FBD_tests2: Test for differences in FBD parameter values

In EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Test for differences in FBD parameter values

Description

FBD_tests2() performs t-tests and Mann-Whitney U-tests to compare the average value of fossilized birth–death process (FBD) parameters between time bins.

Usage

FBD_tests2(posterior, p.adjust.method = "fdr")

Arguments

posterior	A data frame of posterior parameter estimates containing a single "Time_bin" column and one column for each FBD parameter value. Such data frame can be imported using combine_log followed by FBD_reshape.
p.adjust.method	The method use to adjust the p-values for multiple testing. See p.adjust for details and options. Default if "fdr" for the Benjamini-Hochberg false discovery rate correction.

Details

pairwise.t.test and pairwise.wilcox.test are used to calculate, respectively, the t-test and Mann-Whitney U-tests statistics and p-values. Because the power of these tests depends on the number of posterior samples, it can be helpful to examine the distributions of FBD parameter posteriors using FBD_dens_plot instead of relying heavily on the tests.

Value

A list with an element for each test, each of which contains a list of test results for each parameter. The results are in the form of a data frame containing the sample sizes and unadjusted and adjusted p-values for each comparison.

See Also

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

combine_log for producing a single data set of parameter posterior samples from individual parameter log files.

FBD_reshape for converting posterior parameter table from wide to long format.

FBD_dens_plot, FBD_normality_plot, FBD_tests1, and FBD_tests2 for other functions used to summarize and display the distributions of the parameter posteriors.

pairwise.t.test and pairwise.wilcox.test for the tests used.

Examples

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

data("posterior3p")

posterior3p_long <- FBD_reshape(posterior3p)

FBD_tests2(posterior3p_long)

EvoPhylo documentation built on Nov. 4, 2022, 1:06 a.m.