estPD: Estimate asymptotic phylogenetic diversity

In iNextPD: Interpolation and Extrapolation for Phylogenetic Diversity

Description

estPD: Estimate asymptotic phylogenetic diversity with order q = 0, 1, 2.

Usage

estPD(x, labels, phy, q = 0, datatype = "abundance", se = FALSE,
  conf = 0.95)

Arguments

x	a vector/matrix/list of species abundances or a matrix of raw incidence table.
labels	a vector of species name for input data.
phy	a phylogenetic tree with "phylog" class.
q	a numeric value specifying the diversity order of Hill number.
datatype	data type of input data: individual-based abundance data (datatype = "abundance"), species by sampling-units incidence matrix (datatype = "incidence_raw").
se	a logical variable to calculate the bootstrap standard error and conf confidence interval.
conf	a positive number < 1 specifying the level of confidence interval, default is 0.95.

Value

a data.frame with sample size and sample coverage.

Examples

# abundance-based example
data(bird)
bird.abu <- bird$abun
bird.lab <- rownames(bird$abun)
bird.phy <- ade4::newick2phylog(bird$tre)
estPD(bird.abu, labels=bird.lab, phy=bird.phy, q=0, datatype="abundance")

# incidence_based example
bird.inc <- bird$inci
estPD(bird.inc, labels=bird.lab, phy=bird.phy, q=0, datatype="incidence_raw", se=TRUE)

iNextPD documentation built on May 2, 2019, 3:31 a.m.