Files in USCbiostats/phylogenetic
Statistical Inference and Prediction of Annotations in Phylogenetic Trees
.Rbuildignore
.github/.gitignore
.github/workflows/ci.yml
.github/workflows/update-docker.yml
.github/workflows/website.yml
.gitignore
.travis.yml.old
ChangeLog
DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS.md
R/RcppExports.R
R/accuracy_sifter.R
R/ape.R
R/aphylo-ape-info.R
R/aphylo-package.R
R/aphylo_from_data_frame.R
R/aphylo_hier.R
R/aphylo_mcmc.R
R/aphylo_mle.R
R/balance.R
R/color-palettes.R
R/cv.R
R/data-management.R
R/estimation.R
R/formulas.R
R/impute_duplications.R
R/indexing.R
R/list_offspring.R
R/loglike.R
R/misc.r
R/multiaphylo.R
R/panther.R
R/pie.r
R/plot.R
R/plot_logLik.R
R/polygon.r
R/predict.R
R/prediction_score.R
R/priors.R
R/prune.R
R/read_nhx.R
R/read_sifter.R
R/simulation.R
README.md
README.qmd
aphylo.Rproj
aphylo.code-workspace
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
docker/Dockerfile
docker/Dockerfile-clang
docker/Dockerfile.dev
docker/Dockerfile.flexiblas
docker/Makefile
inst/CITATION
inst/CODECOV_EXCLUSIONS
inst/NEWS
inst/include/pruner.hpp
inst/include/tree_bones.hpp
inst/include/tree_meat.hpp
inst/include/treeiterator_bones.hpp
inst/include/treeiterator_meat.hpp
inst/include/typedefs.hpp
inst/tinytest/test-aphylo-ape-info.r
inst/tinytest/test-aphylo_from_data_frame.R
inst/tinytest/test-auc.r
inst/tinytest/test-balance.r
inst/tinytest/test-cv.R
inst/tinytest/test-data-management.r
inst/tinytest/test-formula.r
inst/tinytest/test-impute_duplications.R
inst/tinytest/test-indexing.R
inst/tinytest/test-loglikelihood.r
inst/tinytest/test-panther.r
inst/tinytest/test-parameter-estimates-and-formulas.r
inst/tinytest/test-parameter-estimates.r
inst/tinytest/test-plot_loglike.r
inst/tinytest/test-predict-ans0.rds
inst/tinytest/test-predict-ans1.rds
inst/tinytest/test-predict.r
inst/tinytest/test-pseq-reduce.r
inst/tinytest/test-sim_phylo.r
inst/tree.tree
man-roxygen/edges.r
man-roxygen/estimates.R
man-roxygen/loo.r
man-roxygen/parameters.r
man/LogLike.Rd
man/accuracy_sifter.Rd
man/ape-methods.Rd
man/aphylo-class.Rd
man/aphylo-index.Rd
man/aphylo-info.Rd
man/aphylo-methods.Rd
man/aphylo-model.Rd
man/aphylo-package.Rd
man/aphylo_cv.Rd
man/aphylo_estimates.Rd
man/aphylo_from_data_frame.Rd
man/aphylo_mcmc.Rd
man/aphylo_mle.Rd
man/as.phylo.Rd
man/auc.Rd
man/balance_ann.Rd
man/bprior.Rd
man/fakeexperiment.Rd
man/faketree.Rd
man/figures/MCMC-1.png
man/figures/MCMC-2.png
man/figures/MLE-1.png
man/figures/Predict-1.png
man/figures/get-offspring-1.png
man/figures/get-offspring-2.png
man/figures/logo-raw.svg
man/figures/logo.svg
man/imputate_duplications.Rd
man/list_offspring.Rd
man/mislabel.Rd
man/multiAphylo.Rd
man/new_aphylo_pruner.Rd
man/panther-tree.Rd
man/plot.aphylo_prediction_score.Rd
man/plot_logLik.Rd
man/plot_multivariate.Rd
man/posterior-probabilities.Rd
man/prediction_score.Rd
man/raphylo.Rd
man/rdrop_annotations.Rd
man/read_nhx.Rd
man/read_pli.Rd
man/sim_fun_on_tree.Rd
man/sim_tree.Rd
man/states.Rd
man/write_pli.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/cpp-classes.cpp
playground/eta.Rmd
playground/eta.pdf
playground/exact-distribution-pscore.R
playground/leave-one-out.R
playground/multivariate-bernoulli.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/eac2018/notation-def.tex
playground/presentations/eac2018/p2-eac2018.Rmd
playground/presentations/eac2018/p2-eac2018.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/pruning.r
playground/reduced_peeling.r
playground/retreat2018.rmd
playground/root_node_prob.Rmd
playground/root_node_prob_fixed.pdf
playground/sim_phylo.cpp
src/Makevars.in
src/Makevars.win
src/RcppExports.cpp
src/TreeData.hpp
src/aphylo_pruner.cpp
src/auc.cpp
src/loglikelihood.h
src/misc.cpp
src/misc.h
src/predict.cpp
src/prediction_score_rand.cpp
src/sim_phylo.cpp
tests/tinytest.R
vignettes/example.Rmd
