Nothing
fbed.glmm.reg <- function(target, dataset, id, prior = NULL, reps = NULL, ini = NULL, threshold = 0.05, wei = NULL, K = 0, method = "LR", gam = NULL, backward = TRUE, test = "testIndGLMMReg") {
if ( length(K) > 1 ) {
result <- kfbed.glmm.reg(y = target, x = dataset, id = id, prior= prior, reps= reps, univ = ini, alpha = threshold, wei = wei, K = K, method = method, gam = gam, backward = backward, test = test)
} else {
#check for NA values in the dataset and replace them with the variable median or the mode
if ( any( is.na(dataset) ) ) {
#dataset = as.matrix(dataset);
warning("The dataset contains missing values (NA) and they were replaced automatically by the variable (column) median (for numeric) or by the most frequent level (mode) if the variable is factor")
dataset <- apply( dataset, 2, function(x){ x[which(is.na(x))] = median(x, na.rm = TRUE) ; return(x) } )
}
if ( method =="LR" ) {
if ( test == "testIndGLMMOrdinal" ) {
if ( !is.null(reps) ) {
result <- fbed.glmm.ordinal.reps(y = target, x = dataset, id = id, prior = prior, reps = reps, univ = ini, alpha = threshold, wei = wei, K = K)
} else result <- fbed.glmm.ordinal(y = target, x = dataset, id = id, prior = prior, univ = ini, alpha = threshold, wei = wei, K = K)
} else if ( test == "testIndGLMMCR" ) {
result <- fbed.glmm.cr(y = target, x = dataset, id, prior = prior, univ = ini, alpha = threshold, wei = wei, K = K)
} else if ( test == "testIndGLMMReg" ) {
if ( !is.null(reps) ) {
result <- fbed.lmm.reps(y = target, x = dataset, id = id, prior = prior, reps = reps, univ = ini, alpha = threshold, wei = wei, K = K)
} else result <- fbed.lmm(y = target, x = dataset, id = id, prior = prior, univ = ini, alpha = threshold, wei = wei, K = K)
} else if ( test == "testIndGLMMNB" ) {
if ( !is.null(reps) ) {
result <- fbed.glmm.nb.reps(y = target, x = dataset, id = id, prior = prior, reps = reps, univ = ini, alpha = threshold, wei = wei, K = K)
} else result <- fbed.glmm.nb(y = target, x = dataset, id = id, prior = prior, univ = ini, alpha = threshold, wei = wei, K = K)
} else {
if ( !is.null(reps) ) {
result <- fbed.glmm.reps(y = target, x = dataset, id = id, prior = prior, reps = reps, univ = ini, alpha = threshold, wei = wei, K = K, test = test)
} else result <- fbed.glmm(y = target, x = dataset, id = id, prior = prior, univ = ini, alpha = threshold, wei = wei, K = K, test = test)
}
result$back.rem <- 0
result$back.n.tests <- 0
if ( backward ) {
if (result$info[1, 1] > 0) {
if ( test == "testIndGLMMOrdinal" ) {
if ( !is.null(reps) ) {
a <- glmm.ordinal.reps.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, reps = reps, threshold = threshold, wei = wei)
} else a <- glmm.ordinal.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, threshold = threshold, wei = wei)
} else if ( test == "testIndGLMMCR" ) {
a <- glmm.cr.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, threshold = threshold, wei = wei)
} else if ( test == "testIndGLMMNB" ) {
if ( !is.null(reps) ) {
a <- glmm.nb.reps.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, reps = reps, threshold = threshold, wei = wei)
} else a <- glmm.nb.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, threshold = threshold, wei = wei)
} else if ( test == "testIndGLMMReg" ) {
if ( !is.null(reps) ) {
a <- lmm.reps.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, reps = reps, threshold = threshold, wei = wei)
} else a <- lmm.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, threshold = threshold, wei = wei)
} else {
if ( !is.null(reps) ) {
a <- glmm.reps.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, reps = reps, threshold = threshold, wei = wei, test = test)
} else a <- MXM::glmm.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, threshold = threshold, wei = wei, test = test)
}
if ( typeof(a) == "list" ) {
result$back.rem <- result$res[a$info[, 1], 1]
back.n.tests <- sum( dim(result$res)[1] : dim(a$mat)[1] )
sel <- result$res[a$mat[, 1], 1]
stat <- a$mat[, 3]
pval <- a$mat[, 2]
result$res <- cbind(sel, stat, pval)
result$back.n.tests <- back.n.tests
result$runtime <- result$runtime + a$runtime
} else {
back.rem <- 0
back.n.tests <- 0
result$back.rem <- back.rem
result$back.n.tests <- back.n.tests
result$runtime <- result$runtime
} ## end if ( typeof(a) == "list" )
} ## end if (result$info[1, 1] > 0)
} ## end if ( backward )
} else {
if (test == "testIndGLMMOrdinal") {
if ( !is.null(reps) ) {
result <- ebic.fbed.glmm.ordinal.reps(target, dataset, id, reps = reps, univ = ini, gam = gam, wei = wei, K = K)
} else result <- ebic.fbed.glmm.ordinal(target, dataset, id, univ = ini, gam = gam, wei = wei, K = K)
} else if ( test == "testIndGLMMCR" ) {
result <- ebic.fbed.glmm.cr(target, dataset, id, univ = ini, gam = gam, wei = wei, K = K)
} else if (test == "testIndGLMMReg") {
if ( !is.null(reps) ) {
result <- ebic.fbed.lmm.reps(target, dataset, id, reps = reps, univ = ini, gam = gam, wei = wei, K = K)
} else result <- ebic.fbed.lmm(target, dataset, id, univ = ini, gam = gam, wei = wei, K = K)
} else {
if ( !is.null(reps) ) {
result <- ebic.fbed.glmm.reps(target, dataset, id, reps = reps, univ = ini, gam = gam, wei = wei, K = K, test = test)
} else result <- ebic.fbed.glmm(target, dataset, id, univ = ini, gam = gam, wei = wei, K = K, test = test)
}
result$back.rem <- 0
result$back.n.tests <- 0
if ( backward ) {
if (result$info[1, 1] > 0) {
if ( test == "testIndGLMMOrdinal" ) {
if ( !is.null(reps) ) {
a <- ebic.glmm.ordinal.reps.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, reps = reps, wei = wei, gam = gam)
} else a <- ebic.glmm.ordinal.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, wei = wei, gam = gam)
} else if ( test == "testIndGLMMCR" ) {
a <- ebic.glmm.cr.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, wei = wei, gam = gam)
} else {
if ( !is.null(reps) ) {
a <- ebic.glmm.reps.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, reps = reps, wei = wei, gam = gam, test = test)
} else a <- ebic.glmm.bsreg(target, dataset[, result$res[, 1], drop = FALSE], id, wei = wei, gam = gam, test = test)
}
if ( typeof(a) == "list" ) {
back.n.tests <- sum( dim(result$res)[1] : length(a$mat[, 1]) )
result$back.rem <- result$res[a$info[, 1], 1]
sel <- result$res[ a$mat[, 1], 1]
val <- a$mat[, 2]
result$res <- cbind(sel, val)
colnames(result$res) <- c("Vars", "eBIC")
result$back.n.tests <- back.n.tests
result$runtime <- result$runtime + a$runtime
} else {
back.rem <- 0
back.n.tests <- 0
result$back.rem <- back.rem
result$back.n.tests <- back.n.tests
result$runtime <- result$runtime
}
} ## end if (result$info[1, 1] > 0)
} ## end if ( backward )
} ## end if ( method == "LR" )
} ## end ( if length(K) > 1 )
result
}
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