print.cophy: Print a cophylogenetic set

In treeducken: Nested Phylogenetic Tree Simulator

Description

Prints a cophylogenetic set or a list of cophylogenetic sets.

Usage

host_tree(cophy)

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

## S3 method for class 'multiCophy'
host_tree(cophy)

symb_tree(cophy)

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

## S3 method for class 'multiCophy'
symb_tree(cophy)

association_mat(cophy)

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

## S3 method for class 'multiCophy'
association_mat(cophy)

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

## S3 method for class 'cophy'
print(x, ...)

## S3 method for class 'multiCophy'
print(x, details = FALSE, ...)

Arguments

cophy	An object of class 'cophy'
x	An object of class 'cophy' or class 'multiCophy'
...	Further arguments used in generic classes
details	A logical value, outputs brief summary of each set in the list.

Details

The association matrix is output with symbionts in columns and hosts in rows. The event history data frame has codes for the following events: "CSP" = cospeciation/codivergence, "HSP" = host speciation, "HX" = host extinction, "SSP" = symbiont speciation, "SX" = Symbiont extinction, "DISP" = Symbiont dispersal, and "EXTP" = symbiont extirpation, "SHE" symbiont speciation with host spread or host switch.

Value

Print returns NULL. host_tree returns NULL, symb_tree returns NULL, association_mat returns the dimensions of the matrix, event_history returns NULL.

Functions

• host_tree: Returns host tree of a cophylogenetic set

• host_tree.cophy: Returns host tree of a cophylogenetic set

• host_tree.multiCophy: Returns host tree of each member of a list of cophylogenetic sets

• symb_tree: Returns symb tree of a cophylogenetic set

• symb_tree.cophy: Returns symb tree of a cophylogenetic set

• symb_tree.multiCophy: Returns symb tree of each member of a list of cophylogenetic sets

• association_mat: Returns association matrix of a cophylogenetic set

• association_mat.cophy: Returns association matrix of a cophylogenetic set

• association_mat.multiCophy: Returns association matrix for each member of a list of cophylogenetic sets

• event_history.multiCophy: Returns event_history for each member of a list of cophylogenetic sets

• print.multiCophy: Prints a list of cophylogenetic sets

Author(s)

Wade Dismukes, Ben Bolker, and Emmanuel Paradis

See Also

sim_cophylo_bdp, print 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 = 4)
print(host_symb_sets[[1]])
host_tree(host_symb_sets[[1]])
symb_tree(host_symb_sets[[1]])
association_mat(host_symb_sets[[1]])
event_history(host_symb_sets[[1]])
print(host_symb_sets)

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