https://github.com/cran/GsymPoint
Tip revision: 158c572b6991bd851086fb65dec3157d2ba15647 authored by Mónica López-Ratón on 31 October 2023, 18:30:02 UTC
version 1.1.2
version 1.1.2
Tip revision: 158c572
gsym.point.R
gsym.point <-
function(methods, data, marker, status, tag.healthy, categorical.cov = NULL, CFN = 1, CFP = 1, control = control.gsym.point(), confidence.level = 0.95, trace = FALSE, seed = FALSE, value.seed = 3, verbose = FALSE)
{
# Possible errors:
if(missing(methods) || is.null(methods))
{
stop("'methods' argument required.", call.=FALSE)
}
if(any(!(methods %in% c("GPQ","EL","auto"))))
{
stop ("You have entered an invalid method.", call. = FALSE)
}
if ((length(methods)== 3) | (length(methods)== 2 & "auto" %in% methods))
{
stop ("You have entered an invalid option. The only possible options are 'GPQ', 'EL','auto', or both methods 'GPQ' and 'EL'", call. = FALSE)
}
if (missing(data)|| is.null(data))
{
stop("'data' argument required.", call. = FALSE)
}
if (missing(marker)|| is.null(marker))
{
stop("'marker' argument required.", call. = FALSE)
}
if (missing(status)|| is.null(status))
{
stop("'status' argument required.", call. = FALSE)
}
if (missing(tag.healthy)|| is.null(tag.healthy))
{
stop("'tag.healthy' argument required.", call. = FALSE)
}
if (control$c_sampling <= 0)
{
stop("the constant for resampling in EL method must be a positive value.", call. = FALSE)
}
if (control$c_F <= 0)
{
stop("the constant for estimating the distribution in EL method must be a positive value.", call. = FALSE)
}
if (control$c_ELq <= 0)
{
stop("the constant for estimating the empirical likelihood function in EL method must be a positive value.", call. = FALSE)
}
if (control$c_R <= 0)
{
stop("the constant for estimating the ROC curve in EL method must be a positive value.", call. = FALSE)
}
if (control$B <= 0)
{
stop("the number of samples in EL method must be a positive value.", call. = FALSE)
}
if (control$I <= 0)
{
stop("the number of samples in GPQ method must be a positive value", call. = FALSE)
}
if (confidence.level < 0 | confidence.level > 1 | length(confidence.level) != 1)
{
stop("'confidence.level' must be a single number between 0 and 1.", call. = FALSE)
}
if (is.logical(trace) == FALSE)
{
stop("'trace' must be a logical-type argument.", call. = FALSE)
}
if (is.logical(seed) == FALSE)
{
stop("'seed' must be a logical-type argument.", call. = FALSE)
}
if (is.logical(verbose) == FALSE)
{
stop("'verbose' must be a logical-type argument.", call. = FALSE)
}
if (length(value.seed) != 1)
{
stop("'value.seed' must be a single number.", call. = FALSE)
}
if(!all(c(marker,status,categorical.cov) %in% names(data))) {
stop("Not all needed variables are supplied in 'data'.", call. = FALSE)
}
# NA's deleted
data <- na.omit(data[, c(marker,status,categorical.cov)])
# A data frame with the results is created:
res <- vector("list", length(methods))
names(res) <- methods
if(!is.null(categorical.cov))
{
if(!is.factor(data[, categorical.cov])) data[, categorical.cov] <- factor(data[, categorical.cov])
data[, categorical.cov] <- droplevels(data[, categorical.cov])
levels.cat <- levels(data[, categorical.cov])
for (i in 1: length(methods))
{
res[[i]] <- vector("list", length(levels.cat))
names(res[[i]]) <- levels.cat
}
}
else
{
levels.cat = 1
for (i in 1: length(methods))
{
res[[i]] <- vector("list", 1)
names(res[[i]]) <- "Global"
}
}
# Calculate the needed parameters:
n0 <- length(data[data[,status] == tag.healthy, marker])
n1 <- length(data[data[,status] != tag.healthy, marker])
# Each method is called up:
for (i in 1: length(methods))
{
for(j in 1:length(levels.cat))
{
if(trace)
{
cat("*************************************************\n")
text <- paste("Method: ", methods[i], sep = "")
if(length(levels.cat) > 1) {
text <- paste(text, ". Level: ", levels.cat[j], sep = "")
}
cat(text)
cat("\nAnalysing ...")
