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#' @title Checking Plots
#'
#' @description Function that creates four graphs that can be used to help assess independence, normality, and constant variance
#'
#' @param model an aov or lm object
#' @param n.id the number of points to identify
#' @param COL vector of two colors
#'
#' @author Alan T. Arnholt <arnholtat@@appstate.edu>
#'
#' @seealso \code{\link{twoway.plots}}, \code{\link{oneway.plots}}
#'
#'
#' @export
#'
#' @examples
#' mod.aov <- aov(StopDist ~ tire, data = Tire)
#' checking.plots(mod.aov)
#' rm(mod.aov)
#'
#'
#' @keywords hplot
#'
############## added density plot and 2*2 design 6/27/13 ###
## Change type from "b" to "o" 11/04/14
checking.plots <- function(model, n.id = 3, COL=c("#0080FF", "#A9E2FF")){
Identify <- function(x, y, n.id = 3, AD = 0.2){
y <- y[!is.na(y)]
y <- y[is.finite(y)]
n <- length(y)
pos <- as.numeric(names(y))
oy <- order(abs(y))
b <- y*AD
W <- oy[(n - n.id + 1):n]
text(x[W], y[W]+b[W], as.character(pos[W]))
}
par(mfrow=c(2, 2), pty = "m")
varmodel <- deparse(substitute(model))
y <- rstandard(model)
mAx <- max(abs(y[is.finite(y)])) + .5
n <- length(y)
plot( (1:n), y, ylab = "standardized residuals", col = COL[1],
xlab = "ordered values", ylim=c(-mAx, mAx), type = "o",
main = paste("Standardized residuals versus \n ordered values for", varmodel))
Identify((1:n), y, n.id)
abline(h = 0, lty = 2, col = COL[2])
abline(h = c(2, 3), col = COL, lty = 2)
abline(h = c(-2, -3), col = COL, lty = 2)
qqnorm(y, col = COL[1], ylab = "standardized residuals", xlim = c(-mAx, mAx),
ylim = c(-mAx, mAx), main = paste("Normal Q-Q plot of standardized \n residuals from", varmodel))
abline(a = 0, b = 1, col = COL[2])
junk <- qqnorm(y, plot.it = FALSE)
Identify(junk$x, junk$y, n.id)
plot(fitted(model), y, col = COL[1], xlab = "fitted values", ylab = "standardized residuals",
ylim = c(-mAx, mAx), main = paste("Standardized residuals versus \n fitted values for", varmodel))
abline(h = 0, lty = 2, col = COL[2])
abline(h = c(2, 3), col = COL, lty = 2)
abline(h = c(-2, -3), col = COL, lty = 2)
Identify(fitted(model), y, n.id)
#
plot(density(y), main = paste("Density plot of standardized\nresiduals for", varmodel), col = COL[1])
par(mfrow = c(1, 1), pty = "m")
#
}
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