Files in xavierdidelot/BactDating
BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees
.Rbuildignore
.gitignore
.travis.yml
BactDating.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R/RcppExports.R
R/clustered.R
R/data.R
R/dualScale.R
R/extractSample.R
R/loadCFML.R
R/loadGubbins.R
R/main.R
R/methods.R
R/package.R
R/probs.R
R/roototip.R
R/simu/anaSimu.R
R/simu/simu.R
R/simu/simu.sh
R/simu/superscript.sh
R/simulate.R
README.Rmd
README.md
data/staph.rda
docs/404.html
docs/LICENSE-text.html
docs/articles/Staph.html
docs/articles/Staph_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/Staph_files/figure-html/unnamed-chunk-1-1.png
docs/articles/Staph_files/figure-html/unnamed-chunk-2-1.png
docs/articles/Staph_files/figure-html/unnamed-chunk-3-1.png
docs/articles/Staph_files/figure-html/unnamed-chunk-4-1.png
docs/articles/Staph_files/figure-html/unnamed-chunk-5-1.png
docs/articles/Staph_files/figure-html/unnamed-chunk-6-1.png
docs/articles/clustered.html
docs/articles/clustered_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/clustered_files/figure-html/unnamed-chunk-2-1.png
docs/articles/clustered_files/figure-html/unnamed-chunk-3-1.png
docs/articles/clustered_files/figure-html/unnamed-chunk-4-1.png
docs/articles/exampleRec.html
docs/articles/exampleRec_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/exampleRec_files/figure-html/unnamed-chunk-4-1.png
docs/articles/exampleRec_files/figure-html/unnamed-chunk-5-1.png
docs/articles/exampleRec_files/figure-html/unnamed-chunk-6-1.png
docs/articles/exampleRec_files/figure-html/unnamed-chunk-7-1.png
docs/articles/exampleRelaxed.html
docs/articles/exampleRelaxed_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/exampleRelaxed_files/figure-html/unnamed-chunk-2-1.png
docs/articles/exampleRelaxed_files/figure-html/unnamed-chunk-3-1.png
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docs/articles/exampleRelaxed_files/figure-html/unnamed-chunk-7-1.png
docs/articles/exampleRelaxed_files/figure-html/unnamed-chunk-8-1.png
docs/articles/exampleTest.html
docs/articles/exampleTest_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/exampleTest_files/figure-html/unnamed-chunk-2-1.png
docs/articles/exampleTest_files/figure-html/unnamed-chunk-3-1.png
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docs/articles/exampleTest_files/figure-html/unnamed-chunk-6-1.png
docs/articles/exampleTest_files/figure-html/unnamed-chunk-7-1.png
docs/articles/index.html
docs/articles/yourData.html
docs/articles/yourData_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/yourData_files/figure-html/unnamed-chunk-1-1.png
docs/articles/yourData_files/figure-html/unnamed-chunk-2-1.png
docs/articles/yourData_files/figure-html/unnamed-chunk-3-1.png
docs/articles/yourData_files/figure-html/unnamed-chunk-4-1.png
docs/articles/yourData_files/figure-html/unnamed-chunk-5-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/BactDating.html
docs/reference/allDates.html
docs/reference/as.mcmc.resBactDating.html
docs/reference/as.treedata.resBactDating.html
docs/reference/bactdate.html
docs/reference/clusteredTest.html
docs/reference/coalpriorR.html
docs/reference/collapse.singles.useRec.html
docs/reference/drop.tip.useRec.html
docs/reference/dualScale.html
docs/reference/extractSample.html
docs/reference/figures/unnamed-chunk-3-1.png
docs/reference/figures/unnamed-chunk-4-1.png
docs/reference/figures/unnamed-chunk-5-1.png
docs/reference/index.html
docs/reference/initRoot.html
docs/reference/leafDates.html
docs/reference/likelihoodArc.html
docs/reference/likelihoodCarc.html
docs/reference/likelihoodGamma.html
docs/reference/likelihoodNegbin.html
docs/reference/likelihoodPoisson.html
docs/reference/likelihoodRelaxedgamma.html
docs/reference/loadCFML.html
docs/reference/loadGubbins.html
docs/reference/modelcompare.html
docs/reference/nodeDates.html
docs/reference/plot.resBactDating.html
docs/reference/plotDualScale.html
docs/reference/print.resBactDating.html
docs/reference/roottotip.html
docs/reference/simcoaltree.html
docs/reference/simdatedtree.html
docs/reference/simobsphy.html
docs/reference/staph.html
docs/reference/summary.resBactDating.html
docs/sitemap.xml
figures/README-unnamed-chunk-3-1.png
figures/README-unnamed-chunk-4-1.png
figures/README-unnamed-chunk-5-1.png
inst/CITATION
man/BactDating.Rd
man/allDates.Rd
man/as.mcmc.resBactDating.Rd
man/as.treedata.resBactDating.Rd
man/bactdate.Rd
man/clusteredTest.Rd
man/coalpriorR.Rd
man/collapse.singles.useRec.Rd
man/drop.tip.useRec.Rd
man/dualScale.Rd
man/extractSample.Rd
man/figures/unnamed-chunk-3-1.png
man/figures/unnamed-chunk-4-1.png
man/figures/unnamed-chunk-5-1.png
man/initRoot.Rd
man/leafDates.Rd
man/likelihoodArc.Rd
man/likelihoodCarc.Rd
man/likelihoodGamma.Rd
man/likelihoodNegbin.Rd
man/likelihoodPoisson.Rd
man/likelihoodRelaxedgamma.Rd
man/loadCFML.Rd
man/loadGubbins.Rd
man/modelcompare.Rd
man/nodeDates.Rd
man/plot.resBactDating.Rd
man/plotDualScale.Rd
man/print.resBactDating.Rd
man/roottotip.Rd
man/simcoaltree.Rd
man/simdatedtree.Rd
man/simobsphy.Rd
man/staph.Rd
man/summary.resBactDating.Rd
src/RcppExports.cpp
src/probs.cpp
tests/testthat.R
tests/testthat/test.out.em.txt
tests/testthat/test.out.importation_status.txt
tests/testthat/test.out.labelled_tree.newick
tests/testthat/test.out.position_cross_reference.txt
tests/testthat/test2.final_tree.tre
tests/testthat/test2.node_labelled.final_tree.tre
tests/testthat/test2.per_branch_statistics.csv
tests/testthat/test_likelihoods.R
tests/testthat/test_priors.R
tests/testthat/test_running.R
tests/testthat/test_utils.R
vignettes/Staph.Rmd
vignettes/clustered.Rmd
vignettes/exampleRec.Rmd
vignettes/exampleRelaxed.Rmd
vignettes/exampleTest.Rmd
vignettes/tmp-pdfcrop-79225.tex
vignettes/yourData.Rmd
