plotDivRates: Plot Diversification Rates

In revbayes/RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Plot Diversification Rates

Description

Plots the output of an episodic diversification rate analysis

Usage

plotDivRates(rates, facet = TRUE)

Arguments

rates	(list of dataframes; no default) A list of dataframes, such as produced by processDivRates(), containing the data on rates and interval times for each type of rate to be plotted (e.g. speciation rate, etc.).
facet	(logical; TRUE) plot rates in separate facets.

Details

Plots the output of episodic diversification rate analyses. Takes as input the output of processDivRates() and plotting parameters. For now, only variable names (under "item") that contain the word "rate" are included in the plot.

The return object can be manipulated. For example, you can change the axis labels, the color palette, whether the axes are to be linked, or the overall plotting style/theme, just as with any ggplot object.

Value

A ggplot object

Examples

# download the example datasets to working directory

url_ex_times <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_extinction_times.log"
dest_path_ex_times <- "primates_EBD_extinction_times.log"
download.file(url_ex_times, dest_path_ex_times)

url_ex_rates <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_extinction_rates.log"
dest_path_ex_rates <- "primates_EBD_extinction_rates.log"
download.file(url_ex_rates, dest_path_ex_rates)

url_sp_times <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_times.log"
dest_path_sp_times <- "primates_EBD_speciation_times.log"
download.file(url_sp_times, dest_path_sp_times)

url_sp_rates <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_rates.log"
dest_path_sp_rates <- "primates_EBD_speciation_rates.log"
download.file(url_sp_rates, dest_path_sp_rates)

# to run on your own data, change this to the path to your data file
speciation_time_file <- dest_path_sp_times
speciation_rate_file <- dest_path_sp_rates
extinction_time_file <- dest_path_ex_times
extinction_rate_file <- dest_path_ex_rates

rates <- processDivRates(speciation_time_log = speciation_time_file,
                         speciation_rate_log = speciation_rate_file,
                         extinction_time_log = extinction_time_file,
                         extinction_rate_log = extinction_rate_file,
                         burnin = 0.25)

# then plot results:
p <- plotDivRates(rates = rates);p

# change the x-axis
p <- p + ggplot2::xlab("Thousands of years ago");p

# change the colors
p <- p + ggplot2::scale_fill_manual(values = c("red",
                                               "green",
                                               "yellow",
                                               "purple")) +
  ggplot2::scale_color_manual(values = c("red",
                                         "green",
                                         "yellow",
                                         "purple"));p

# let's say we don't want to plot relative-extinction rate,
# and use the same y-axis for all three rates
rates <- rates[!grepl("relative-extinction", rates$item),]
p2 <- plotDivRates(rates)
p2 <- p2 + ggplot2::facet_wrap(ggplot2::vars(item), scale = "fixed");p2

# remove files
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_sp_times, dest_path_ex_times,
            dest_path_sp_rates, dest_path_ex_rates)

revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.