shannon.evaluate.core-deprecated {EvaluateCore} | R Documentation |
Shannon-Weaver Diversity Index
Description
Compute the Shannon-Weaver Diversity Index (\(H'\)), Maximum diversity (\(H'_{max}\)) and Shannon Equitability Index (\(E_{H}\)) (Shannon and Weaver 1949) to compare the phenotypic diversity for qualitative traits between entire collection (EC) and core set (CS).
Usage
shannon.evaluate.core(data, names, qualitative, selected)
Details
Shannon-Weaver Diversity Index (\(H'\)) is computed as follows.
\[H' = -\sum_{i=1}^{k}p_{i} \ln(p_{i})\]Where \(p_{i}\) denotes the proportion in the group \(k\).
The maximum value of the index (\(H'_{max}\)) is \(\ln(k)\). This value occurs when each group has the same frequency.
The Shannon equitability index (\(E_{H}\)) is the Shannon diversity index divided by the maximum diversity.
\[E_{H} = \frac{H'}{\ln{(k)}}\]Value
A data frame with the following columns.
Trait |
The qualitative trait. |
EC_H |
The Shannon-Weaver Diversity Index (\(H'\)) for EC. |
EC_H |
The Shannon-Weaver Diversity Index (\(H'\)) for CS. |
EC_Hmax |
The Maximum diversity value (\(H'_{max}\)) for EC. |
CS_Hmax |
The Maximum diversity value (\(H'_{max}\)) for CS. |
EC_EH |
The Shannon Equitability Index (\(E_{H}\)) for EC. |
CS_EH |
The Shannon Equitability Index (\(E_{H}\)) for CS. |
References
Shannon CE, Weaver W (1949). The Mathematical Theory of Communication, number v. 2 in The Mathematical Theory of Communication. University of Illinois Press.
See Also
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)