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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]

# 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:

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.

Target	Result	Time
linux-devel-arm64	NOTE	182
linux-devel-x86_64	NOTE	198
source / vignettes	OK	315
linux-release-arm64	NOTE	207
linux-release-x86_64	NOTE	180
macos-release-arm64	NOTE	162
macos-release-x86_64	NOTE	343
macos-oldrel-arm64	FAIL	90
macos-oldrel-x86_64	FAIL	172
windows-devel	NOTE	172
windows-release	NOTE	175
windows-oldrel	FAIL	70
wasm-release	OK	146

Exports:add_events add_scalebar association_mat association_mat.cophy association_mat.multiCophy ave_tips_lt ave_tips_st build_historical_association_matrix c.cophy c.multiCophy calculate_expected_leaves_locustree calculate_expected_leaves_sptree collapse_clade collapse_locus_subtree convert_assoc_table_to_matrix convert_to_cophy cophy_summary_stat cophy_summary_stat_by_indx count_cherries draw_cophy draw_curve drop_extinct estimate_node_heights event_history event_history.cophy event_history.multiCophy genetree_summary_stat get_ana_events get_assoc get_child_gts get_loci get_parent_gts get_tip_labels_tree_list get_tipnames host_tree host_tree.cophy host_tree.multiCophy is_extinct is.cophy is.multiCophylo make_mat make_textbox node_heights parafit_stat parafit_test plot.cophy plot.multiCophy print.cophy print.multiCophy retrieve_child_genetrees retrieve_parent_genetrees sim_cophyBD sim_cophyBD_ana sim_cophylo_bdp sim_cophylo_bdp_ana sim_locustree_bdp sim_ltBD sim_mlc sim_msc sim_multilocus_coal sim_multispecies_coal sim_sptree_bdp sim_sptree_bdp_time sim_stBD sim_stBD_t str.multiCophy summarize_1cophy summarize_cophy summarize_gt summary.cophy symb_tree symb_tree.cophy symb_tree.multiCophy to_cophy

Dependencies:ape apTreeshape coda cubature digest lattice MASS Matrix MatrixModels nlme pbapply quantreg Rcpp RcppArmadillo SparseM survival

Cophylogenetic simulation

Rendered fromcophylogenetic_sim.Rmdusingknitr::rmarkdown

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

Help page	Topics
treeducken: simulates cophylogenetic systems & nested phylogenies	treeducken-package treeducken
Add events from sim_cophyBD to plot.cophy	add_events
Add scale bar to cophylo plot	add_scalebar
Reconstruct historical association matrix	build_historical_association_matrix get_assoc
Combine cophylogenetic sets into a multiCophy object	c.cophy c.multiCophy
Calculate expected leaves of a locus tree	ave_tips_lt calculate_expected_leaves_locustree
Calculate expected leaves of a species tree	ave_tips_st calculate_expected_leaves_sptree
Collapse a clade into a single tip	collapse_clade collapse_locus_subtree
Convert a table with host and symbiont associations to a matrix	convert_assoc_table_to_matrix make_mat
Converts an object into an object of type cophy	convert_to_cophy to_cophy
Calculates summary statistics for cophylogenetic objects	cophy_summary_stat cophy_summary_stat_by_indx summarize_1cophy summarize_cophy
Calculate cherry statistic for gene-trees	count_cherries
Internal tree plot function	draw_cophy
Curve draw function	draw_curve
Drops extinct tips from tree	drop_extinct
Calculate expected time to branching point of a species tree	estimate_node_heights node_heights
Summarize a cophylogenetic set	event_history event_history.cophy summary.cophy
Calculate summary statistics for gene trees	genetree_summary_stat summarize_gt
Separate a locus tree into loci	get_loci
Get all the tip labels of a `multiPhylo` object	get_tipnames get_tip_labels_tree_list
Print a cophylogenetic set	association_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 tree	is_extinct
Test for the cophylogenetic set object	is.cophy is.multiCophylo
Internal tree plot function	make_textbox
Calculate the ParafitGlobal statistic on 2 trees and their association matrix	parafit_stat parafit_test
Plot host and symbiont pair with current associations	plot.cophy plot.multiCophy
Retrieve all gene trees of the parent tree from a list generated from sim_mlc	get_child_gts get_parent_gts retrieve_child_genetrees retrieve_parent_genetrees
Simulates a host-symbiont system using a cophylogenetic birth-death process	sim_cophyBD sim_cophylo_bdp
Simulates a host-symbiont system using a cophylogenetic birth-death process	sim_cophyBD_ana sim_cophylo_bdp_ana
Simulates locus tree using constant rate birth-death-transfer process	sim_locustree_bdp sim_ltBD
Simulate multispecies coalescent on a species tree	sim_msc sim_multispecies_coal
Simulates multi-locus coalescent on a given locus tree	sim_mlc sim_multilocus_coal
Simulates species trees using constant rate birth-death process	sim_sptree_bdp sim_stBD
Simulates species tree using constant rate birth-death process to a time	sim_sptree_bdp_time sim_stBD_t
Retrieve the structure of a class multiCophy	str.multiCophy

Package: treeducken 1.1.0.9999

treeducken: Nested Phylogenetic Tree Simulator

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