summary.cophy: Summarize a cophylogenetic set

In treeducken: Nested Phylogenetic Tree Simulator

Description

Several utility functions for cophylogenetic set summarization. Including functions for printing an entire summary, and a summary of each part: host_tree, symb_tree, association_mat, and event_history.

Usage

event_history(cophy)

## S3 method for class 'cophy'
event_history(cophy)

## S3 method for class 'cophy'
summary(object, ...)

Arguments

cophy	Cophylogenetic set
object	An object of class 'cophy'
...	Further arguments used in generic classes

Details

The summary for a cophylogenetic set outputs a summary of the host tree and the symbiont tree. The number of rows and columns of the association matrix, and a summary of the event_history.

Value

Summary returns NULL.

Functions

• event_history: Returns event history of a cophylogenetic set

• event_history.cophy: Returns event history of a cophylogenetic set

Author(s)

Wade Dismukes and Emmanuel Paradis

See Also

sim_cophylo_bdp, summary for the generic, multiCophy, c.cophy

Examples

h_lambda <- 1.0
h_mu <- 0.3
c_lambda <- 0.0
s_lambda <- 1.0
s_mu <- 0.3
s_her <- 0.0
host_symb_sets <- sim_cophylo_bdp(hbr = h_lambda,
                                  hdr = h_mu,
                                  sbr = s_lambda,
                                  cosp_rate = c_lambda,
                                  sdr = s_mu,
                                  host_exp_rate = s_her,
                                  time_to_sim = 1.0,
                                  numbsim = 1)
summary(host_symb_sets[[1]])

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