Conduct pairwise t-tests between node rates and clock base rates from a BEAST2 output.
get_pwt_rates_BEAST2.RdProduces a data frame containing the results of 1-sample t-tests for the mean of posterior clock rates against each node's absolute clock rate.
Arguments
- rate_table
A data frame containing a single "value" column (for all rate values) and one column for the "clock" variable (indicating to which clock partition each rate values refers to), such as from the output of
get_clockrate_table_MrBayeswith an extracladecolumn added, and followed byclock_reshape.- posterior
A data frame of posterior parameter estimates including a "clockrate" column indicating the base of the clock rate estimate for each generation that will be used for pairwise t-tests. Such data frame can be imported using
combine_log(no need to reshape from wide to long). See theposterior1porposterior3pdatasets for an examples of how the input file should look.
Details
get_pwt_rates_BEAST2() first transforms relative clock rates to absolute rate values for each node and each clock, by multiplying these by the mean posterior clock rate base value. Then, for each node and clock, a one-sample t-test is performed with the null hypothesis that the mean of the posterior clockrates is equal to that node and clock's absolute clock rate.
Value
A long data frame with one row per node per clock and the following columns:
- clade
The name of the clade, taken from the "clade" column of
rate_table- nodes
The node number, taken from the "node" column of
rate_table- clock
The clock partition number
- background.rate(mean)
The absolute background clock rate (mean clock rate for the whole tree) sampled from the posterior log file
- relative.rate(mean)
The relative mean clock rate per branch, taken from the "rates" columns of
rate_table- absolute.rate(mean)
The absolute mean clock rate per branch; the relative clock rate multiplied by the mean of the posterior clock rates
- p.value
The p-value of the test comparing the mean ofthe posterior clockrates to each absolute clockrate
Examples
if (FALSE) {
# See vignette("rates-selection") for how to use this
# function as part of an analysis pipeline
# Load example rate table and posterior data sets
RateTable_Means_Clades <- system.file("extdata", "RateTable_Means_Clades.csv", package = "EvoPhylo")
RateTable_Means_Clades <- read.csv(RateTable_Means_Clades, header = TRUE)
posterior <- system.file("extdata", "Penguins_log.log", package = "EvoPhylo")
posterior <- read.table(posterior, header = TRUE)
get_pwt_rates_BEAST2(RateTable_Means_Clades, posterior)
}