plot_glm: Plots the results of a GLM analysis from BEAST

Description Usage Arguments Value Author(s)

Description

Plots the results of a GLM analysis from BEAST

Usage

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plot_glm(Names, Log, prob_zero = 0.5, cutoffs = c(3, 50),
  intercept = FALSE, alpha = 0.95, conditional = TRUE,
  burnin = 0.2, title = "", export = TRUE, file_name = "GLM_plot")

Arguments

Names

a character vector with the predictor names (labels)

Log

a dataframe with traces without burnin

prob_zero

a scalar specifying the probability that no predictors are included (default: 0.5)

cutoffs

a numeric vector with the Bayes factor cutoffs to be used (dotted lines in the plot, default: 3 and 50)

intercept

a boolean specifying whether the model has an intercept (default: FALSE)

alpha

a scalar with the credibility level to be used for credibility intervals (default:0.95)

conditional

a boolean specifying whether the coeffcients should be plotted conditionally

burnin

a scalar specifying the *proportion* of the samples to discard as burn-in/warm-up

title

a character with the title in the plot (default: none)

export

a boolean (default: TRUE)

file_name

a character specifying the name of the output PDF file. Ignored if export = FALSE.

Value

a (ggplot) plot object showing inclusion probabilities, Bayes factors and coefficient estimates

Author(s)

Luiz Max Carvalho/Philippe Lemey/Nuno Faria


beast-dev/RBeast documentation built on May 12, 2019, 10:02 a.m.