clockrate_summary {EvoPhylo}R Documentation

Compute rate summary statistics across clades and clocks


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


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



A data frame of clock rates, such as from the output of get_clockrate_table_MrBayes with an extra "clade" column.


An optional file path where the resulting table will be stored using write.csv.


The number of digits to round the summary results to. Default is 3. See round.


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.


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).

See Also

vignette("rates-selection") for the use of this function as part of an analysis pipeline.

get_clockrate_table_MrBayes, summary


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



[Package EvoPhylo version 0.3.2 Index]