EvaluateCore (version 0.1.1)

signtest.evaluate.core: Sign Test

Description

Test difference between means and variances of entire collection (EC) and core set (CS) for quantitative traits by Sign test ( versus ) basigalup_development_1995,tai_core_2001EvaluateCore.

Usage

signtest.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.

Value

A data frame with the following components.

Comparison

The comparison measure.

ChiSq

The test statistic ().

p.value

The p value for the test statistic.

significance

The significance of the test statistic (*: p 0.01; **: p 0.05; ns: p 0.05).

Details

The test statistic for Sign test () is computed as follows.

Where, where is the number of variables for which the mean or variance of the CS is greater than the mean or variance of the EC (number of signs); is the number of variables for which the mean or variance of the CS is less than the mean or variance of the EC (number of signs). The value of is compared with a Chi-square distribution with 1 degree of freedom.

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

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


# }