Nothing
IsoGene1 <- function(x, y){
y<-as.numeric(y)
ordx <- order(x)
x <- x[ordx]
y <- y[ordx]
unx <- unique(x)
n.p <- table(x)
n.g <- length(n.p)
y.m <- tapply(y, as.factor(x), mean)
y.m.tot <- rep(mean(y), length(unx))
y.is.u <- pava(y = y.m, w = n.p )
y.is.d <- pava(y = y.m, w = n.p, decreasing=TRUE)
iso.u <- rep.iso.u <- rep.iso.d <- y.m.all <- NULL
rep.iso.d <- rep(y.is.d, n.p)
rep.iso.u <- rep(y.is.u, n.p)
y.m.all <- rep(y.m, n.p)
SST0 <- sum((y - mean(y))^2)
SSIS.u1<-sum((rep.iso.u-y)^2)
SSIS.d1<-sum((rep.iso.d-y)^2)
SST<-sum((y-y.m.all)^2)
direction <- if (SSIS.u1 <= SSIS.d1) "u" else "d" # no ifelse
lambda1.up <- SSIS.u1 / SST0 # no brackets
Esquare.up <- 1 - lambda1.up
iso.u <- y.is.u
# w.up <- (y.is.u[n.g]-y.m[1])/ sqrt(2*SST/(sum(n.p)-n.g)/(n.g-1))
# w.c.up <- (y.is.u[n.g]-y.is.u[1])/ sqrt(2*SST/(sum(n.p)-n.g)/(n.g-1))
w.up <- (y.is.u[n.g]-y.m[1])/sqrt(sum((y-y.m.all)^2)/(sum(n.p)-n.g)*(1/n.p[1]+1/n.p[n.g]))
w.c.up <- (y.is.u[n.g]-y.is.u[1])/sqrt(sum((y-y.m.all)^2)/(sum(n.p)-n.g)*(1/n.p[1]+1/n.p[n.g]))
m.up <- (y.is.u[n.g]-y.is.u[1])/sqrt(SSIS.u1/(sum(n.p)-n.g))
i.up <- (y.is.u[n.g]-y.is.u[1])/sqrt(SSIS.u1/(sum(n.p)-length(unique(y.is.u))))
lambda1.dn <- SSIS.d1 / SST0
Esquare.dn <- 1 - lambda1.dn
iso.u <- y.is.d
# n.pSum <- sum(n.p)
# w.dn <- (y.is.d[n.g]-y.m[1])/ sqrt(2*SST / (n.pSum-n.g)/(n.g-1))
# w.c.dn <- (y.is.d[n.g]-y.is.d[1]) / sqrt(2*SST/(n.pSum-n.g)/(n.g-1))
w.dn <- (y.is.d[n.g]-y.m[1])/sqrt(sum((y-y.m.all)^2)/(sum(n.p)-n.g)*(1/n.p[1]+1/n.p[n.g]))
w.c.dn <- (y.is.d[n.g]-y.is.d[1])/sqrt(sum((y-y.m.all)^2)/(sum(n.p)-n.g)*(1/n.p[1]+1/n.p[n.g]))
m.dn <- (y.is.d[n.g]-y.is.d[1]) / sqrt(SSIS.d1/(sum(n.p)-n.g))
i.dn <- (y.is.d[n.g]-y.is.d[1]) / sqrt(SSIS.d1/(sum(n.p)-length(unique(y.is.d))))
res <- list(E2.up = Esquare.up,
Williams.up = as.numeric(w.up),
Marcus.up = as.numeric(w.c.up),
M.up = as.numeric(m.up),
ModM.up = as.numeric(i.up),
E2.dn = Esquare.dn,
Williams.dn = as.numeric(w.dn),
Marcus.dn = as.numeric(w.c.dn),
M.dn = as.numeric(m.dn),
ModM.dn = as.numeric(i.dn),
direction = direction)
return(res)
}
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