Phylogenetic entropy or diversity.

Entropy or diversity against the height of the phylogenetic or functional tree.

Usage

is.PhyloValue(x)
# S3 method for class 'PhyloValue'
autoplot(object, xlab = expression(italic("T")), ylab = NULL, main = NULL,
          col = ggplot2::GeomLine$default_aes$colour,
          lty = ggplot2::GeomLine$default_aes$linetype,
          lwd = ggplot2::GeomLine$default_aes$size,
          ...)
# S3 method for class 'PhyloValue'
plot(x, xlab = expression(italic("T")), ylab = NULL, main = NULL, ...)
# S3 method for class 'PhyloValue'
summary(object, ...)

Arguments

x

An object of class PhyloValue, including PhyloDiversity and PhyloEntropy objects.

xlab

The X axis label, "T" by default for Time.

ylab

The Y axis label. if NULL (by default), "Entropy" or "Diversity" or nothing is chosen according to the object class.

main

The main title of the plot. if NULL (by default), a default value is used.

object

A PhyloValue object to be summarized.

col

The color of the geom objects. See "Color Specification" in par.

lty

The type of the lines. See lines.

lwd

The width of the lines. See lines.

...

Additional arguments to be passed to plot.

Details

PhyloValue objects are the result of PhyloApply.

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
#      and their taxonomy)
data(Paracou618)
# Calculate richness along the tree
# (Cuts are 1=species, 2=genus, 3=family)
summary(r <- PhyloApply(Paracou618.Taxonomy, FUN=Richness,
  NorP=Paracou618.MC$Ns, Normalize=TRUE))
#> Richness applied to Paracou618.MC$Ns along the tree: Paracou618.Taxonomy
#> 
#> Results are normalized
#> 
#> The average value is: 191
#> 
#> Values along the tree are:
#>   1   2   3 
#> 359 156  58 
autoplot(r)