get.diversity: get.diversity
In rtk: Rarefaction Tool Kit

Description Usage Arguments Details Author(s) References See Also Examples

View source: R/rarefaction.R

Collectorscurves visualize the richness gained by picking more samples.

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	get.diversity(obj, div = "richness", multi = FALSE)
	get.mean.diversity(obj, div = "richness")
	get.median.diversity(obj, div = "richness")

`obj`	Object of type rtk
`div`	diversity measure as string e.g "richness"
`multi`	Argument set to true if called recursivly and class should not be checked. Should not be set in normal use case.

This set of functions allows fast and easy access to calculated diversity measures by rtk. It returns a matrix, when rarefaction was only performed to one depth and a list of matrices or vectors if rarefaction was done for multiple depths.

Falk Hildebrand, Paul Saary

Saary, Paul, et al. "RTK: efficient rarefaction analysis of large datasets." Bioinformatics (2017): btx206.

Use rt before calling this function.

require("rtk")
# Collectors Curve dataset should be broad and contain many samples (columns)
data            <- matrix(sample(x = c(rep(0, 15000), rep(1:10, 100)),
                          size = 10000, replace = TRUE), ncol = 80)
data.r 			<- rtk(data, depth = min(colSums(data)))
get.diversity(data.r)
get.median.diversity(data.r)
get.mean.diversity(data.r)