Compute rate summary statistics across clades and clocks
clockrate_summary.RdComputes summary statistics for each clade and/or each clock partition. The input must have a "clade" column.
Arguments
- rate_table
A data frame of clock rates, such as from the output of
get_clockrate_table_MrBayeswith 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.
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).
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)
#> clade clock n mean sd min Q1 median Q3 max
#> 1 Dipnomorpha 1 8 1.100 0.110 0.944 1.020 1.098 1.194 1.231
#> 2 Elpisostegalia 1 14 1.605 0.216 1.133 1.451 1.682 1.797 1.806
#> 3 Osteolepididae 1 11 0.632 0.264 0.165 0.442 0.811 0.836 0.872
#> 4 Rhizodontidae 1 14 0.572 0.304 0.030 0.330 0.667 0.834 0.890
#> 5 Tristichopteridae 1 21 0.714 0.036 0.615 0.695 0.722 0.739 0.782
#> 6 Other 1 11 0.885 0.358 0.541 0.689 0.782 0.941 1.807
#> 7 Dipnomorpha 2 8 0.751 0.181 0.518 0.624 0.747 0.891 0.981
#> 8 Elpisostegalia 2 14 1.361 0.099 1.029 1.360 1.377 1.412 1.423
#> 9 Osteolepididae 2 11 0.345 0.153 0.066 0.278 0.382 0.452 0.532
#> 10 Rhizodontidae 2 14 0.327 0.183 0.019 0.174 0.384 0.443 0.557
#> 11 Tristichopteridae 2 21 0.342 0.059 0.270 0.315 0.327 0.332 0.545
#> 12 Other 2 11 0.747 0.253 0.388 0.610 0.717 0.782 1.352
#> 13 Dipnomorpha 3 8 0.869 0.110 0.720 0.791 0.887 0.948 1.006
#> 14 Elpisostegalia 3 14 0.834 0.163 0.626 0.671 0.892 0.987 1.001
#> 15 Osteolepididae 3 11 0.320 0.128 0.074 0.274 0.333 0.416 0.486
#> 16 Rhizodontidae 3 14 0.318 0.167 0.022 0.205 0.395 0.429 0.521
#> 17 Tristichopteridae 3 21 0.520 0.085 0.374 0.435 0.536 0.586 0.639
#> 18 Other 3 11 0.731 0.166 0.466 0.640 0.699 0.813 1.002