Nothing
ebic.fbed.glmm.ordinal.reps <- function(y, x, id, reps = NULL, univ = NULL, gam = NULL, wei = NULL, K = 0) {
dm <- dim(x)
n <- dm[1]
p <- dm[2]
ind <- 1:p
lik2 <- numeric(p)
sela <- NULL
card <- 0
zevar <- Rfast::check_data(x)
if ( sum( zevar > 0 ) > 0 ) x[, zevar] <- rnorm( n * length(zevar) )
if ( is.null(gam) ) {
con <- 2 - log(p) / log(n)
} else con <- 2 * gam
if ( (con) < 0 ) con <- 0
lik1 <- BIC( ordinal::clmm(y ~ 1 + reps + (1|id), weights = wei) )
runtime <- proc.time()
if ( is.null(univ) ) {
for ( i in ind ) {
fit2 <- ordinal::clmm( y ~ x[, i] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * log(p)
}
lik2[zevar] <- Inf
n.tests <- p
stat <- lik1 - lik2
univ <- list()
univ$ebic <- lik2
} else {
n.tests <- 0
lik2 <- univ$ebic
lik2[zevar] <- Inf
stat <- lik1 - lik2
}
s <- which(stat > 0)
if ( length(s) > 0 ) {
sel <- which.max(stat)
sela <- sel
s <- s[ - which(s == sel) ]
lik1 <- lik2[sel]
sa <- stat[sel]
lik2 <- rep( lik1, p )
#########
while ( sum(s > 0) > 0 ) {
M <- length(sela) + 1
for ( i in ind[s] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests <- n.tests + length(ind[s])
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
}
card <- length(sela)
if (K == 1) {
M <- length(sela) + 1
for ( i in ind[-c(sela, zevar)] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests[2] <- length( ind[-c(sela, zevar)] )
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
while ( sum(s > 0) > 0 ) {
M <- length(sela) + 1
for ( i in ind[s] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests[2] <- n.tests[2] + length( ind[s] )
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
} ## end while ( sum(s > 0) > 0 )
card <- c(card, sum(sela > 0) )
} ## end if ( K == 1 )
if ( K > 1) {
M <- length(sela) + 1
for ( i in ind[-c(sela, zevar)] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests[2] <- length(ind[-c(sela, zevar)])
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
while ( sum(s > 0) > 0 ) {
M <- length(sela) + 1
for ( i in ind[s] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests[2] <- n.tests[2] + length(ind[s])
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
} ## end while ( sum(s > 0) > 0 )
vim <- 1
card <- c(card, sum(sela > 0) )
while ( vim < K & card[vim + 1] - card[vim] > 0 ) {
vim <- vim + 1
M <- length(sela) + 1
for ( i in ind[-c(sela, zevar)] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests[vim + 1] <- length(ind[-c(sela, zevar)])
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
while ( sum(s > 0) > 0 ) {
M <- length(sela) + 1
for ( i in ind[s] ) {
fit2 <- ordinal::clmm( y ~ x[, c(sela, i)] + reps + (1|id), weights = wei )
lik2[i] <- BIC(fit2) + con * lchoose(p, M)
}
n.tests[vim + 1] <- n.tests[vim + 1] + length(ind[s])
stat <- lik1 - lik2
s <- which(stat > 0)
sel <- which.max(stat) * ( length(s)>0 )
sa <- c(sa, stat[sel])
sela <- c(sela, sel[sel>0])
s <- s[ - which(s == sel) ]
if (sel > 0) {
lik1 <- lik2[sel]
lik2 <- rep(lik1, p)
}
} ## end while ( sum(s > 0) > 0 )
card <- c(card, sum(sela > 0) )
} ## end while ( vim < K )
} ## end if ( K > 1)
} ## end if ( length(s) > 0 )
runtime <- proc.time() - runtime
len <- sum( sela > 0 )
if (len > 0) {
res <- cbind(sela[1:len], sa[1:len] )
info <- matrix(nrow = length(card), ncol = 2)
info[, 1] <- card
info[, 2] <- n.tests
} else {
res <- matrix(c(0, 0), ncol = 2)
info <- matrix(c(0, p), ncol = 2)
}
colnames(res) <- c("Vars", "eBIC difference")
rownames(info) <- paste("K=", 1:length(card)- 1, sep = "")
colnames(info) <- c("Number of vars", "Number of tests")
list(univ = univ, res = res, info = info, runtime = runtime)
}
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