Aggregate data by given taxonomic rank

Aggregate data by given taxonomic rank

Usage

rankagg(data = NULL, datacol = NULL, rank = NULL, fxn = "sum")

Arguments

data

A data.frame. Column headers must have capitalized ranks (e.g., Genus, Tribe, etc.) (data.frame)

datacol

The data column (character)

rank

Taxonomic rank to aggregate by (character)

fxn

Arithmetic function or vector or functions (character)

Examples

if (require(vegan)) {
data(dune.taxon, dune, package='vegan')
dat <- dune.taxon
dat$abundance <- colSums(dune)
rankagg(data=dat, datacol="abundance", rank="Genus")
rankagg(data=dat, "abundance", rank="Family")
rankagg(data=dat, "abundance", rank="Genus", fxn="mean")
rankagg(data=dat, "abundance", rank="Subclass")
rankagg(data=dat, "abundance", rank="Subclass", fxn="sd")
}
#> Loading required package: vegan
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.6-8
#>      Subclass       sd
#> 1     Bryidae 27.57716
#> 2 Magnoliidae 18.45558