cat("\n*************************************************\n")
}
data.m <- if(length(levels.cat) != 1) data[data[,categorical.cov] == levels.cat[j], ] else data
rho = CFP/CFN
res[[i]][[j]] <- eval(parse(text = paste("function.", methods[i], sep = "")))(data = data.m, marker = marker, status = status, tag.healthy = tag.healthy, CFN = CFN, CFP = CFP, control = control, confidence.level = confidence.level, seed = seed, value.seed = value.seed)
}
}
res$methods <- methods
if(verbose)
{
if(length(methods) > 1)
{
if (is.null(categorical.cov))
{
if(!"normality.transformed" %in% names(res$GPQ$Global))
{
cat(paste("According to the Shapiro-Wilk normality test, the marker can be \n"))
cat(paste("considered normally distributed in both groups.\n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
cat("\n")
print(matrix(c(round(res$GPQ$Global$pvalue.healthy,4), round(res$GPQ$Global$pvalue.diseased,4)), ncol=2, byrow=T, dimnames=list(c("Original marker"),c("Group 0","Group 1"))))
}
else
{
if (res$GPQ$Global$normality.transformed == "yes")
{
cat(paste("According to the Shapiro-Wilk normality test, the marker can not \n"))
cat(paste("be considered normally distributed in both groups.\n"))
cat(paste("However, after transforming the marker using the Box-Cox \n"))
cat(paste("transformation estimate, the Shapiro-Wilk normality test \n"))
cat(paste("indicates that the transformed marker can be considered \n"))
cat(paste("normally distributed in both groups.\n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$GPQ$Global$lambda,4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
print(matrix(c(round(res$GPQ$Global$pvalue.healthy,4), round(res$GPQ$Global$pvalue.diseased,4), round(res$GPQ$Global$pvalue.healthy.transformed,4), round(res$GPQ$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
else if (res$GPQ$Global$normality.transformed == "no")
{
if (is.null(res$GPQ$Global$pvalue.healthy) | is.null(res$GPQ$Global$pvalue.diseased))
{
cat(paste("Due to the sample size, the Shapiro-Wilk normality test can not be performed \n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the results obtained with the GPQ method may not be reliable.\n"))
cat(paste("You must use the EL method instead.\n"))
}
else
{
cat(paste("According to the Shapiro-Wilk normality test, the original marker \n"))
cat(paste("can not be considered normally distributed in both groups.\n"))
cat(paste("After transforming the marker using the Box-Cox transformation \n"))
cat(paste("estimate, the Shapiro-Wilk normality test indicates that the \n"))
cat(paste("transformed marker can not be considered normally distributed \n"))
cat(paste("in both groups.\n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the results obtained with the GPQ method may not be reliable.\n"))
cat(paste("You must use the EL method instead.\n"))
}
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$GPQ$Global$lambda,4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
if (!is.null(res$GPQ$Global$pvalue.healthy) & !is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c(round(res$GPQ$Global$pvalue.healthy,4), round(res$GPQ$Global$pvalue.diseased,4), round(res$GPQ$Global$pvalue.healthy.transformed,4), round(res$GPQ$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$GPQ$Global$pvalue.healthy) & !is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c("NULL", round(res$GPQ$Global$pvalue.diseased,4), "NULL", round(res$GPQ$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (!is.null(res$GPQ$Global$pvalue.healthy) & is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c(round(res$GPQ$Global$pvalue.healthy,4),"NULL", round(res$GPQ$Global$pvalue.healthy.transformed,4), "NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$GPQ$Global$pvalue.healthy) & is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c("NULL","NULL","NULL","NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
}
}
}
else
{
for(i in 1:length(levels.cat))
{
if(!"normality.transformed" %in% names(res$EL[[i]]))
{
cat(paste(levels.cat[i],": \n"))
cat(paste("According to the Shapiro-Wilk normality test, the marker can be \n"))
cat(paste("considered normally distributed in both groups.\n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
cat("\n")
print(matrix(c(round(res$EL[[i]][["pvalue.healthy"]],4), round(res$EL[[i]][["pvalue.diseased"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker"),c("Group 0","Group 1"))))
