Plots distribution of background rates extracted from posterior log files.

Plots The distribution and mean of background rates extracted from the posterior log files from Mr. Bayes or BEAST2, as well as the distribution of background rates if log transformed to test for normality of data distribution.

Usage

plot_back_rates(type = c("MrBayes", "BEAST2"),
                           posterior,
                           clock = 1,
                           trans = c("none", "log", "log10", "z"),
                           size = 12, quantile = 0.95)

Arguments

type: Whether to use data output from "Mr.Bayes" or "BEAST2".
posterior: A data frame of posterior parameter estimates (log file). From Mr.Bayes, it includes a "clockrate" column indicating the mean (background) 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 the posterior1p or posterior3p datasets for an examples of how the input file should look. From BEAST2, it will include at least one "rate<filename>.mean" column indicating the mean (background) clock rate estimate for each generation. If there are "P" unlinked clock partitions in BEAST2, there will be P x "rate<filename>.mean" columns (one for each partition) in the posterior log file.
clock: The clock partition number to calculate selection mode. Ignored if only one clock is available.
trans: Type of data transformation to perform on background rates extracted from the posterior log file from Mr. Bayes or BEAST2. Options include "none" (if rates are normally distributed), natural log transformation "log", and log of base 10 transformation "log10", and "z" FOR A z-transformation. The necessity of using data transformation can be tested using the function plot_back_rates.
size: Font size for title of plot
quantile: Upper limit for X axis (passed on to 'xlim') to remove outliers from histogram. The quantile can be any value between "0" and "1", but values equal or above "0.95" provide good results in most cases in which the data distribution is right skewed.

Details

Plots The distribution and mean (red dotted line) of background rates extracted from the posterior log files from Mr. Bayes or BEAST2, as well as the distribution of background rates if log transformed. Background rates should be normally distributed for meeting the assumptions of t-tests and other tests passed on by downstream functions, including get_pwt_rates_MrBayes, get_pwt_rates_BEAST2, and plot_treerates_sgn.

Value

It produces a ggplot object that can be manipulated using ggplot2 syntax (e.g., to change the theme or labels).

Examples

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

## MrBayes example
# Load example tree and posterior

data("posterior3p")

P <- plot_back_rates (type = "MrBayes", posterior3p, clock = 1,
                      trans = "log10", size = 10, quantile = 0.95)
P
#> Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(density)` instead.
#> ℹ The deprecated feature was likely used in the EvoPhylo package.
#>   Please report the issue at <https://github.com/tiago-simoes/EvoPhylo/issues>.
#> Warning: Use of `posterior.final$clockrate.log` is discouraged.
#> ℹ Use `clockrate.log` instead.
#> Warning: Use of `posterior.final$clockrate.log` is discouraged.
#> ℹ Use `clockrate.log` instead.
#> Warning: Use of `posterior.final$clockrate.log` is discouraged.
#> ℹ Use `clockrate.log` instead.