summarize.trends: Summarize trends in the congruence class

In ACDC: Analysis of Congruent Diversification Classes

Description

Summarize trends in the congruence class

Usage

summarize.trends(model_set, threshold = 0.005, rate_name = "lambda", 
return_data = FALSE, rm_singleton = FALSE, relative_deltas = FALSE, group_names = NULL)

Arguments

model_set	an object of type "ACDCset"
threshold	a threshold for when Δ λ i should be interpreted as decreasing, flat, or increasing
rate_name	either "lambda" or "mu" or "delta"
return_data	instead of plots, return the plotting dataframes
rm_singleton	whether or not to remove singletons. Pass starting at present, going towards ancient
relative_deltas	whether to divide Δ λ i by the local lambda value
group_names	a vector of prefixes, if you want to group the models in a facet. For example 'c("reference", "model")'

Value

a patchwork object

Examples

data(primates_ebd)
lambda <- approxfun(primates_ebd$time, primates_ebd$lambda)
mu <- approxfun(primates_ebd$time, primates_ebd$mu)
times <- seq(0, max(primates_ebd$time), length.out = 500)

reference <- create.model(lambda, mu, times = times)

mus <- list(function(t) exp(0.01*t) - 0.01*t - 0.9,
            function(t) exp(-0.02*t) - 0.2,
            function(t) exp(-0.07*t) + 0.02*t - 0.5,
            function(t) 0.2 + 0.01*t,
            function(t) 0.2)


model_set <- congruent.models(reference, mus = mus)

p <- summarize.trends(model_set, 0.02)

ACDC documentation built on Jan. 13, 2022, 1:08 a.m.