estimatePD: Compute phylogenetic diversity with a particular of sample...

Description Usage Arguments Value Examples

View source: R/estimatePD.R

Description

estimatePD: computes phylogenetic diversity (Hill numbers with q = 0, 1 and 2) with a particular user-specified level of sample size or sample coverage.

Usage

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estimatePD(x, labels, phy, datatype = "abundance", base = "size",
  level = NULL, conf = 0.95, digits = 4)

Arguments

x

a data.frame or list of species abundances or incidence frequencies.
If datatype = "incidence", then the first entry of the input data must be total number of sampling units, followed by species incidence frequencies in each column or list.

labels

species names for object x

phy

a phylog objcet for input phylo-tree

datatype

data type of input data: individual-based abundance data (datatype = "abundance"), or species by sampling-units incidence matrix (datatype = "incidence_raw").

base

comparison base: sample-size-based (base="size") or coverage-based
(base="coverage").

level

an integer specifying a particular sample size or a number (between 0 and 1) specifying a particular value of sample coverage. If base="size" and level=NULL, then this function computes the diversity estimates for the minimum sample size among all sites. If base="coverage" and level=NULL, then this function computes the diversity estimates for the minimum sample coverage among all sites.

conf

a positive number < 1 specifying the level of confidence interval, default is 0.95. Remove C.I. by setting conf=NULL.

digits

integer indicating the number of decimal places round to be used.

Value

a data.frame of phylogenetic diversity table including the sample size, sample coverage, method (rarefaction or extrapolation), and diversity estimates with q = 0, 1, and 2 for the user-specified sample size or sample coverage.

Examples

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data(bird)
bird.abu <- bird$abun
bird.lab <- rownames(bird$abun)
bird.phy <- ade4::newick2phylog(bird$tre)
estimatePD(bird.abu, bird.lab, bird.phy, "abundance", base="size", level=NULL, conf=NULL)
## Not run: 
estimatePD(bird.abu, bird.lab, bird.phy, "abundance", base="size", level=NULL)

## End(Not run)

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