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#' Genotypic Variance-Covariance Analysis
#'
#' @param data traits to be analyzed
#' @param genotypes vector containing genotypes/treatments
#' @param replication vector containing replication
#'
#' @return A Genotypic Variance-Covariance Matrix
#' @export
#'
#' @examples
#' gen.varcov(data=seldata[,3:9], genotypes=seldata$treat,replication=seldata$rep)
gen.varcov<- function (data, genotypes, replication)
{
convrt<- function(data1) {
data1<- as.data.frame(sapply(data1, as.numeric))
data1<- as.list(data1)
return(data1)
}
datam<- convrt(data)
colnumber<- ncol(data)
headings<- names(data)
analysis<- function(genotypes, replication, trait1, trait2) {
genotypes<- as.factor(genotypes)
replication<- as.factor(replication)
sumch1<- tapply(trait1, genotypes, sum)
sumch2<- tapply(trait2, genotypes, sum)
sumr1<- tapply(trait1, replication, sum)
sumr2<- tapply(trait2, replication, sum)
repli<- nlevels(replication)
genotype<- nlevels(genotypes)
GT1<- sum(trait1)
GT2<- sum(trait2)
CF<- (GT1 * GT2)/(repli * genotype)
TSP<- round(sum(trait1 * trait2) - CF, 4)
GSP<- round((sum(sumch1 * sumch2)/repli) - CF, 4)
RSP<- round((sum(sumr1 * sumr2)/genotype) - CF, 4)
ESP<- TSP - GSP - RSP
DFR<- repli - 1
DFG<- genotype - 1
DFE<- DFR * DFG
RMP<- round(RSP/DFR, 4)
GMP<- round(GSP/DFG, 4)
EMP<- round(ESP/DFE, 4)
ECov<- EMP
GCov<- round((GMP - EMP)/repli, 4)
return(GCov)
}
genetic.cov<- c()
index = 0
for (i in 1:(colnumber)) {
for (j in 1:colnumber) {
index = index + 1
genetic.cov[index]<- analysis(genotypes, replication,
datam[[i]], datam[[j]])
}
}
matrix1<- matrix(genetic.cov, nrow = colnumber,
dimnames = list(headings, headings))
return(matrix1)
}
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