#'Calculate Fisher's Least Significant Difference (LSD)
#'@description Adapted from the 'agricolae' package
#'@param y Input Y
#'@param trt Input trt
#'@param alpha Numeric, default is 0.05
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
my.lsd.test <- function(y, trt, alpha = 0.05){
clase<-c("aov","lm")
name.y <- paste(deparse(substitute(y)))
name.t <- paste(deparse(substitute(trt)))
if("aov"%in%class(y) | "lm"%in%class(y)){
A<-y$model
DFerror<-df.residual(y)
MSerror<-deviance(y)/DFerror
y<-A[,1]
ipch<-pmatch(trt,names(A))
name.t <-names(A)[ipch]
trt<-A[,ipch]
name.y <- names(A)[1]
}
junto <- subset(data.frame(y, trt), is.na(y) == FALSE)
means <- tapply.stat(junto[, 1], junto[, 2], stat="mean") #change
sds <- tapply.stat(junto[, 1], junto[, 2], stat="sd") #change
nn <- tapply.stat(junto[, 1], junto[, 2], stat="length") #change
std.err <- sds[, 2]/sqrt(nn[, 2])
Tprob <- qt(1 - alpha/2, DFerror)
LCL <- means[,2]-Tprob*std.err
UCL <- means[,2]+Tprob*std.err
means <- data.frame(means, std.err, replication = nn[, 2], LCL, UCL)
names(means)[1:2] <- c(name.t, name.y)
#row.names(means) <- means[, 1]
ntr <- nrow(means)
nk <- choose(ntr, 2)
nr <- unique(nn[, 2])
comb <- combn(ntr, 2)
nn <- ncol(comb)
dif <- rep(0, nn)
LCL1<-dif
UCL1<-dif
sig<-NULL
pvalue <- rep(0, nn)
for (k in 1:nn) {
i <- comb[1, k]
j <- comb[2, k]
if (means[i, 2] < means[j, 2]){
comb[1, k]<-j
comb[2, k]<-i
}
dif[k] <- abs(means[i, 2] - means[j, 2])
sdtdif <- sqrt(MSerror * (1/means[i, 4] + 1/means[j,4]))
pvalue[k] <- 2 * (1 - pt(dif[k]/sdtdif, DFerror));
pvalue[k] <- round(pvalue[k],6);
LCL1[k] <- dif[k] - Tprob*sdtdif
UCL1[k] <- dif[k] + Tprob*sdtdif
sig[k]<-" "
if (pvalue[k] <= 0.001) sig[k]<-"***"
else if (pvalue[k] <= 0.01) sig[k]<-"**"
else if (pvalue[k] <= 0.05) sig[k]<-"*"
else if (pvalue[k] <= 0.1) sig[k]<-"."
}
tr.i <- means[comb[1, ],1]
tr.j <- means[comb[2, ],1]
output<-data.frame("Difference" = dif, pvalue = pvalue,sig,LCL=LCL1,UCL=UCL1)
rownames(output)<-paste(tr.i,tr.j,sep=" - ");
output;
}
tapply.stat <-function (y, x, stat = "mean"){
cx<-deparse(substitute(x))
cy<-deparse(substitute(y))
x<-data.frame(c1=1,x)
y<-data.frame(v1=1,y)
nx<-ncol(x)
ny<-ncol(y)
namex <- names(x)
namey <- names(y)
if (nx==2) namex <- c("c1",cx)
if (ny==2) namey <- c("v1",cy)
namexy <- c(namex,namey)
for(i in 1:nx) {
x[,i]<-as.character(x[,i])
}
z<-NULL
for(i in 1:nx) {
z<-paste(z,x[,i],sep="&")
}
w<-NULL
for(i in 1:ny) {
m <-tapply(y[,i],z,stat)
m<-as.matrix(m)
w<-cbind(w,m)
}
nw<-nrow(w)
c<-rownames(w)
v<-rep("",nw*nx)
dim(v)<-c(nw,nx)
for(i in 1:nw) {
for(j in 1:nx) {
v[i,j]<-strsplit(c[i],"&")[[1]][j+1]
}
}
rownames(w)<-NULL
junto<-data.frame(v[,-1],w)
junto<-junto[,-nx]
names(junto)<-namexy[c(-1,-(nx+1))]
return(junto)
}
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