cat("\n")
}
else
{
if (res$EL[[i]][["normality.transformed"]] == "yes")
{
cat(paste(levels.cat[i],":\n"))
cat(paste("According to the Shapiro-Wilk normality test, the marker can not \n"))
cat(paste("be considered normally distributed in both groups.\n"))
cat(paste("However, after transforming the marker using the Box-Cox \n"))
cat(paste("transformation estimate, the Shapiro-Wilk normality test \n"))
cat(paste("indicates that the transformed marker can be considered \n"))
cat(paste("normally distributed in both groups.\n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$EL[[i]][["lambda"]],4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
print(matrix(c(round(res$EL[[i]][["pvalue.healthy"]],4), round(res$EL[[i]][["pvalue.diseased"]],4), round(res$EL[[i]][["pvalue.healthy.transformed"]],4), round(res$EL[[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
cat("\n")
}
else if (res$EL[[i]][["normality.transformed"]] == "no")
{
cat(paste(levels.cat[i],":\n"))
if (is.null(res$EL[[i]][["pvalue.healthy"]]) | is.null(res$EL[[i]][["pvalue.diseased"]]))
{
cat(paste("Due to the sample size, the Shapiro-Wilk normality test can not be performed \n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the results obtained with the GPQ method may not be reliable.\n"))
cat(paste("You must use the EL method instead.\n"))
}
else
{
cat(paste("According to the Shapiro-Wilk normality test, the original marker \n"))
cat(paste("can not be considered normally distributed in both groups.\n"))
cat(paste("After transforming the marker using the Box-Cox transformation \n"))
cat(paste("estimate, the Shapiro-Wilk normality test indicates that the \n"))
cat(paste("transformed marker can not be considered normally distributed \n"))
cat(paste("in both groups.\n"))
cat(paste("Therefore, although the results of both methods will be shown,\n"))
cat(paste("the results obtained with the GPQ method may not be reliable.\n"))
cat(paste("You must use the EL method instead.\n"))
}
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$EL[[i]][["lambda"]],4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
if (!is.null(res$EL[[i]][["pvalue.healthy"]]) & !is.null(res$EL[[i]][["pvalue.diseased"]]))
{
print(matrix(c(round(res$EL[[i]][["pvalue.healthy"]],4), round(res$EL[[i]][["pvalue.diseased"]],4), round(res$EL[[i]][["pvalue.healthy.transformed"]],4), round(res$EL[[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$EL[[i]][["pvalue.healthy"]]) & !is.null(res$EL[[i]][["pvalue.diseased"]]))
{
print(matrix(c("NULL", round(res$EL[[i]][["pvalue.diseased"]],4), "NULL", round(res$EL[[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (!is.null(res$EL[[i]][["pvalue.healthy"]]) & is.null(res$EL[[i]][["pvalue.diseased"]]))
{
print(matrix(c(round(res$EL[[i]][["pvalue.healthy"]],4),"NULL", round(res$EL[[i]][["pvalue.healthy.transformed"]],4), "NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$EL[[i]][["pvalue.healthy"]]) & is.null(res$EL[[i]][["pvalue.diseased"]]))
{
print(matrix(c("NULL","NULL","NULL","NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
cat("\n")
}
}
}
}
}
else
{
if (methods == "EL")
{
if (is.null(categorical.cov))
{
if(!"normality.transformed" %in% names(res$EL$Global))
{
cat(paste("According to the Shapiro-Wilk normality test, the marker can be \n"))
cat(paste("considered normally distributed in both groups.\n"))
cat(paste("Therefore the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
cat("\n")
print(matrix(c(round(res$EL$Global$pvalue.healthy,4), round(res$EL$Global$pvalue.diseased,4)), ncol=2, byrow=T, dimnames=list(c("Original marker"),c("Group 0","Group 1"))))
}
else
{
if (res$EL$Global$normality.transformed == "yes")
{
cat(paste("According to the Shapiro-Wilk normality test, the marker can not \n"))
cat(paste("be considered normally distributed in both groups.\n"))
cat(paste("However, after transforming the marker using the Box-Cox \n"))
cat(paste("transformation estimate, the Shapiro-Wilk normality test \n"))
cat(paste("indicates that the transformed marker can be considered \n"))
cat(paste("normally distributed in both groups.\n"))
cat(paste("Therefore the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$EL$Global$lambda,4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
print(matrix(c(round(res$EL$Global$pvalue.healthy,4), round(res$EL$Global$pvalue.diseased,4), round(res$EL$Global$pvalue.healthy.transformed,4), round(res$EL$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
