Nothing
plot.GPvam <-
function (x, ..., alpha=.1)
{
#plotCI is taken from R package gplots
plotCI<-function (x, y = NULL, uiw, liw = uiw, ui, li, err = "y", ylim = NULL,
xlim = NULL, type = "p", col = par("col"), barcol = col,
pt.bg = par("bg"), sfrac = 0.01, gap = 1, lwd = par("lwd"),
lty = par("lty"), labels, add = FALSE, xlab, ylab,
minbar, maxbar, ...)
{
if (is.list(x)) {
y <- x$y
x <- x$x
}
if (is.null(y)) {
if (is.null(x))
stop("both x and y NULL")
y <- as.numeric(x)
x <- seq(along = x)
}
li<-y - uiw
ui<-y + uiw
if (err == "y")
z <- y
else z <- x
if (FALSE)
uiw <- NA
if (FALSE)
liw <- NA
if (FALSE)
ui <- z + uiw
if (FALSE)
li <- z - liw
if (FALSE)
li <- ifelse(li < minbar, minbar, li)
if (FALSE)
ui <- ifelse(ui > maxbar, maxbar, ui)
if (err == "y") {
if (is.null(ylim))
ylim <- range(c(y, ui, li), na.rm = TRUE)
if (is.null(xlim) )
xlim <- range(x, na.rm = TRUE)
}
else if (err == "x") {
if (is.null(xlim))
xlim <- range(c(x, ui, li), na.rm = TRUE)
if (is.null(ylim) )
ylim <- range(x, na.rm = TRUE)
}
if (!add) {
if (FALSE)
plot(x, y, ylim = ylim, xlim = xlim, col = col, xlab = xlab,
ylab = ylab, ...)
else {
plot(x, y, ylim = ylim, xlim = xlim, col = col, type = "n",
xlab = xlab, ylab = ylab, ...)
text(x, y, label =labels, col = col, ...)
}
}
if (err == "y") {
if (gap != FALSE)
gap <- strheight("O") * gap
smidge <- par("fin")[1] * sfrac
if (!is.null(li))
suppressWarnings(arrows(x, li, x, pmax(y - gap, li), col = barcol,
lwd = lwd, lty = lty, angle = 90, length = smidge,
code = 1))
if (!is.null(ui))
suppressWarnings(arrows(x, ui, x, pmin(y + gap, ui), col = barcol,
lwd = lwd, lty = lty, angle = 90, length = smidge,
code = 1))
}
else {
if (gap != FALSE)
gap <- strwidth("O") * gap
smidge <- par("fin")[2] * sfrac
if (!is.null(li))
arrows(li, y, pmax(x - gap, li), y, col = barcol,
lwd = lwd, lty = lty, angle = 90, length = smidge,
code = 1)
if (!is.null(ui))
arrows(ui, y, pmin(x + gap, ui), y, col = barcol,
lwd = lwd, lty = lty, angle = 90, length = smidge,
code = 1)
}
points(x, y, col = col, lwd = lwd, bg = pt.bg, type = type,
...)
invisible(list(x = x, y = y))
}
devAskNewPage(ask = TRUE)
c.level <- qnorm(1 - alpha/2)
for (i in 1:length(unique(x$teach.effects$teacher_year))) {
if(x$persistence=="GP"){
for (j in i:length(unique(x$teach.effects$teacher_year))) {
temp.df <- x$teach.effects[x$teach.effects$teacher_year ==
i & x$teach.effects$effect_year == j, ]
temp.df <- temp.df[order(temp.df$EBLUP), ]
plotCI(temp.df$EBLUP, uiw = c.level * temp.df$std_error, labels=temp.df$teacher,
barcol = 2, xlab = "Ranked Teachers", ylab = "Teacher Effect")
title(paste("Year ", i, " Teachers' Year ", j," Effect\nwith ",(1-alpha)*100,"% Confidence Intervals", sep = ""))
abline(h = 0)
}
}else if(x$persistence=="rGP"){
for (j in i:min((i+1),length(unique(x$teach.effects$teacher_year)))) {
temp.df <- x$teach.effects[x$teach.effects$teacher_year ==
i & x$teach.effects$effect_year == j, ]
temp.df <- temp.df[order(temp.df$EBLUP), ]
plotCI(temp.df$EBLUP, uiw = c.level * temp.df$std_error, labels=temp.df$teacher,
barcol = 2, xlab = "Ranked Teachers", ylab = "Teacher Effect")
title(paste("Year ", i, " Teachers' Year ", j," Effect\nwith ",(1-alpha)*100,"% Confidence Intervals", sep = ""))
abline(h = 0)
}
}else{
for (j in i) {
temp.df <- x$teach.effects[x$teach.effects$teacher_year ==
i & x$teach.effects$effect_year == j, ]
temp.df <- temp.df[order(temp.df$EBLUP), ]
plotCI(temp.df$EBLUP, uiw = c.level * temp.df$std_error, labels=temp.df$teacher,
barcol = 2, xlab = "Ranked Teachers", ylab = "Teacher Effect")
title(paste("Year ", i, " Teachers' Year ", j," Effect\nwith ",(1-alpha)*100,"% Confidence Intervals", sep = ""))
abline(h = 0)
}
}
}
qqnorm(x$cresid, main = "Normal Q-Q Plot\n for raw conditional residuals")
qqline(x$cresid)
qqnorm(x$sresid, main = "Normal Q-Q Plot\n for scaled conditional residuals")
qqline(x$sresid)
plot(x$yhat.s, x$sresid, main = "Scaled Conditional Residuals\n(by inverse Cholesky root\nof conditional error matrix)",
xlab = "Predicted", ylab = "Residuals")
plot(x$yhat, x$cresid, main = "Raw conditional residuals",
xlab = "Predicted", ylab = "Residuals")
plot(x$yhat.m, x$mresid, main = "Raw marginal residuals",
xlab = "Predicted", ylab = "Residuals")
devAskNewPage(ask = FALSE)
invisible(x)
}
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