Man pages for treeducken
Nested Phylogenetic Tree Simulator

add_eventsAdd events from sim_cophyBD to plot.cophy
add_scalebarAdd scale bar to cophylo plot
build_historical_association_matrixReconstruct historical association matrix
calculate_expected_leaves_locustreeCalculate expected leaves of a locus tree
calculate_expected_leaves_sptreeCalculate expected leaves of a species tree
c.cophyCombine cophylogenetic sets into a multiCophy object
collapse_locus_subtreeCollapse a clade into a single tip
convert_assoc_table_to_matrixConvert a table with host and symbiont associations to a...
convert_to_cophyConverts an object into an object of type cophy
cophy_summary_statCalculates summary statistics for cophylogenetic objects
count_cherriesCalculate cherry statistic for gene-trees
draw_cophyInternal tree plot function
draw_curveCurve draw function
drop_extinctDrops extinct tips from tree
estimate_node_heightsCalculate expected time to branching point of a species tree
genetree_summary_statCalculate summary statistics for gene trees
get_ana_eventsInternal function for plotting anagenetic events
get_lociSeparate a locus tree into loci
get_tip_labels_tree_listGet all the tip labels of a 'multiPhylo' object
is.cophyTest for the cophygenetic set object
is_extinctIdentify extinct tips from tree
make_textboxInternal tree plot function
parafit_statCalculate the ParafitGlobal statistic on 2 trees and their...
plot.cophyPlot host and symbiont pair with current associations
print.cophyPrint a cophylogenetic set
retrieve_parent_genetreesRetrieve all gene trees of the parent tree from a list...
sim_cophyBDSimulates a host-symbiont system using a cophylogenetic...
sim_cophyBD_anaSimulates a host-symbiont system using a cophylogenetic...
sim_ltBDSimulates locus tree using constant rate birth-death-transfer...
sim_mscSimulate multispecies coalescent on a species tree
sim_multilocus_coalSimulates multi-locus coalescent on a given locus tree
sim_stBDSimulates species trees using constant rate birth-death...
sim_stBD_tSimulates species tree using constant rate birth-death...
str.multiCophyRetrieve the structure of a class multiCophy
summary.cophySummarize a cophylogenetic set
treeducken-packagetreeducken: simulates cophylogenetic systems & nested...
treeducken documentation built on March 3, 2021, 1:11 a.m.