}
}
else
{
for(i in 1:length(levels.cat))
{
if(!"normality.transformed" %in% names(res[[1]][[i]]))
{
cat(paste(levels.cat[i],":\n"))
cat(paste("According to the Shapiro-Wilk normality test, the marker can be \n"))
cat(paste("considered normally distributed in both groups. \n"))
cat(paste("Therefore the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
cat("\n")
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4), round(res[[1]][[i]][["pvalue.diseased"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker"),c("Group 0","Group 1"))))
cat("\n")
}
else
{
if (res[[1]][[i]][["normality.transformed"]] == "yes")
{
cat(paste(levels.cat[i],":\n"))
cat(paste("According to the Shapiro-Wilk normality test, the marker can not \n"))
cat(paste("be considered normally distributed in both groups.\n"))
cat(paste("However, after transforming the marker using the Box-Cox \n"))
cat(paste("transformation estimate, the Shapiro-Wilk normality test \n"))
cat(paste("indicates that the transformed marker can be considered \n"))
cat(paste("normally distributed in both groups.\n"))
cat(paste("Therefore the GPQ method would be more suitable for this dataset.\n"))
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res[[1]][[i]][["lambda"]],4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4), round(res[[1]][[i]][["pvalue.diseased"]],4), round(res[[1]][[i]][["pvalue.healthy.transformed"]],4), round(res[[1]][[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
cat("\n")
}
}
}
}
}
if (methods == "auto")
{
if (is.null(categorical.cov))
{
if(!"normality.transformed" %in% names(res$auto$Global))
{
cat(paste("According to the Shapiro-Wilk normality test, the marker can be \n"))
cat(paste("considered normally distributed in both groups.\n"))
cat(paste("Therefore the program selects automatically the GPQ method for this dataset.\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
cat("\n")
print(matrix(c(round(res$auto$Global$pvalue.healthy,4), round(res$auto$Global$pvalue.diseased,4)), ncol=2, byrow=T, dimnames=list(c("Original marker"),c("Group 0","Group 1"))))
}
else
{
if (res$auto$Global$normality.transformed == "yes")
{
cat(paste("According to the Shapiro-Wilk normality test, the marker can not \n"))
cat(paste("be considered normally distributed in both groups.\n"))
cat(paste("However, after transforming the marker using the Box-Cox \n"))
cat(paste("transformation estimate, the Shapiro-Wilk normality test \n"))
cat(paste("indicates that the transformed marker can be considered \n"))
cat(paste("normally distributed in both groups.\n"))
cat(paste("Therefore the program selects automatically the GPQ method for this dataset.\n"))
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$auto$Global$lambda,4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
print(matrix(c(round(res$auto$Global$pvalue.healthy,4), round(res$auto$Global$pvalue.diseased,4), round(res$auto$Global$pvalue.healthy.transformed,4), round(res$auto$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (res$auto$Global$normality.transformed == "no")
{
if (is.null(res$auto$Global$pvalue.healthy) | is.null(res$auto$Global$pvalue.diseased))
{
cat(paste("Due to the sample size, the Shapiro-Wilk normality test can not be performed \n"))
cat(paste("Therefore, the program selects automatically the EL method. \n"))
}
else
{
cat(paste("According to the Shapiro-Wilk normality test, the original marker \n"))
cat(paste("can not be considered normally distributed in both groups.\n"))
cat(paste("After transforming the marker using the Box-Cox transformation \n"))
cat(paste("estimate the Shapiro-Wilk normality test indicates that the \n"))
cat(paste("transformed marker can not be considered normally distributed \n"))
cat(paste("in both groups. \n"))
cat(paste("Therefore, the program selects automatically the EL method for this dataset. \n"))
}
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$auto$Global$lambda,4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
if (!is.null(res$auto$Global$pvalue.healthy) & !is.null(res$auto$Global$pvalue.diseased))
{
print(matrix(c(round(res$auto$Global$pvalue.healthy,4), round(res$auto$Global$pvalue.diseased,4), round(res$auto$Global$pvalue.healthy.transformed,4), round(res$auto$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$auto$Global$pvalue.healthy) & !is.null(res$auto$Global$pvalue.diseased))
