estShannonf: Estimate the Shannon-Wiener index

In MCPAN: Multiple Comparisons Using Normal Approximation

Description

Calculate estimates of the Shannon-Wiener index after pooling over several samples, grouped by a factor variable.

Usage

estShannonf(X, f)

Arguments

X	a data.frame of dimension n times p with integer entries, where n is the number of samples and p is the number of species
f	a factor variable of length n, grouping the observations in X

Details

The function splits X according to the levels of the grouping variable f, builds the sum over each column and calculates the Shannon index ove the resulting counts.

Value

A list, containing the elements:

estimae	a named numeric vector, the groupwise Shannon indices with bias correction according to Fritsch and Hsu (1999)
estraw	a named numeric vector, the groupwise Shannon indices, without bias correction
varest	a named numeric vector, the groupwise variance estimates of the Shannon indices
table	a matrix, giving the summarized counts of the groups in the rows

References

Fritsch, KS, and Hsu, JC (1999): Multiple Comparison of Entropies with Application to Dinosaur Biodiversity. Biometrics 55, 1300-1305.

Examples

data(HCD)
HCD

# Groupwise point estimates:

est<-estShannonf(X=HCD[,-1], f=HCD[,1])

est

MCPAN documentation built on May 1, 2019, 8:04 p.m.