plotTrend: Graphical representation of search.trend results
In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

plotTrend

R Documentation

Graphical representation of search.trend results

Description

This function generates customized functions to produce plots of phenotype versus time and absolute evolutionary rates versus time regressions for the entire phylogeny and individual clades. Each custom function takes as the only argument the index or name of the variable (as in the search.trend output in $trends.data$phenotypeVStime) to be plotted.

Usage

plotTrend(ST)

Arguments

`ST`	an object produced by `search.trend`.

Value

The function returns a list of functions:

$plotPhen returns the plot of rescaled phenotype versus age regression. The 95% confidence intervals of slopes produced by regressing phenotypes simulated under the Brownian motion are plotted as a shaded area.

$plotRates returns the plot of log rescaled rates versus age regression. The 95% confidence intervals of slopes produced by regressing rates simulated under the Brownian motion are plotted as a shaded area.

$plotPhenNode returns plots of rescaled phenotype versus age regression for individual clades. For each plot, the gray line represents the slope of phenotype versus age regression for the rest of the tree.

$plotRatesNode returns plots of absolute rates versus age regression for individual clades. For each plot, the gray line represents the slope of absolute rates versus age regression for the rest of the tree.

Author(s)

Silvia Castiglione, Carmela Serio, Pasquale Raia

References

Castiglione, S., Serio, C., Mondanaro, A., Di Febbraro, M., Profico, A., Girardi, G., & Raia, P. (2019) Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species. PLoS ONE, 14: e0210101. https://doi.org/10.1371/journal.pone.0210101

Examples

 ## Not run: 
data("DataOrnithodirans")
DataOrnithodirans$treedino->treedino
DataOrnithodirans$massdino->massdino
cc<- 2/parallel::detectCores()

# Extract Pterosaurs tree and data
library(ape)
extract.clade(treedino,746)->treeptero
massdino[match(treeptero$tip.label,names(massdino))]->massptero
massptero[match(treeptero$tip.label,names(massptero))]->massptero

RRphylo(tree=treeptero,y=log(massptero))->RRptero

search.trend(RR=RRptero, y=log(massptero), nsim=100, node=143, clus=cc,cov=NULL)->ST

plotTrends(ST)->plotST

plotST$plotPhen(1) # to plot phenotypic trend through time for entire tree
plotST$plotPhen("y") # equivalent to the previuous line

plotST$plotRates(1) # to plot rates trend through time for entire tree

plotST$plotPhenNode("y") # to plot phenotypic trend through time for the clade
plotST$plotRatesNode("y") # to plot rates trend through time for the clade

   
## End(Not run)

RRphylo documentation built on May 9, 2022, 9:08 a.m.