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/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/figure-html/unnamed-chunk-1-1.png
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docs/articles/clustered.html
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docs/articles/exampleRec.html
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docs/articles/exampleTest.html
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docs/articles/index.html
docs/articles/yourData.html
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docs/authors.html
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/figures/unnamed-chunk-3-1.png
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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
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/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/yourData.Rmd
xavierdidelot/BactDating documentation built on April 8, 2020, 4:59 p.m.