.html
docs/reference/hmodel2list.html
docs/reference/index.html
docs/reference/logLik.msm.html
docs/reference/lrtest.msm.html
docs/reference/medists-1.png
docs/reference/medists.html
docs/reference/model.frame.msm.html
docs/reference/msm-package.html
docs/reference/msm.form.qoutput.html
docs/reference/msm.html
docs/reference/msm.object.html
docs/reference/msm2Surv.html
docs/reference/odds.msm.html
docs/reference/paramdata.object.html
docs/reference/pearson.msm.html
docs/reference/pexp-1.png
docs/reference/pexp-2.png
docs/reference/pexp.html
docs/reference/phasemeans.msm.html
docs/reference/plot.msm.html
docs/reference/plot.prevalence.msm.html
docs/reference/plot.survfit.msm.html
docs/reference/plotprog.msm.html
docs/reference/pmatrix.msm.html
docs/reference/pmatrix.piecewise.msm.html
docs/reference/pnext.msm.html
docs/reference/ppass.msm.html
docs/reference/prevalence.msm.html
docs/reference/print.msm.html
docs/reference/printold.msm.html
docs/reference/psor.html
docs/reference/qcmodel.object.html
docs/reference/qgeneric.html
docs/reference/qmatrix.msm.html
docs/reference/qmodel.object.html
docs/reference/qratio.msm.html
docs/reference/recreate.olddata.html
docs/reference/scoreresid.msm.html
docs/reference/sim.msm.html
docs/reference/simfitted.msm.html
docs/reference/simmulti.msm.html
docs/reference/sojourn.msm.html
docs/reference/statetable.msm.html
docs/reference/summary.msm.html
docs/reference/surface.msm.html
docs/reference/tidy.msm.est.html
docs/reference/tidy.msm.estbystate.html
docs/reference/tidy.msm.html
docs/reference/tidy.msm.prevalence.html
docs/reference/tnorm-1.png
docs/reference/tnorm.html
docs/reference/totlos.msm.html
docs/reference/transient.msm.html
docs/reference/twophase.html
docs/reference/updatepars.msm.html
docs/reference/viterbi.msm.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/NEWS
man/MatrixExp.Rd man/aneur.Rd man/boot.msm.Rd man/bos.Rd man/cav.Rd man/cmodel.object.Rd man/coef.msm.Rd man/crudeinits.msm.Rd man/deltamethod.Rd man/draic.msm.Rd man/ecmodel.object.Rd man/efpt.msm.Rd man/ematrix.msm.Rd man/emodel.object.Rd man/fev.Rd man/hazard.msm.Rd man/hmm-dists.Rd man/hmmMV.Rd man/hmodel.object.Rd man/hmodel2list.Rd man/logLik.msm.Rd man/lrtest.msm.Rd man/medists.Rd man/model.frame.msm.Rd man/msm-package.Rd man/msm.Rd man/msm.form.qoutput.Rd man/msm.object.Rd man/msm2Surv.Rd man/odds.msm.Rd man/paramdata.object.Rd man/pearson.msm.Rd man/pexp.Rd man/phasemeans.msm.Rd man/plot.msm.Rd man/plot.prevalence.msm.Rd man/plot.survfit.msm.Rd man/plotprog.msm.Rd man/pmatrix.msm.Rd man/pmatrix.piecewise.msm.Rd man/pnext.msm.Rd man/ppass.msm.Rd man/prevalence.msm.Rd man/print.msm.Rd man/printold.msm.Rd man/psor.Rd man/qcmodel.object.Rd man/qgeneric.Rd man/qmatrix.msm.Rd man/qmodel.object.Rd man/qratio.msm.Rd man/recreate.olddata.Rd man/scoreresid.msm.Rd man/sim.msm.Rd man/simfitted.msm.Rd man/simmulti.msm.Rd man/sojourn.msm.Rd man/statetable.msm.Rd man/summary.msm.Rd man/surface.msm.Rd man/tidy.msm.Rd man/tidy.msm.est.Rd man/tidy.msm.estbystate.Rd man/tidy.msm.prevalence.Rd man/tnorm.Rd man/totlos.msm.Rd man/transient.msm.Rd man/twophase.Rd man/updatepars.msm.Rd man/viterbi.msm.Rd
src/Makevars
src/analyticp.c
src/expm.h
src/hmm.c
src/hmm.h
src/hmmderiv.c
src/lik.c
src/msm-init.c
src/msm.h
src/pijt.c
