FBD_reshape: Convert an FBD posterior parameter table from wide to long...

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

Convert an FBD posterior parameter table from wide to long format

Description

Converts FBD posterior parameter table, such as those imported using combine_log, from wide to long format.

Usage

FBD_reshape(posterior, variables = NULL, log.type = c("MrBayes", "BEAST2"))

Arguments

posterior	Single posterior parameter sample dataset with skyline FBD parameters produced with combine_log.
variables	Names of FBD rate variables in the log. If NULL (default), will attempt to auto-detect the names and log type.
log.type	Name of the software which produced the log (currently supported: MrBayes or BEAST2). Has to be set if variables is not NULL.

Details

The posterior parameters log files produced by Bayesian evolutionary analyses using skyline birth-death tree models, including the skyline FBD model, result into two or more estimates for each FBD parameter, one for each time bin. This function will convert a table of parameters with skyline FBD parameters from wide to long format, with one row per generation per time bin and a new column "Time_bin" containing the respective time bins as a factor. The long format is necessary for downstream analyses using FBD_summary, FBD_dens_plot, FBD_normality_plot, FBD_tests1, or FBD_tests2, as similarly done by clock_reshape for clock rate tables.

The format of the log files can either be specified using the variables and log.type or auto-detected by the function. The "posterior" data frame can be obtained by reading in a log file directly (e.g. using the read.table function) or by combining several output log files from Mr. Bayes using combine_log.

Value

A data frame of posterior parameter estimates containing a single "Time_bin" column and one column for each FBD parameter value.

See Also

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

combine_log, reshape

Examples

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

data("posterior3p")

head(posterior3p)

## Reshape FBD table to long format
posterior3p_long <- FBD_reshape(posterior3p)

head(posterior3p_long)

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