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

treeducken documentation built on March 3, 2021, 1:11 a.m.