| clockrate_summary {EvoPhylo} | R Documentation |
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)
Arguments
rate_table |
A data frame of clock rates, such as from the output of |
file |
An optional file path where the resulting table will be stored using |
digits |
The number of digits to round the summary results to. Default is 3. See |
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.
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).
See Also
vignette("rates-selection") for the use of this function as part of an analysis pipeline.
get_clockrate_table_MrBayes, summary
Examples
# 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)