plot.phyloglmhp: Plot for a 'phyloglm.hp' object

In phylolm.hp: Hierarchical Partitioning of R2 for Phylogenetic Linear Regression

Plot for a phyloglm.hp object

Description

Plot for a phyloglm.hp object

Usage

## S3 method for class 'phyloglmhp'
plot(x, plot.perc = FALSE, commonality = FALSE, color = NULL, dig = 4, ...)

Arguments

x	A phyloglm.hp object.
plot.perc	Logical;if TRUE, the bar plot (based on ggplot2 package) of the percentage to individual effects of variables and phylogenetic signal towards total explained variation, the default is FALSE to show plot with original individual effects.
commonality	Logical; If TRUE, the result of commonality analysis is shown, the default is FALSE.
color	Color of variables.
dig	Integer; number of decimal places in Venn diagram.
...	unused

Value

a ggplot object

Author(s)

Jiangshan Lai [e-mail]

Examples

library(phylolm)
library(rr2)
set.seed(123456)
tre <- rtree(50)
x1 <- rTrait(n=1, phy=tre)  
x2 <- rTrait(n=1, phy=tre)
X <- cbind(rep(1, 50), x1, x2)
y <- rbinTrait(n=1, phy=tre, beta=c(-1, 0.8, 0.9), alpha=1, X=X)
dat <- data.frame(trait01=y, predictor1=x1, predictor2=x2)
fit <- phyloglm(trait01 ~ predictor1 + predictor2, phy=tre, data=dat)
plot(phyloglm.hp(fit,commonality=TRUE))
plot(phyloglm.hp(fit,commonality=TRUE),commonality=TRUE)

phylolm.hp documentation built on April 4, 2025, 5:12 a.m.