PhyloValue: Phylogenetic entropy or diversity.

In entropart: Entropy Partitioning to Measure Diversity

Phylogenetic entropy or diversity.

Description

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))
autoplot(r)

entropart documentation built on Sept. 11, 2024, 6:20 p.m.