sensi_plot.sensiIntra_Clade: Graphical diagnostics for class 'sensiIntra_Clade'

In sensiPhy: Sensitivity Analysis for Comparative Methods

Description

Plot results from intra_clade_phylm and intra_clade_phyglm

Usage

## S3 method for class 'sensiIntra_Clade'
sensi_plot(x, clade = NULL, graphs = "all", ...)

Arguments

x	output from intra_clade_phylm or intra_clade_phyglm
clade	The name of the clade to be evaluated (see details)
graphs	Choose which graph should be printed on the output ("all", 1 or 2). Defaults to "all".
...	further arguments to methods.

Details

For 'x' from intra_clade_phylm or intra_clade_phyglm:

Graph 1: Estimated slopes after clade removal (reduced data) across multiple simulations. Small dots represent estimates reruns between simulations while larger dots represents the average estimate between all simulations for each clade. The solid black line represents the average slope estimate among trees using the full dataset.

Graph 2: The effect of clade removal on slope estimate across all individual simulations for each clade analyzed. The black line indicates estimates with the full dataset while the red line represent estimates without the focal clade (reduced data) across different simulation The blue dots represent null expectation estimates after removing the same number of species of the focal clade, with dots falling outside the red line area indicating a larger than expected absolute effect.

Author(s)

Gustavo Paterno, Caterina Penone

See Also

intra_clade_phylm

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