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.

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.

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)
#> $t_tests #>$t_tests$net_speciation #> parameter Time_bin1 Time_bin2 n1 n2 p-value p-value adj #> 1 net_speciation 1 2 10000 10000 0.000000e+00 0.000000e+00 #> 2 net_speciation 1 3 10000 10000 0.000000e+00 0.000000e+00 #> 3 net_speciation 1 4 10000 10000 6.233495e-24 6.233495e-24 #> 4 net_speciation 2 3 10000 10000 2.211519e-178 2.653822e-178 #> 5 net_speciation 2 4 10000 10000 0.000000e+00 0.000000e+00 #> 6 net_speciation 3 4 10000 10000 0.000000e+00 0.000000e+00 #> #>$t_tests$relative_extinction #> parameter Time_bin1 Time_bin2 n1 n2 p-value p-value adj #> 1 relative_extinction 1 2 10000 10000 0.000000e+00 0.000000e+00 #> 2 relative_extinction 1 3 10000 10000 0.000000e+00 0.000000e+00 #> 3 relative_extinction 1 4 10000 10000 0.000000e+00 0.000000e+00 #> 4 relative_extinction 2 3 10000 10000 3.621037e-48 3.621037e-48 #> 5 relative_extinction 2 4 10000 10000 0.000000e+00 0.000000e+00 #> 6 relative_extinction 3 4 10000 10000 0.000000e+00 0.000000e+00 #> #>$t_tests$relative_fossilization #> parameter Time_bin1 Time_bin2 n1 n2 p-value #> 1 relative_fossilization 1 2 10000 10000 5.666499e-179 #> 2 relative_fossilization 1 3 10000 10000 1.447373e-164 #> 3 relative_fossilization 1 4 10000 10000 1.030473e-05 #> 4 relative_fossilization 2 3 10000 10000 0.000000e+00 #> 5 relative_fossilization 2 4 10000 10000 4.449998e-129 #> 6 relative_fossilization 3 4 10000 10000 3.026156e-220 #> p-value adj #> 1 1.133300e-178 #> 2 2.171060e-164 #> 3 1.030473e-05 #> 4 0.000000e+00 #> 5 5.339997e-129 #> 6 9.078469e-220 #> #> #>$mwu_tests
#> $mwu_tests$net_speciation
#>        parameter Time_bin1 Time_bin2    n1    n2       p-value   p-value adj
#> 1 net_speciation         1         2 10000 10000  0.000000e+00  0.000000e+00
#> 2 net_speciation         1         3 10000 10000  0.000000e+00  0.000000e+00
#> 3 net_speciation         1         4 10000 10000  1.687839e-20  1.687839e-20
#> 4 net_speciation         2         3 10000 10000 7.102785e-263 8.523342e-263
#> 5 net_speciation         2         4 10000 10000  0.000000e+00  0.000000e+00
#> 6 net_speciation         3         4 10000 10000  0.000000e+00  0.000000e+00
#>
#> $mwu_tests$relative_extinction
#>             parameter Time_bin1 Time_bin2    n1    n2       p-value
#> 1 relative_extinction         1         2 10000 10000  0.000000e+00
#> 2 relative_extinction         1         3 10000 10000  0.000000e+00
#> 3 relative_extinction         1         4 10000 10000  0.000000e+00
#> 4 relative_extinction         2         3 10000 10000 3.308183e-304
#> 5 relative_extinction         2         4 10000 10000  0.000000e+00
#> 6 relative_extinction         3         4 10000 10000  0.000000e+00
#> 1  0.000000e+00
#> 2  0.000000e+00
#> 3  0.000000e+00
#> 4 3.308183e-304
#> 5  0.000000e+00
#> 6  0.000000e+00
#>
#> $mwu_tests$relative_fossilization
#>                parameter Time_bin1 Time_bin2    n1    n2 p-value p-value adj
#> 1 relative_fossilization         1         2 10000 10000       0           0
#> 2 relative_fossilization         1         3 10000 10000       0           0
#> 3 relative_fossilization         1         4 10000 10000       0           0
#> 4 relative_fossilization         2         3 10000 10000       0           0
#> 5 relative_fossilization         2         4 10000 10000       0           0
#> 6 relative_fossilization         3         4 10000 10000       0           0
#>
#>