vr.evaluate.core {EvaluateCore} R Documentation

## Variable Rate of Coefficient of Variation

### Description

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).

### Usage

vr.evaluate.core(data, names, quantitative, 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 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 names column.

### 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

### Value

The $$VR$$ value.

### 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


####################################
# 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)))

core <- rownames(dactylis_CC)

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

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

vr.evaluate.core(data = ec, names = "genotypes",
quantitative = quant, selected = core)



[Package EvaluateCore version 0.1.2 Index]