Nothing
fbed.glmm.reps <- function(y, x, id, prior = NULL, reps, univ = NULL, alpha = 0.05, wei = NULL, K = 0, test = "testIndGLMMLogistic") {
if (test == "testIndGLMMLogistic") {
oiko <- binomial(logit)
} else if (test == "testIndGLMMPois") {
oiko <- poisson(log)
} else if (test == "testIndGLMMGamma") {
oiko <- Gamma(log)
} else if (test == "testIndGLMMNormLog") {
oiko <- gaussian(log)
}
dm <- dim(x)
p <- dm[2]
n <- dm[1]
ind <- 1:p
sig <- log(alpha)
if ( is.null(prior) ) {
lik1 <- logLik( lme4::glmer(y ~ 1 + reps + (1|id), family = oiko, weights = wei, nAGQ = 0) )
} else lik1 <- logLik( lme4::glmer(y ~ prior + reps + (1|id), family = oiko, weights = wei, nAGQ = 0) )
lik2 <- numeric(p)
sela <- NULL
card <- 0
sa <- NULL
pva <- NULL
zevar <- Rfast::check_data(x)
if ( sum( zevar > 0 ) > 0 ) x[, zevar] <- rnorm( n * length(zevar) )
priorindex <- NULL
if ( !is.null(prior) ) {
x <- cbind(x, prior)
priorindex <- c( (p + 1):dim(x)[2] )
}
runtime <- proc.time()
if ( is.null(univ) ) {
for ( i in ind ) {
fit2 <- lme4::glmer( y ~ x[, c(i, priorindex)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests <- p
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
univ <- list()
univ$stat <- stat
univ$pvalue <- pval
univ$stat[zevar] <- 0
univ$pvalue[zevar] <- 0
} else {
n.tests <- 0
stat <- univ$stat
pval <- univ$pvalue
lik2 <- 0.5 * stat + lik1
}
s <- which(pval < sig)
if ( length(s) > 0 ) {
sel <- which.min(pval)
sela <- sel
s <- s[ - which(s == sel) ]
lik1 <- lik2[sel]
sa <- stat[sel]
pva <- pval[sel]
lik2 <- rep( lik1, p )
#########
while ( sum(s>0) > 0 ) {
for ( i in ind[s] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests <- n.tests + length( ind[s] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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 <- sum(sela > 0)
if (K == 1) {
for ( i in ind[-c(sela, zevar)] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests[2] <- length( ind[-c(sela, zevar)] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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 ) {
for ( i in ind[s] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests[2] <- n.tests[2] + length( ind[s] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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) {
for ( i in ind[-c(sela, zevar)] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests[2] <- length( ind[-c(sela, zevar)] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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 ) {
for ( i in ind[s] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests[2] <- n.tests[2] + length( ind[s] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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) )
vim <- 1
while ( vim < K & card[vim + 1] - card[vim] > 0 ) {
vim <- vim + 1
for ( i in ind[-c(sela, zevar)] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests[vim + 1] <- length( ind[-c(sela, zevar)] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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 ) {
for ( i in ind[s] ) {
fit2 <- lme4::glmer( y ~ x[, c(priorindex, sela, i)] + reps + (1|id), family = oiko, weights = wei, nAGQ = 0 )
lik2[i] <- logLik(fit2)
}
n.tests[vim + 1] <- n.tests[vim + 1] + length( ind[s] )
stat <- 2 * (lik2 - lik1)
pval <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
s <- which(pval < sig)
sel <- which.min(pval) * ( length(s)>0 )
sa <- c(sa, stat[sel])
pva <- c(pva, pval[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], pva[1:len] )
info <- matrix(nrow = length(card), ncol = 2)
info[, 1] <- card
info[, 2] <- n.tests
} else {
res <- matrix(c(0, 0, 0), ncol = 3)
info <- matrix(c(0, p), ncol = 2)
}
colnames(res) <- c("Vars", "stat", "log p-value")
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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