shannon.evaluate.core-deprecated: Shannon-Weaver Diversity Index

In EvaluateCore: Quality Evaluation of Core Collections

Shannon-Weaver Diversity Index

Description

Compute the Shannon-Weaver Diversity Index (\mjseqnH'), Maximum diversity (\mjseqnH'_max) and Shannon Equitability Index (\mjseqnE_H) \insertCiteshannon_mathematical_1949EvaluateCore to compare the phenotypic diversity for qualitative traits between entire collection (EC) and core set (CS). \loadmathjax

Usage

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

Details

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

\mjsdeqn

H' = -\sum_i=1^kp_i \ln(p_i)

Where \mjseqnp_i denotes the proportion in the group \mjseqnk.

The maximum value of the index (\mjseqnH'_max) is \mjseqn\ln(k). This value occurs when each group has the same frequency.

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

\mjsdeqn

E_H = \fracH'\ln(k)

Value

A data frame with the following columns.

Trait	The qualitative trait.
EC_H	The Shannon-Weaver Diversity Index (\mjseqnH') for EC.
EC_H	The Shannon-Weaver Diversity Index (\mjseqnH') for CS.
EC_Hmax	The Maximum diversity value (\mjseqnH'_max) for EC.
CS_Hmax	The Maximum diversity value (\mjseqnH'_max) for CS.
EC_EH	The Shannon Equitability Index (\mjseqnE_H) for EC.
CS_EH	The Shannon Equitability Index (\mjseqnE_H) for CS.

References

\insertAllCited

See Also

shannon

EvaluateCore-deprecated

Examples

data("cassava_CC")
data("cassava_EC")

ec <- cbind(genotypes = rownames(cassava_EC), cassava_EC)
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL

core <- rownames(cassava_CC)

quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
           "ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
          "ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
          "PSTR")

ec[, qual] <- lapply(ec[, qual],
                     function(x) factor(as.factor(x)))

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

EvaluateCore documentation built on July 3, 2022, 5:06 p.m.