Files in USCbiostats/phylogenetic
Statistical Inference of Annotated Phylogenetic Trees

.Rbuildignore
.gitignore
.travis.yml
ChangeLog
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/RcppExports.R R/ape.r R/aphylo-package.r R/data-management.r R/estimation.r R/formulas.r R/loglike.r R/panther.r R/plot_logLik.r R/predict-bis.r R/predict.r
R/prune.r
R/simulation.r README.Rmd README.md
README_files/figure-markdown_github-ascii_identifiers/Get offspring-1.png
README_files/figure-markdown_github-ascii_identifiers/Get offspring-2.png
README_files/figure-markdown_github-ascii_identifiers/MCMC-1.png
README_files/figure-markdown_github-ascii_identifiers/MCMC-2.png
README_files/figure-markdown_github-ascii_identifiers/MLE-1.png
README_files/figure-markdown_github-ascii_identifiers/Predict-1.png
README_files/figure-markdown_github/Get offspring-1.png
README_files/figure-markdown_github/Get offspring-2.png
README_files/figure-markdown_github/MCMC-1.png
README_files/figure-markdown_github/MCMC-2.png
README_files/figure-markdown_github/MLE-1.png
README_files/figure-markdown_github/Predict-1.png
README_files/figure-markdown_github/Predict-2.png
aphylo.Rproj
appveyor.yml
cleanup
codecov.yml
configure
configure.ac
data-raw/fakeexperiment.csv
data-raw/fakeexperiment.r
data-raw/faketree.csv
data-raw/faketree.r
data/fakeexperiment.rda
data/faketree.rda
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/data_imputation.html
docs/articles/index.html
docs/articles/peeling_phylo.html
docs/authors.html
docs/docsearch.css
docs/index.html
docs/index_files/figure-html/Get offspring-1.png
docs/index_files/figure-html/Get offspring-2.png
docs/index_files/figure-html/MLE-1.png
docs/index_files/figure-html/Predict-1.png
docs/index_files/figure-html/Predict-2.png
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/LogLike.html
docs/reference/aphylo-class-1.png
docs/reference/aphylo-class-2.png
docs/reference/aphylo-class.html
docs/reference/aphylo-methods.html
docs/reference/aphylo-model.html
docs/reference/aphylo-package.html
docs/reference/aphylo.html
docs/reference/aphylo_estimates-class-1.png
docs/reference/aphylo_estimates-class-2.png
docs/reference/aphylo_estimates-class.html
docs/reference/approx_geodesic.html
docs/reference/as.phylo-1.png
docs/reference/as.phylo-2.png
docs/reference/as.phylo.html
docs/reference/fakeexperiment.html
docs/reference/faketree.html
docs/reference/index.html
docs/reference/list_offspring.html
docs/reference/mislabel.html
docs/reference/panther-tree.html
docs/reference/piechart-1.png
docs/reference/piechart-2.png
docs/reference/piechart.html
docs/reference/plot.aphylo_prediction_score.html
docs/reference/plot_LogLike-1.png
docs/reference/plot_LogLike-2.png
docs/reference/plot_LogLike.html
docs/reference/plot_logLik-1.png
docs/reference/plot_logLik-2.png
docs/reference/plot_logLik.html
docs/reference/plot_multivariate-1.png
docs/reference/plot_multivariate.html
docs/reference/posterior-probabilities.html
docs/reference/rdrop_annotations.html
docs/reference/sim_annotated_tree.html
docs/reference/sim_fun_on_tree.html
docs/reference/sim_tree-1.png
docs/reference/sim_tree-2.png
docs/reference/sim_tree.html
docs/reference/states.html
inst/NEWS
inst/tree.tree
makefile
man-roxygen/edges.r man-roxygen/parameters.r man/LogLike.Rd man/aphylo-class.Rd man/aphylo-methods.Rd man/aphylo-model.Rd man/aphylo-package.Rd man/aphylo_estimates-class.Rd man/approx_geodesic.Rd man/as.phylo.Rd man/fakeexperiment.Rd man/faketree.Rd man/list_offspring.Rd man/mislabel.Rd man/panther-tree.Rd man/plot.aphylo_prediction_score.Rd man/plot_logLik.Rd man/plot_multivariate.Rd man/posterior-probabilities.Rd man/rdrop_annotations.Rd man/sim_annotated_tree.Rd man/sim_fun_on_tree.Rd man/sim_tree.Rd man/states.Rd playground/20180102-test-bias.r playground/20180315-jmor-trees.r playground/FormatTreeR_24Oct2012.pdf playground/annotations.r playground/ape_now_supports_singletons.md playground/ape_now_supports_singletons.rmd
playground/ape_now_supports_singletons_files/figure-markdown_github-ascii_identifiers/benchmark-plot-1.png
playground/ape_recode.cpp
playground/compare_prunseq_with_po_packages.r playground/core_meeting.rmd playground/eta.Rmd playground/eta.pdf playground/leave-one-out.r playground/new_mle_test.r playground/postorder.r playground/preorder.r playground/presentations/aphylo.pdf playground/presentations/aphylo.rmd
playground/presentations/aphylo.sty
playground/presentations/aphylo.tex
playground/presentations/bias_trees_of_size_[57,138).pdf playground/presentations/gelmans_right_prior.pdf playground/presentations/mcmc_right_prior_prediction.pdf
playground/presentations/simple_tree.dia
playground/presentations/simple_tree.pdf
playground/presentations/simple_tree.tex
playground/presentations/simple_tree_leaf2.tex
playground/presentations/simple_tree_leaf4.tex
playground/presentations/simple_tree_leaf5.tex
playground/presentations/simple_tree_leafs.tex
playground/presentations/simple_tree_likelihood.tex
playground/presentations/simple_tree_names.dia
playground/presentations/simple_tree_names.tex
playground/presentations/simple_tree_node0.tex
playground/presentations/simple_tree_node1.tex
playground/presentations/simple_tree_node3.tex
playground/reduced_peeling.r playground/retreat2018.rmd playground/root_node_prob.Rmd playground/root_node_prob_fixed.pdf
playground/sim_phylo.cpp
src/Makevars
src/Makevars.in
src/Makevars.win
src/RcppExports.cpp
src/misc.cpp
src/misc.h
src/phylo.cpp
src/phylo.h
src/predict.cpp
src/quality.cpp
src/sim_phylo.cpp
src/tree.cpp
tests/testthat.R tests/testthat/test-data-management.r tests/testthat/test-examples.r tests/testthat/test-formula.r tests/testthat/test-geodesic.r tests/testthat/test-loglikelihood.r tests/testthat/test-panther.r tests/testthat/test-parameter-estimates-and-formulas.r tests/testthat/test-parameter-estimates.r tests/testthat/test-pies.r tests/testthat/test-plot_loglike.r tests/testthat/test-predict.r tests/testthat/test-sim_phylo.r tests/testthat/test-tree-cpp.r vignettes/data_imputation.rmd vignettes/peeling_phylo.rmd
USCbiostats/phylogenetic documentation built on Oct. 17, 2018, 8:11 p.m.