estPD: Estimate asymptotic phylogenetic diversity

Description Usage Arguments Value Examples

View source: R/estPD.R

Description

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

Usage

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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

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# 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.