sensi_plot.sensiTree.TraitEvol: Graphical diagnostics for class 'sensiTree.TraitEvol'

In sensiPhy: Sensitivity Analysis for Comparative Methods

Description

sensi_plot.sensiTree.TraitEvol Plot results from tree_discrete and tree_continuous.

Usage

## S3 method for class 'sensiTree.TraitEvol'
sensi_plot(x, graphs = "all", ...)

Arguments

x	output from tree_fitDiscrete or tree_fitContinuous
graphs	choose which graph should be printed in the output ("all", "q12", "q21", "aic" or" "optpar")
...	further arguments to methods

Author(s)

Gijsbert Werner

See Also

ggplot, tree_discrete tree_continuous

The following graphs are printed.

Graph aicc: Distribution of estimated AICc-values across each tree. Red vertical line represents the mean value among all estimates. Blue vertical line represents the median value among all estimates.

Graph optpar: Distribution of estimated values for optimisation parameter specified using 'transform' (if applicable) Red vertical line represents the mean value among all estimates. Blue vertical line represents the median value among all estimates.

Additionally, only for tree_discrete the function creates the following graphs.

Graph q12: Distribution of estimated parameter values for transition rates q12 for each tree. Red vertical line represents the mean value among all estimates. Blue vertical line represents the median value among all estimates.

Graph q21: Distribution of estimated parameter values for transition rates q21 for each tree. Red vertical line represents the mean value among all estimates. Blue vertical line represents the median value among all estimates.

While only for tree_continuous the function creates the following graphs.

Graph sigsq: Distribution of estimated parameter values for rate of evolution sigsq for each tree. Red vertical line represents the mean value among all estimates. Blue vertical line represents the median value among all estimates.

Graph z0: Distribution of estimated parameter values for z0 for each tree. Red vertical line represents the mean value among all estimates. Blue vertical line represents the median value among all estimates.

sensiPhy documentation built on April 14, 2020, 7:15 p.m.