add_events: Add events from sim_cophyBD to plot.cophy

In treeducken: Nested Phylogenetic Tree Simulator

Description

This will plot the classical cophylogenetic events onto the plot from plot.cophy if event_history is non-empty. At present this only works with phylograms.

Usage

add_events(
  cophy_obj,
  legend = TRUE,
  pch = NULL,
  col = NULL,
  gap = 1,
  fsize = 1,
  type = "phylogram",
  show_tip_label = TRUE
)

Arguments

cophy_obj	Cophylogenetic object
legend	Boolean to turn on or off the legend
pch	Length 8 vector of plotting symbols to be used
col	Length 8 vector of colors to be used in plot
gap	the gap between the two trees
fsize	the font size of tips (this must be set the same as used in plot.cophy)
type	the type of graph ("phylogram" or "cladogram")
show_tip_label	Boolean indicating whether the plot has tip labels or not

Details

The pch and color vectors place symbols or colors for the different events. The order this vector is input determines which symbol corresponds to which event. * Position 1 = cospeciation * Position 2 = host speciation * Position 3 = host extinction * Position 4 = symbiont speciation * Position 5 = symbiont extinction * Position 6 = host spread or host-switch symbiont speciation * Position 7 = anagenetic symbiont dispersal * Position 8 = anadenetic symbiont extirpation

By default a color vector is used in this order: purple, red, blue, darkorange, cyan, yellow, brown, seagreen

Examples

host_mu <- 1.0 # death rate
host_lambda <- 2.0 # birth rate
numb_replicates <- 10
time <- 1.0
symb_mu <- 0.2
symb_lambda <- 0.4
host_shift_rate <- 0.0
cosp_rate <- 2.0

cophylo_pair <- sim_cophyBD(hbr = host_lambda,
                           hdr = host_mu,
                           cosp_rate = cosp_rate,
                           host_exp_rate = host_shift_rate,
                           sdr = symb_mu,
                           sbr = symb_lambda,
                           numbsim = numb_replicates,

                           time_to_sim = time)
plot.cophy(cophylo_pair[[1]])
add_events(cophylo_pair[[1]], legend = FALSE)

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