#' Performs DIF detection using SIBTEST method. (internal function)
#'
#' @description Internal function substituting the `difSIBTEST()` function of
#' the `difR` package.
#'
#' @keywords internal
#' @noRd
#'
#' @importFrom difR sibTest
.difSIBTEST_edited <- function(Data, group, focal.name, type = "udif", anchor = NULL,
alpha = 0.05, purify = FALSE, nrIter = 10, p.adjust.method = NULL,
puriadjType = "simple",
save.output = FALSE, output = c("out", "default")) {
internalSIBTEST <- function() {
if (length(group) == 1) {
if (is.numeric(group)) {
gr <- Data[, group]
DATA <- Data[, (1:ncol(Data)) != group]
colnames(DATA) <- colnames(Data)[(1:ncol(Data)) != group]
} else {
gr <- Data[, colnames(Data) == group]
DATA <- Data[, colnames(Data) != group]
colnames(DATA) <- colnames(Data)[colnames(Data) != group]
}
} else {
gr <- group
DATA <- Data
}
Group <- as.numeric(gr == focal.name)
df <- data.frame(DATA, Group, check.names = F)
if (any(is.na(DATA))) {
warning("'Data' contains missing values. Observations with missing values are discarded.",
call. = FALSE
)
}
if (any(is.na(Group))) {
warning("'group' contains missing values. Observations with missing values are discarded.",
call. = FALSE
)
}
df <- df[complete.cases(df), ]
Group <- df[, "Group"]
DATA <- as.data.frame(df[, !(colnames(df) %in% c("Group"))])
colnames(DATA) <- colnames(df)[!(colnames(df) %in% c("Group"))]
if (is.null(anchor)) {
ANCHOR <- 1:ncol(DATA)
anchor.names <- NULL
} else {
if (is.numeric(anchor)) {
ANCHOR <- anchor
anchor.names <- anchor
} else {
ANCHOR <- which(colnames(DATA) %in% anchor)
anchor.names <- anchor
}
}
if (purify) {
if (is.null(p.adjust.method)) {
puri.adj.method <- "none"
adj.method <- "none"
} else {
if (puriadjType == "simple") {
puri.adj.method <- "none"
adj.method <- p.adjust.method
} else {
puri.adj.method <- p.adjust.method
adj.method <- p.adjust.method
}
}
} else {
adj.method <- ifelse(is.null(p.adjust.method), "none", p.adjust.method)
}
if (!purify | !is.null(anchor)) {
PROV <- sibTest(DATA, Group, type = type, anchor = ANCHOR)
PVAL <- PROV$p.value
P.ADJUST <- p.adjust(PVAL, method = adj.method)
if (min(P.ADJUST, na.rm = TRUE) >= alpha) {
DIFitems <- "No DIF item detected"
} else {
DIFitems <- which(!is.na(PVAL) & P.ADJUST < alpha)
}
if (is.null(p.adjust.method)) {
adjusted.p <- NULL
} else {
adjusted.p <- P.ADJUST
}
RES <- list(
Beta = PROV$Beta, SE = PROV$SE, X2 = PROV$X2,
df = PROV$df, p.value = PROV$p.value, type = type,
alpha = alpha, DIFitems = DIFitems, p.adjust.method = p.adjust.method,
adjusted.p = adjusted.p, purification = purify, names = colnames(DATA),
anchor.names = anchor.names, save.output = save.output,
output = output
)
if (!is.null(anchor)) {
RES$Beta[ANCHOR] <- NA
RES$SE[ANCHOR] <- NA
RES$X2[ANCHOR] <- NA
RES$df[ANCHOR] <- NA
RES$p.value[ANCHOR] <- NA
RES$DIFitems <- RES$DIFitems[!RES$DIFitems %in% ANCHOR]
}
} else {
nrPur <- 0
difPur <- NULL
noLoop <- FALSE
prov1 <- sibTest(DATA, Group, type = type)
pval1 <- prov1$p.value
p.adjust1 <- p.adjust(pval1, method = puri.adj.method)
if (min(p.adjust1, na.rm = TRUE) >= alpha) {
DIFitems <- "No DIF item detected"
noLoop <- TRUE
} else {
dif <- which(!is.na(pval1) & p.adjust1 < alpha)
difPur <- rep(0, length(pval1))
difPur[dif] <- 1
repeat {
if (nrPur >= nrIter) {
break
} else {
nrPur <- nrPur + 1
nodif <- NULL
if (is.null(dif)) {
nodif <- 1:ncol(DATA)
} else {
nodif <- which(!1:ncol(DATA) %in% dif)
}
prov2 <- sibTest(DATA, Group,
type = type,
anchor = nodif
)
pval2 <- prov2$p.value
p.adjust2 <- p.adjust(pval2, method = puri.adj.method)
if (min(p.adjust2, na.rm = TRUE) >= alpha) {
dif2 <- NULL
} else {
dif2 <- which(!is.na(pval2) & p.adjust2 < alpha)
}
difPur <- rbind(difPur, rep(0, ncol(DATA)))
difPur[nrPur + 1, dif2] <- 1
if (length(dif) != length(dif2)) {
dif <- dif2
} else {
dif <- sort(dif)
dif2 <- sort(dif2)
if (sum(dif == dif2) == length(dif)) {
noLoop <- TRUE
break
} else {
dif <- dif2
}
}
}
}
pval1 <- pval2
p.adjust1 <- p.adjust(pval1, method = adj.method)
prov1 <- prov2
if (min(p.adjust1, na.rm = TRUE) >= alpha) {
DIFitems <- "No DIF item detected"
} else {
DIFitems <- which(!is.na(pval1) & p.adjust1 < alpha)
}
}
if (!is.null(difPur)) {
rownames(difPur) <- paste0("Step", 1:nrow(difPur) - 1)
colnames(difPur) <- colnames(DATA)
}
if (is.null(p.adjust.method)) {
adjusted.p <- NULL
} else {
adjusted.p <- p.adjust1
}
RES <- list(
Beta = prov1$Beta, SE = prov1$SE, X2 = prov1$X2,
df = prov1$df, p.value = pval1, type = type,
alpha = alpha, DIFitems = DIFitems, p.adjust.method = p.adjust.method,
adjusted.p = adjusted.p, puriadjType = puriadjType, purification = purify, nrPur = nrPur,
difPur = difPur, convergence = noLoop, names = colnames(DATA),
anchor.names = NULL, save.output = save.output,
output = output
)
}
class(RES) <- "SIBTEST"
return(RES)
}
resToReturn <- internalSIBTEST()
if (save.output) {
if (output[2] == "default") {
wd <- paste(getwd(), "/", sep = "")
} else {
wd <- output[2]
}
fileName <- paste(wd, output[1], ".txt", sep = "")
capture.output(resToReturn, file = fileName)
}
return(resToReturn)
}
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