Package: treeducken 1.1.0.9999

Wade Dismukes

treeducken: Nested Phylogenetic Tree Simulator

Simulates nested phylogenetic trees (gene trees in species tree, symbiont trees in host trees) using birth-death processes and transfers between lineages. Simulations of gene trees within species trees are performed using a three-tree model with species trees, locus trees, and gene trees. The cophylogenetic birth-death process is used to simulate sets of host and symbiont trees with extant associations between tips. For more information about the three-tree model see: Mallo et al. (2015) <doi:10.1093/sysbio/syv082>, Rasmussen and Kellis (2012) <doi:10.1101/gr.123901.111>.

Authors:Wade Dismukes [aut, cre], Tracy A. Heath [aut], Josh Justison [ctb], Damien de Vienne [ctb], Liam Revell [ctb], Emmanuel Paradis [ctb], Klaus Schliep [ctb], Ben Bolker [ctb], Luke J. Harmon [ctb], Joseph W. Brown [ctb]

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manual.pdf |manual.html✨
card.svg |card.png
treeducken/json (API)
NEWS

# Install 'treeducken' in R:
install.packages('treeducken', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wadedismukes/treeducken/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

3.72 score 4 stars 26 scripts 13 downloads 74 exports 16 dependencies

Last updated from:032b92e3b4. Checks:8 NOTE, 2 OK, 3 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE182
linux-devel-x86_64NOTE198
source / vignettesOK315
linux-release-arm64NOTE207
linux-release-x86_64NOTE180
macos-release-arm64NOTE162
macos-release-x86_64NOTE343
macos-oldrel-arm64FAIL90
macos-oldrel-x86_64FAIL172
windows-develNOTE172
windows-releaseNOTE175
windows-oldrelFAIL70
wasm-releaseOK146

Exports:add_eventsadd_scalebarassociation_matassociation_mat.cophyassociation_mat.multiCophyave_tips_ltave_tips_stbuild_historical_association_matrixc.cophyc.multiCophycalculate_expected_leaves_locustreecalculate_expected_leaves_sptreecollapse_cladecollapse_locus_subtreeconvert_assoc_table_to_matrixconvert_to_cophycophy_summary_statcophy_summary_stat_by_indxcount_cherriesdraw_cophydraw_curvedrop_extinctestimate_node_heightsevent_historyevent_history.cophyevent_history.multiCophygenetree_summary_statget_ana_eventsget_assocget_child_gtsget_lociget_parent_gtsget_tip_labels_tree_listget_tipnameshost_treehost_tree.cophyhost_tree.multiCophyis_extinctis.cophyis.multiCophylomake_matmake_textboxnode_heightsparafit_statparafit_testplot.cophyplot.multiCophyprint.cophyprint.multiCophyretrieve_child_genetreesretrieve_parent_genetreessim_cophyBDsim_cophyBD_anasim_cophylo_bdpsim_cophylo_bdp_anasim_locustree_bdpsim_ltBDsim_mlcsim_mscsim_multilocus_coalsim_multispecies_coalsim_sptree_bdpsim_sptree_bdp_timesim_stBDsim_stBD_tstr.multiCophysummarize_1cophysummarize_cophysummarize_gtsummary.cophysymb_treesymb_tree.cophysymb_tree.multiCophyto_cophy

Dependencies:apeapTreeshapecodacubaturedigestlatticeMASSMatrixMatrixModelsnlmepbapplyquantregRcppRcppArmadilloSparseMsurvival

Cophylogenetic simulation

Wade Dismukes

Rendered fromcophylogenetic_sim.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2021-07-14
Started: 2020-04-03

Readme and manuals

Help Manual

Help pageTopics
treeducken: simulates cophylogenetic systems & nested phylogeniestreeducken-package treeducken
Add events from sim_cophyBD to plot.cophyadd_events
Add scale bar to cophylo plotadd_scalebar
Reconstruct historical association matrixbuild_historical_association_matrix get_assoc
Combine cophylogenetic sets into a multiCophy objectc.cophy c.multiCophy
Calculate expected leaves of a locus treeave_tips_lt calculate_expected_leaves_locustree
Calculate expected leaves of a species treeave_tips_st calculate_expected_leaves_sptree
Collapse a clade into a single tipcollapse_clade collapse_locus_subtree
Convert a table with host and symbiont associations to a matrixconvert_assoc_table_to_matrix make_mat
Converts an object into an object of type cophyconvert_to_cophy to_cophy
Calculates summary statistics for cophylogenetic objectscophy_summary_stat cophy_summary_stat_by_indx summarize_1cophy summarize_cophy
Calculate cherry statistic for gene-treescount_cherries
Internal tree plot functiondraw_cophy
Curve draw functiondraw_curve
Drops extinct tips from treedrop_extinct
Calculate expected time to branching point of a species treeestimate_node_heights node_heights
Summarize a cophylogenetic setevent_history event_history.cophy summary.cophy
Calculate summary statistics for gene treesgenetree_summary_stat summarize_gt
Separate a locus tree into lociget_loci
Get all the tip labels of a `multiPhylo` objectget_tipnames get_tip_labels_tree_list
Print a cophylogenetic setassociation_mat association_mat.cophy association_mat.multiCophy event_history.multiCophy host_tree host_tree.cophy host_tree.multiCophy print.cophy print.multiCophy symb_tree symb_tree.cophy symb_tree.multiCophy
Identify extinct tips from treeis_extinct
Test for the cophylogenetic set objectis.cophy is.multiCophylo
Internal tree plot functionmake_textbox
Calculate the ParafitGlobal statistic on 2 trees and their association matrixparafit_stat parafit_test
Plot host and symbiont pair with current associationsplot.cophy plot.multiCophy
Retrieve all gene trees of the parent tree from a list generated from sim_mlcget_child_gts get_parent_gts retrieve_child_genetrees retrieve_parent_genetrees
Simulates a host-symbiont system using a cophylogenetic birth-death processsim_cophyBD sim_cophylo_bdp
Simulates a host-symbiont system using a cophylogenetic birth-death processsim_cophyBD_ana sim_cophylo_bdp_ana
Simulates locus tree using constant rate birth-death-transfer processsim_locustree_bdp sim_ltBD
Simulate multispecies coalescent on a species treesim_msc sim_multispecies_coal
Simulates multi-locus coalescent on a given locus treesim_mlc sim_multilocus_coal
Simulates species trees using constant rate birth-death processsim_sptree_bdp sim_stBD
Simulates species tree using constant rate birth-death process to a timesim_sptree_bdp_time sim_stBD_t
Retrieve the structure of a class multiCophystr.multiCophy