EvaluateCore (version 0.1.1)

shannon.evaluate.core: Shannon-Weaver Diversity Index

Description

Compute the Shannon-Weaver Diversity Index (), Maximum diversity () and Shannon Equitability Index () shannon_mathematical_1949EvaluateCore to compare the phenotypic diversity for qualitative traits between entire collection (EC) and core set (CS).

Usage

shannon.evaluate.core(data, names, qualitative, selected)

Arguments

data

The data as a data frame object. The data frame should possess one row per individual and columns with the individual names and multiple trait/character data.

names

Name of column with the individual names as a character string

qualitative

Name of columns with the qualitative traits as a character vector.

selected

Character vector with the names of individuals selected in core collection and present in the names column.

Value

A data frame with the following columns.

Trait

The qualitative trait.

EC_H

The Shannon-Weaver Diversity Index () for EC.

EC_H

The Shannon-Weaver Diversity Index () for CS.

EC_Hmax

The Maximum diversity value () for EC.

CS_Hmax

The Maximum diversity value () for CS.

EC_EH

The Shannon Equitability Index () for EC.

CS_EH

The Shannon Equitability Index () for CS.

Details

Shannon-Weaver Diversity Index () is computed as follows.

Where denotes the proportion in the group .

The maximum value of the index () is . This value occurs when each group has the same frequency.

The Shannon equitability index () is the Shannon diversity index divided by the maximum diversity.

References

See Also

shannon

Examples

# NOT RUN {
####################################
# Use data from R package ccChooser
####################################

library(ccChooser)
data("dactylis_CC")
data("dactylis_EC")

ec <- cbind(genotypes = rownames(dactylis_EC), dactylis_EC[, -1])
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL
ec[, c("X1", "X6", "X7")] <- lapply(ec[, c("X1", "X6", "X7")],
                                    function(x) cut(x, breaks = 4))
ec[, c("X1", "X6", "X7")] <- lapply(ec[, c("X1", "X6", "X7")],
                                    function(x) factor(as.numeric(x)))
head(ec)

core <- rownames(dactylis_CC)

quant <- c("X2", "X3", "X4", "X5", "X8")
qual <- c("X1", "X6", "X7")

####################################
# EvaluateCore
####################################

shannon.evaluate.core(data = ec, names = "genotypes",
                      qualitative = qual, selected = core)


# }