xaxt <- NULL
#' Plot function for an RM object
#'
#' Generic plot function for \code{RM} objects: Returns a plot of the mean
#' values along with confidence intervals for a specified RM-model.
#'
#' @param x An object of class \code{RM}
#' @param leg Logical: Should a legend be plotted?
#' @param ... Additional parameters to be passed to plot()
#'
#' @export
plot.RM <- function (x, leg = TRUE, ...) {
object <- x
dots <- list(...)
a <- object$plotting
b <- object$Descriptive
nf <- a$nf
# to automatically create axis if not specified by user
exist2 <- hasArg(xaxt)
ax <- TRUE
if(exist2){
ax <- FALSE
}
if(!(hasArg(gap))){
gap <- 0.1
} else {
gap <- dots$gap
}
label.x <- names(a$fl[nf])
sum.fac <- sum(a$fl)
xmax <- a$fl[nf]+ (sum.fac-a$fl[nf])*gap
miny <- min(b$`Lower 95 % CI`)
maxy <- max(b$`Upper 95 % CI`)
# default values
args <- list(a,
b,
lwd = 2, ylab = "Means", xlab = label.x,
col = 1:(sum.fac-a$fl[nf]),
pch = 1:18, legendpos = "topright",
xlim = c(0.8, xmax + 0.1),
ylim =c(miny, maxy), gap = 0.1, xaxt = "n", ax,
leg, leg.cex = 0.5)
args[names(dots)] <- dots
do.call(RMplotting, args = args)
}
#' Display MANOVA object
#'
#' Returns a short summary of the results (test statistics with p-values)
#'
#' @param x A MANOVA object
#' @param ... Additional parameters (currently not used)
#'
#' @export
print.MANOVA <- function(x, ...) {
object <- x
a <- object$input
# avoid printing zeros
WTS <- object$WTS
WTS[WTS[, "p-value"] == 0, "p-value"] <- "<0.001"
res <- object$resampling
res[res == 0] <- "<0.001"
cat("Call:", "\n")
print(a$formula)
cat("\n", "Wald-Type Statistic (WTS):", "\n", sep = "")
print(WTS)
# cat("\n", "ANOVA-Type Statistic (ATS):", "\n", sep = "")
# print(x$ATS)
cat("\n", "modified ANOVA-Type Statistic (MATS):", "\n", sep = "")
print(object$MATS)
cat("\n", "p-values resampling:", "\n", sep = "")
print(res)
}
#' Summarizing a MANOVA object
#'
#' Returns a summary of the results including mean vectors and sample sizes for all groups as well
#' as test statistics with degrees of freedom and p-values
#'
#' @param object A MANOVA object
#' @param ... Additional parameters (currently not used)
#'
#' @export
summary.MANOVA <- function (object, ...) {
a <- object$input
b <- object$other
# avoid printing zeros
WTS <- object$WTS
WTS[WTS[, "p-value"] == 0, "p-value"] <- "<0.001"
res <- object$resampling
res[res == 0] <- "<0.001"
cat("Call:", "\n")
print(a$formula)
if(!is.null(b$within)){
cat("A multivariate repeated measures analysis with ", b$no.subf, "within-subject factor(s) (", b$within, ")and ", b$no.whole,
"between-subject factor(s).", "\n")
}
cat("\n", "Descriptive:", "\n", sep = "")
print(object$Descriptive)
cat("\n", "Wald-Type Statistic (WTS):", "\n", sep = "")
print(WTS)
cat("\n", "modified ANOVA-Type Statistic (MATS):", "\n", sep = "")
print(object$MATS)
cat("\n", "p-values resampling:", "\n", sep = "")
print(res)
}
#' Display an RM object
#'
#' Returns a short summary of the results (test statistics with p-values)
#'
#' @param x An RM object
#' @param ... Additional parameters (currently not used)
#'
#' @export
print.RM <- function(x, ...) {
object <- x
a <- object$input
# avoid printing zeros
WTS <- object$WTS
ATS <- object$ATS
WTS[WTS[, "p-value"] == 0, "p-value"] <- "<0.001"
ATS[ATS[, "p-value"] == 0, "p-value"] <- "<0.001"
res <- object$resampling
res[res == 0] <- "<0.001"
cat("Call:", "\n")
print(a$formula)
cat("\n", "Wald-Type Statistic (WTS):", "\n", sep = "")
print(WTS)
cat("\n", "ANOVA-Type Statistic (ATS):", "\n", sep = "")
print(ATS)
cat("\n", "p-values resampling:", "\n", sep = "")
if(x$input$resampling == "Perm"){
print(res[, 1, drop = FALSE])
} else {
print(res)
}
}
#' Summarizing an RM object
#'
#' Returns a summary of the results including mean values, variances
#' and sample sizes for all groups as well
#' as test statistics with degrees of freedom and p-values
#'
#' @param object An RM object
#' @param ... Additional parameters (currently not used)
#'
#' @export
summary.RM <- function (object, ...) {
a <- object$input
b <- object$plotting
# avoid printing zeros
WTS <- object$WTS
ATS <- object$ATS
WTS[WTS[, "p-value"] == 0, "p-value"] <- "<0.001"
ATS[ATS[, "p-value"] == 0, "p-value"] <- "<0.001"
res <- object$resampling
res[res == 0] <- "<0.001"
cat("Call:", "\n")
print(a$formula)
cat("A repeated measures analysis with", b$no.subf, "within-subject factor(s) (", paste(object$withinfactors, collapse = ","),
") and", b$nf-b$no.subf, "between-subject factor(s).", "\n")
cat("\n", "Descriptive:", "\n", sep = "")
print(object$Descriptive)
cat("\n", "Wald-Type Statistic (WTS):", "\n", sep = "")
print(WTS)
cat("\n", "ANOVA-Type Statistic (ATS):", "\n", sep = "")
print(ATS)
cat("\n", "p-values resampling:", "\n", sep = "")
if(a$resampling == "Perm"){
print(res[, 1, drop = FALSE])
} else {
print(res)
}
}
#' @export
plot.MANOVA <- function(x, ...){
stop("There is no plotting routine for MANOVA objects.")
}
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