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Calculate the rate of host-repertoire evolution

Source: R/events_counter.R
events_counter.Rd

Calculate the number of host gains, host losses, and the effective rate of host repertoire evolution.

Usage

count_events(history)

effective_rate(history, tree)

count_gl(history)

rate_gl(history, tree)

Arguments

history

A data frame containing the character history produced by RevBayes and read by read_history().

tree

A phylogenetic tree of the symbiont clade

Functions

  • count_events(): Get the average number of events along the symbiont tree and the highest posterior density interval with 95% probability (HPD95), based on all MCMC iterations in history.

  • effective_rate(): Get the effective rate of evolution, i.e. number of events per branch unit, along each tree branch. Mean and HP95 are outputted.

  • count_gl(): Get the average number of host gains and host losses

  • rate_gl(): Get the average effective rate of host gain and host loss

Examples

# read data that comes with the package
data_path <- system.file("extdata", package = "evolnets")
tree <- read_tree_from_revbayes(paste0(data_path,"/tree_pieridae.tre"))
history <- read_history(paste0(data_path,"/history_thin_pieridae.txt"), burnin = 0)

# all events
n_events <- count_events(history)
rate <- effective_rate(history,tree)

# gains and losses separately
gl_events <- count_gl(history)
gl_rates <- rate_gl(history, tree)