{
print(matrix(c("NULL", round(res$auto$Global$pvalue.diseased,4), "NULL", round(res$auto$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (!is.null(res$auto$Global$pvalue.healthy) & is.null(res$auto$Global$pvalue.diseased))
{
print(matrix(c(round(res$auto$Global$pvalue.healthy,4),"NULL", round(res$auto$Global$pvalue.healthy.transformed,4), "NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$auto$Global$pvalue.healthy) & is.null(res$auto$Global$pvalue.diseased))
{
print(matrix(c("NULL","NULL","NULL","NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
}
}
}
else
{
for(i in 1:length(levels.cat))
{
if(!"normality.transformed" %in% names(res[[1]][[i]]))
{
cat(paste(levels.cat[i],":\n"))
cat(paste("According to the Shapiro-Wilk normality test, the marker can be \n"))
cat(paste("considered normally distributed in both groups. \n"))
cat(paste("Therefore the program selects automatically the GPQ method for this dataset.\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
cat("\n")
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4), round(res[[1]][[i]][["pvalue.diseased"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker"),c("Group 0","Group 1"))))
cat("\n")
}
else
{
if (res[[1]][[i]][["normality.transformed"]] == "yes")
{
cat(paste(levels.cat[i],":\n"))
cat(paste("According to the Shapiro-Wilk normality test, the marker can not \n"))
cat(paste("be considered normally distributed in both groups.\n"))
cat(paste("However, after transforming the marker using the Box-Cox \n"))
cat(paste("transformation estimate, the Shapiro-Wilk normality test \n"))
cat(paste("indicates that the transformed marker can be considered \n"))
cat(paste("normally distributed in both groups.\n"))
cat(paste("Therefore the program selects automatically the GPQ method for this dataset.\n"))
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res[[1]][[i]][["lambda"]],4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4), round(res[[1]][[i]][["pvalue.diseased"]],4), round(res[[1]][[i]][["pvalue.healthy.transformed"]],4), round(res[[1]][[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
cat("\n")
}
if (res[[1]][[i]][["normality.transformed"]] == "no")
{
cat(paste(levels.cat[i],":\n"))
if (is.null(res[[1]][[i]][["pvalue.healthy"]]) | is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
cat(paste("Due to the sample size, the Shapiro-Wilk normality test can not be performed \n"))
cat(paste("Therefore, the program selects automatically the EL method. \n"))
}
else
{
cat(paste("According to the Shapiro-Wilk normality test, the original marker \n"))
cat(paste("can not be considered normally distributed in both groups.\n"))
cat(paste("After transforming the marker using the Box-Cox transformation \n"))
cat(paste("estimate the Shapiro-Wilk normality test indicates that the \n"))
cat(paste("transformed marker can not be considered normally distributed \n"))
cat(paste("in both groups.\n"))
cat(paste("Therefore, the program selects automatically the EL method for this dataset. \n"))
}
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res[[1]][[i]][["lambda"]],4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
if (!is.null(res[[1]][[i]][["pvalue.healthy"]]) & !is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4), round(res[[1]][[i]][["pvalue.diseased"]],4), round(res[[1]][[i]][["pvalue.healthy.transformed"]],4), round(res[[1]][[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res[[1]][[i]][["pvalue.healthy"]]) & !is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c("NULL", round(res[[1]][[i]][["pvalue.diseased"]],4), "NULL", round(res[[1]][[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (!is.null(res[[1]][[i]][["pvalue.healthy"]]) & is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4),"NULL", round(res[[1]][[i]][["pvalue.healthy.transformed"]],4), "NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res[[1]][[i]][["pvalue.healthy"]]) & is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c("NULL","NULL","NULL","NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
cat("\n")
}
}
}
}
}
if (methods == "GPQ")
{
if (is.null(categorical.cov))
{
if ("normality.transformed" %in% names(res$GPQ$Global))
{
if(res$GPQ$Global$normality.transformed == "no")
{
if (is.null(res$GPQ$Global$pvalue.healthy) | is.null(res$GPQ$Global$pvalue.diseased))
{
