Files in treeducken
Nested Phylogenetic Tree Simulator
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/RcppExports.R
R/is.cophylo.R
R/plot_cophy.R
R/utilities.R
R/build_historical_assoc_mat.R
R/sim_multilocus.R
R/convert_assoc_tab_to_mat.R
R/convert_to_cophylo.R
R/deprecated_sim_functions.R
R/summary_cophylo.R
R/calculate_genetree_summary_stat.R
R/estimate_node_heights.R
R/calculate_cophylo_summary_stat.R
src/Makevars
src/LocusTree.h
src/Cophylo.cpp
src/Tree.h
src/Simulator.cpp
src/RcppExports.cpp
src/rcpp_treeducken.cpp
src/SpeciesTree.h
src/SymbiontTree.cpp
src/Tree.cpp
src/LocusTree.cpp
src/Treeducken.cpp
src/GeneTree.h
src/SpeciesTree.cpp
src/SymbiontTree.h
src/Simulator.h
src/GeneTree.cpp
inst/doc/cophylogenetic_sim.Rmd
inst/doc/cophylogenetic_sim.html
inst/doc/cophylogenetic_sim.R
inst/extdata/lice_bd.tre
inst/extdata/gophers_bd.tre
inst/extdata/gopher_lice_mapping.txt
build/vignette.rds
tests/lldb-testr.sh
tests/testthat.R
tests/testthat/test_locus_gene.R
tests/testthat/test_cophylo_obj.R
tests/testthat/test_sptree_gsa.R
tests/testthat/test_cophylo.R
vignettes/cophylogenetic_sim.Rmd
man/c.cophy.Rd
man/add_scalebar.Rd
man/cophy_summary_stat.Rd
man/sim_cophyBD_ana.Rd
man/sim_stBD_t.Rd
man/calculate_expected_leaves_locustree.Rd
man/draw_cophy.Rd
man/sim_cophyBD.Rd
man/retrieve_parent_genetrees.Rd
man/get_ana_events.Rd
man/estimate_node_heights.Rd
man/sim_stBD.Rd
man/genetree_summary_stat.Rd
man/count_cherries.Rd
man/calculate_expected_leaves_sptree.Rd
man/build_historical_association_matrix.Rd
man/is_extinct.Rd
man/sim_multilocus_coal.Rd
man/collapse_locus_subtree.Rd
man/print.cophy.Rd
man/summary.cophy.Rd
man/get_tip_labels_tree_list.Rd
man/make_textbox.Rd
man/convert_to_cophy.Rd
man/draw_curve.Rd
man/sim_msc.Rd
man/add_events.Rd
man/is.cophy.Rd
man/plot.cophy.Rd
man/sim_ltBD.Rd
man/parafit_stat.Rd
man/str.multiCophy.Rd
man/convert_assoc_table_to_matrix.Rd
man/get_loci.Rd
man/treeducken-package.Rd
man/drop_extinct.Rd
