clockrate_summary: Compute rate summary statistics across clades and clocks

Description

Computes summary statistics for each clade and/or each clock partition. The input must have a "clade" column.

Usage

clockrate_summary(rate_table, file = NULL, digits = 3)

Value

A data frame containing a row for each clade and each clock with summary statistics (n, mean, standard deviation, minimum, 1st quartile, median, third quartile, maximum).

Arguments

rate_table: A data frame of clock rates, such as from the output of get_clockrate_table_MrBayes with an extra "clade" column.
file: An optional file path where the resulting table will be stored using write.csv.
digits: The number of digits to round the summary results to. Default is 3. See round.

Details

The user must manually add clades to the rate table produced by get_clockrate_table_MrBayes before it can be used with this function. This can be doen manually within R, such as by using a graphical user interface for editing data like the DataEditR package, or by writing the rate table to a spreadsheet and reading it back in after adding the clades. The example below uses a table that has had the clades added.

Examples

Run this code

# See vignette("rates-selection") for how to use this
# function as part of an analysis pipeline

data("RateTable_Means_3p_Clades")

clockrate_summary(RateTable_Means_3p_Clades)