EvaluateCore (version 0.1.1)

coverage.evaluate.core: Class Coverage

Description

Compute the Class Coverage kim_powercore_2007EvaluateCore to compare the distribution frequencies of qualitative traits between entire collection (EC) and core set (CS).

Usage

coverage.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

The Class Coverage value.

Details

Class Coverage kim_powercore_2007EvaluateCore is computed as follows.

Where, is the sets of categories in the CS for the th trait, is the sets of categories in the EC for the th trait and is the total number of traits.

References

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
####################################

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


# }