Compute the Variable Rate of Coefficient of Variation (\(VR\)) (Hu et al. 2000) to compare quantitative traits of the entire collection (EC) and core set (CS).
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.
- quantitative
Name of columns with the quantitative traits as a character vector.
- selected
Character vector with the names of individuals selected in core collection and present in the
namescolumn.
Details
The Variable Rate of Coefficient of Variation (\(VR\)) is computed as follows.
\[VR = \left ( \frac{1}{n} \sum_{i=1}^{n} \frac{CV_{CS_{i}}}{CV_{EC_{i}}} \right ) \times 100\]
Where, \(CV_{CS_{i}}\) is the coefficients of variation for the \(i\)th trait in the CS, \(CV_{EC_{i}}\) is the coefficients of variation for the \(i\)th trait in the EC and \(n\) is the total number of traits
References
Hu J, Zhu J, Xu HM (2000). “Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops.” Theoretical and Applied Genetics, 101(1), 264–268.
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)))
vr.evaluate.core(data = ec, names = "genotypes",
quantitative = quant, selected = core)
#> [1] 111.6594