tests/slow/helper.r tests/slow/localdata.r tests/slow/test_boot.R tests/slow/test_fits.r tests/slow/test_fits_hmm.r tests/slow/test_fits_hmmmulti.r tests/slow/test_fits_misc.r tests/slow/test_outputs_slow.r tests/slow/test_phase.r tests/test_base.R tests/testthat/helper.r tests/testthat/test_analyticp.r tests/testthat/test_boot.R tests/testthat/test_datasumm.r tests/testthat/test_deriv.r tests/testthat/test_draic.r tests/testthat/test_hmodel2list.R tests/testthat/test_models.r tests/testthat/test_models_hmm.r tests/testthat/test_models_hmmmulti.r tests/testthat/test_models_misc.r tests/testthat/test_msm2Surv.R tests/testthat/test_pearson.R tests/testthat/test_phase.R tests/testthat/test_ppass.R tests/testthat/test_simul.R tests/testthat/test_tidy.R tests/testthat/test_utils.r tests/testthat/test_viterbi.R tests/testthat/test_weights.R
vignettes/Sweave-local.sty
vignettes/figures/dags/p2q1.odg
vignettes/figures/dags/p2q1.pdf
vignettes/figures/dags/p2q1.ps
vignettes/figures/dags/p2q12.odg
vignettes/figures/dags/p2q12.pdf
vignettes/figures/dags/p2q12.ps
vignettes/figures/dags/p3q12.odg
vignettes/figures/dags/p3q12.pdf
vignettes/figures/dags/p3q12.ps
vignettes/figures/dags/p3q124.odg
vignettes/figures/dags/p3q124.pdf
vignettes/figures/dags/p3q124.ps
vignettes/figures/dags/p3q1246.odg
vignettes/figures/dags/p3q1246.pdf
vignettes/figures/dags/p3q1246.ps
vignettes/figures/dags/p3q135.odg
vignettes/figures/dags/p3q135.pdf
vignettes/figures/dags/p3q135.ps
vignettes/figures/dags/p3q14.odg
vignettes/figures/dags/p3q14.pdf
vignettes/figures/dags/p3q14.ps
vignettes/figures/dags/p3q16.odg
vignettes/figures/dags/p3q16.pdf
vignettes/figures/dags/p3q16.ps
vignettes/figures/dags/p4q13569.odg
vignettes/figures/dags/p4q13569.pdf
vignettes/figures/dags/p4q13569.ps
vignettes/figures/dags/p4q159.odg
vignettes/figures/dags/p4q159.pdf
vignettes/figures/dags/p4q159.ps
vignettes/figures/dags/p5q1_4_6_8_11_12_16.odg
vignettes/figures/dags/p5q1_4_6_8_11_12_16.pdf
vignettes/figures/dags/p5q1_4_6_8_11_12_16.ps
vignettes/figures/dags/p5q1_6_11_16.odg
vignettes/figures/dags/p5q1_6_11_16.pdf
vignettes/figures/dags/p5q1_6_11_16.ps
vignettes/figures/dags/p5q1_6_7_11_12.odg
vignettes/figures/dags/p5q1_6_7_11_12.pdf
vignettes/figures/dags/p5q1_6_7_11_12.ps
vignettes/figures/fev_viterbi.pdf
vignettes/figures/general.eps
vignettes/figures/general.pdf vignettes/figures/hidden.pdf
vignettes/figures/hidden.ps
vignettes/figures/illdeath.eps
vignettes/figures/illdeath.pdf
vignettes/figures/multistate.eps
vignettes/figures/multistate.pdf
vignettes/figures/p2q1.eps
vignettes/figures/p2q1.pdf
vignettes/figures/p2q12.eps
vignettes/figures/p2q12.pdf
vignettes/figures/p3q12.eps
vignettes/figures/p3q12.pdf
vignettes/figures/p3q124.eps
vignettes/figures/p3q124.pdf
vignettes/figures/p3q1246.eps
vignettes/figures/p3q1246.pdf
vignettes/figures/p3q135.eps
vignettes/figures/p3q135.pdf
vignettes/figures/p3q14.eps
vignettes/figures/p3q14.pdf
vignettes/figures/p3q16.eps
vignettes/figures/p3q16.pdf
vignettes/figures/p4q13569.eps
vignettes/figures/p4q13569.pdf
vignettes/figures/p4q159.eps
vignettes/figures/p4q159.pdf
vignettes/figures/p5q1_4_6_8_11_12_16.eps
vignettes/figures/p5q1_4_6_8_11_12_16.pdf
vignettes/figures/p5q1_6_11_16.eps
vignettes/figures/p5q1_6_11_16.pdf
vignettes/figures/p5q1_6_7_11_12.eps
vignettes/figures/p5q1_6_7_11_12.pdf vignettes/figures/sampling.pdf
vignettes/figures/sampling.ps
vignettes/msm-manual.Rnw
vignettes/msm.bib
chjackson/msm documentation built on March 3, 2024, 1:05 a.m.