rpr.evaluate.core: Ratio of Phenotype Retained

In EvaluateCore: Quality Evaluation of Core Collections

Ratio of Phenotype Retained

Description

Compute the Ratio of Phenotype Retained (\mjseqnRPR) \insertCiteli_studies_2002EvaluateCore to compare qualitative traits between entire collection (EC) and core set (CS).

Usage

rpr.evaluate.core(data, names, qualitative, selected, na.omit = TRUE)

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.
na.omit	logical. If TRUE, missing values (NA) are ignored and not included as a distinct factor level for analysis. Default is TRUE.

Details

Ratio of Phenotype Retained (\mjseqnRPR) \insertCitekim_PowerCore_2007EvaluateCore is computed as follows.

\mjsdeqn

RPR = \frac\sum_i=1^n k_CS_i\sum_i=1^n k_EC_i

Where, \mjseqnk_CS_i is the number of phenotypic classes in CS for the \mjseqnith trait, \mjseqnk_EC_i is the number of phenotypic classes in EC for the \mjseqnith trait and \mjseqnn is the total number of traits.

Value

The Ratio of Phenotype Retained value.

References

\insertAllCited

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)))

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

EvaluateCore documentation built on April 22, 2026, 9:07 a.m.