plotTrend | R Documentation |
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.
plotTrend(ST)
ST |
an object produced by |
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.
$plotRatesNode returns plots of absolute rates versus age regression for individual clades. For each plot, the gray line represents the slope of absolute rates versus age regression for the rest of the tree.
Silvia Castiglione, Carmela Serio, Pasquale Raia
Castiglione, S., Serio, C., Mondanaro, A., Di Febbraro, M., Profico, A., Girardi, G., & Raia, P. (2019) Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species. PLoS ONE, 14: e0210101. https://doi.org/10.1371/journal.pone.0210101
## Not run: data("DataOrnithodirans") DataOrnithodirans$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)
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