cat(paste("Due to the sample size, the Shapiro-Wilk normality test can not be performed \n"))
cat(paste("Therefore, the results obtained with the GPQ method may not be \n"))
cat(paste("reliable. You must use the EL method instead.\n"))
}
else
{
cat(paste("According to the Shapiro-Wilk normality test, the original marker \n"))
cat(paste("can not be considered normally distributed in both groups.\n"))
cat(paste("After transforming the marker using the Box-Cox transformation \n"))
cat(paste("estimate the Shapiro-Wilk normality test indicates that the \n"))
cat(paste("transformed marker can not be considered normally distributed \n"))
cat(paste("in both groups. \n"))
cat(paste("Therefore, the results obtained with the GPQ method may not be \n"))
cat(paste("reliable. You must use the EL method instead.\n"))
}
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res$GPQ$Global$lambda,4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
if (!is.null(res$GPQ$Global$pvalue.healthy) & !is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c(round(res$GPQ$Global$pvalue.healthy,4), round(res$GPQ$Global$pvalue.diseased,4), round(res$GPQ$Global$pvalue.healthy.transformed,4), round(res$GPQ$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$GPQ$Global$pvalue.healthy) & !is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c("NULL", round(res$GPQ$Global$pvalue.diseased,4), "NULL", round(res$GPQ$Global$pvalue.diseased.transformed,4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (!is.null(res$GPQ$Global$pvalue.healthy) & is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c(round(res$GPQ$Global$pvalue.healthy,4),"NULL", round(res$GPQ$Global$pvalue.healthy.transformed,4), "NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res$GPQ$Global$pvalue.healthy) & is.null(res$GPQ$Global$pvalue.diseased))
{
print(matrix(c("NULL","NULL","NULL","NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
}
}
}
else
{
for(i in 1:length(levels.cat))
{
if ("normality.transformed" %in% names(res[[1]][[i]]))
{
if (res[[1]][[i]][["normality.transformed"]] == "no")
{
cat(paste(levels.cat[i],":\n"))
if (is.null(res[[1]][[i]][["pvalue.healthy"]]) | is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
cat(paste("Due to the sample size, the Shapiro-Wilk normality test can not be performed \n"))
cat(paste("Therefore, the results obtained with the GPQ method may not be \n"))
cat(paste("reliable. You must use the EL method instead.\n"))
}
else
{
cat(paste("According to the Shapiro-Wilk normality test, the original marker \n"))
cat(paste("can not be considered normally distributed in both groups.\n"))
cat(paste("After transforming the marker using the Box-Cox transformation \n"))
cat(paste("estimate the Shapiro-Wilk normality test indicates that the \n"))
cat(paste("transformed marker can not be considered normally distributed \n"))
cat(paste("in both groups.\n"))
cat(paste("Therefore, the results obtained with the GPQ method may not be \n"))
cat(paste("reliable. You must use the EL method instead.\n"))
}
cat("\n")
cat(paste("Box-Cox lambda estimate =", round(res[[1]][[i]][["lambda"]],4),"\n"))
cat("\n")
cat("Shapiro-Wilk test p-values\n")
if (!is.null(res[[1]][[i]][["pvalue.healthy"]]) & !is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4), round(res[[1]][[i]][["pvalue.diseased"]],4), round(res[[1]][[i]][["pvalue.healthy.transformed"]],4), round(res[[1]][[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res[[1]][[i]][["pvalue.healthy"]]) & !is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c("NULL", round(res[[1]][[i]][["pvalue.diseased"]],4), "NULL", round(res[[1]][[i]][["pvalue.diseased.transformed"]],4)), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (!is.null(res[[1]][[i]][["pvalue.healthy"]]) & is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c(round(res[[1]][[i]][["pvalue.healthy"]],4),"NULL", round(res[[1]][[i]][["pvalue.healthy.transformed"]],4), "NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
if (is.null(res[[1]][[i]][["pvalue.healthy"]]) & is.null(res[[1]][[i]][["pvalue.diseased"]]))
{
print(matrix(c("NULL","NULL","NULL","NULL"), ncol=2, byrow=T, dimnames=list(c("Original marker", "Box-Cox transformed marker"),c("Group 0","Group 1"))))
}
cat("\n")
}
}
}
}
}
}
}
if(length(levels.cat) != 1) res$levels.cat <- levels.cat
res$call <- match.call()
res$data <- data
class(res) <- "gsym.point"
invisible(res)
res
}
