estimatePD: Compute phylogenetic diversity with a particular of sample...
In iNextPD: Interpolation and Extrapolation for Phylogenetic Diversity

Description Usage Arguments Value Examples

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

1 2	estimatePD(x, labels, phy, datatype = "abundance", base = "size", level = NULL, conf = 0.95, digits = 4)

`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.

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.

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)