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plot.infl.rma.uni.r
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plot.infl.rma.uni.r
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plot.infl.rma.uni <- function(x, plotinf=TRUE, plotdfbs=FALSE, dfbsnew=FALSE, logcov=TRUE,
layout, slab.style=1, las=0, pch=21, bg="black", bg.infl="red",
col.na="lightgray", ...) {
mstyle <- .get.mstyle("crayon" %in% .packages())
.chkclass(class(x), must="infl.rma.uni")
na.act <- getOption("na.action")
if (!is.element(na.act, c("na.omit", "na.exclude", "na.fail", "na.pass")))
stop(mstyle$stop("Unknown 'na.action' specified under options()."))
#########################################################################
### check for NAs and stop if there are any when na.act == "na.fail"
any.na <- is.na(as.data.frame(x$inf))
if (any(any.na) && na.act == "na.fail")
stop(mstyle$stop("Missing values in results."))
#########################################################################
### process plotinf argument
if (is.logical(plotinf)) {
if (plotinf) {
which.inf <- seq_len(8)
}
} else {
which.inf <- plotinf
which.inf <- which.inf[(which.inf >= 1) & (which.inf <= 8)]
which.inf <- unique(round(which.inf))
if (length(which.inf) == 0L)
stop(mstyle$stop("Incorrect specification of 'plotinf' argument."))
plotinf <- TRUE
}
### process plotdfbs argument
if (is.logical(plotdfbs)) {
if (plotdfbs) {
which.dfbs <- seq_len(x$p)
}
} else {
which.dfbs <- plotdfbs
which.dfbs <- which.dfbs[(which.dfbs >= 1) & (which.dfbs <= x$p)]
which.dfbs <- unique(round(which.dfbs))
if (length(which.dfbs) == 0L)
stop(mstyle$stop("Incorrect specification of 'plotdfbs' argument."))
plotdfbs <- TRUE
}
#########################################################################
if (!plotinf & !plotdfbs)
stop(mstyle$stop("At least one of the arguments 'plotinf' or 'plotdfbs' argument must be TRUE."))
if (!plotinf & dfbsnew)
dfbsnew <- FALSE
par.mar <- par("mar")
par.mar.adj <- par.mar - c(2,2,2,1)
par.mar.adj[par.mar.adj < 1] <- 1
par(mar = par.mar.adj)
on.exit(par(mar = par.mar))
#########################################################################
### filter out potential arguments to abbreviate() (which cause problems with the various plot functions)
lplot <- function(..., minlength, strict) plot(...)
lpoints <- function(..., minlength, strict) points(...)
llines <- function(..., minlength, strict) lines(...)
laxis <- function(..., minlength, strict) axis(...)
labline <- function(..., minlength, strict) abline(...)
#########################################################################
ids <- switch(slab.style, "1" = x$ids, "2" = x$inf$slab, "3" = abbreviate(x$inf$slab, ...))
#print(ids)
#########################################################################
### plot inf values if requested
if (plotinf) {
### set layout (either defaults or user-specified)
### note: could also use n2mfrow() here, but this behaves slightly differently
par.mfrow <- par("mfrow")
on.exit(par(mfrow = par.mfrow), add=TRUE)
if (missing(layout)) {
if (length(which.inf) == 2L)
par(mfrow=c(2,1))
if (length(which.inf) == 3L)
par(mfrow=c(3,1))
if (length(which.inf) == 4L)
par(mfrow=c(2,2))
if (length(which.inf) == 5L)
par(mfrow=c(5,1))
if (length(which.inf) == 6L)
par(mfrow=c(3,2))
if (length(which.inf) == 7L)
par(mfrow=c(7,1))
if (length(which.inf) == 8L)
par(mfrow=c(4,2))
} else {
layout <- layout[layout >= 1]
layout <- round(layout)
if (length(layout) != 2L)
stop(mstyle$stop("Incorrect specification of 'layout' argument."))
par(mfrow=layout)
}
######################################################################
for (i in seq_len(length(which.inf))) {
if (which.inf[i] == 1) {
zi <- x$inf$rstudent
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- min(zi,-2,na.rm=TRUE)
zi.max <- max(zi, 2,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="rstudent", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=0, lty="dashed", ...)
labline(h=c(qnorm(.025),qnorm(.975)), lty="dotted", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
#if (num.infl)
# text(seq_len(len.ids)[ids.infl], zi[ids.infl], seq_len(len.ids)[ids.infl], pos=ifelse(zi[ids.infl] > 0, 3, 1), ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="rstudent", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 2) {
zi <- x$inf$dffits
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- min(zi,na.rm=TRUE)
zi.max <- max(zi,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="dffits", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h= 0, lty="dashed", ...)
labline(h= 3*sqrt(x$p/(x$k-x$p)), lty="dotted", ...)
labline(h=-3*sqrt(x$p/(x$k-x$p)), lty="dotted", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
#if (num.infl)
# text(seq_len(len.ids)[ids.infl], zi[ids.infl], seq_len(len.ids)[ids.infl], pos=ifelse(zi[ids.infl] > 0, 3, 1), ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="dffits", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 3) {
zi <- x$inf$cook.d
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- min(zi,na.rm=TRUE)
zi.max <- max(zi,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="cook.d", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=qchisq(0.5, df=x$m), lty="dotted", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
#if (num.infl)
# text(seq_len(len.ids)[ids.infl], zi[ids.infl], seq_len(len.ids)[ids.infl], pos=3, ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="cook.d", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 4) {
zi <- x$inf$cov.r
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- min(zi,na.rm=TRUE)
zi.max <- max(zi,na.rm=TRUE)
if (logcov) {
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="cov.r", xlab="", ylab="", las=las, log="y", ...)
} else {
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="cov.r", xlab="", ylab="", las=las, ...)
}
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=1, lty="dashed", ...)
#labline(h=1+3*x$m/(x$k-x$m), lty="dotted", ...)
#labline(h=1-3*x$m/(x$k-x$m), lty="dotted", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
#if (num.infl)
# text(seq_len(len.ids)[ids.infl], zi[ids.infl], seq_len(len.ids)[ids.infl], pos=ifelse(zi[ids.infl] > 1, 3, 1), ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="cov.r", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 5) {
zi <- x$inf$tau2.del
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- min(zi,na.rm=TRUE)
zi.max <- max(zi,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="tau2.del", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=x$tau2, lty="dashed", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="tau2.del", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 6) {
zi <- x$inf$QE.del
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- min(zi,na.rm=TRUE)
zi.max <- max(zi,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="QE.del", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=x$QE, lty="dashed", ...)
#labline(h=qchisq(.95, df=x$k-x$p), lty="dotted")
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="QE.del", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 7) {
zi <- x$inf$hat
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- 0
zi.max <- max(zi,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="hat", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=x$p/x$k, lty="dashed", ...)
labline(h=3*x$p/x$k, lty="dotted", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="hat", xlab="", ylab="", ...)
}
}
if (which.inf[i] == 8) {
zi <- x$inf$weight
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
if (any(!is.na(zi))) {
zi.min <- 0
zi.max <- max(zi,na.rm=TRUE)
lplot(NA, NA, xlim=c(1,len.ids), ylim=c(zi.min,zi.max), xaxt="n", main="weight", xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h=100/x$k, lty="dashed", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
} else {
lplot(NA, NA, xlim=c(0,1), ylim=c(0,1), xaxt="n", yaxt="n", main="weight", xlab="", ylab="", ...)
}
}
}
}
#########################################################################
### plot dfbs values if requested
if (plotdfbs) {
if (dfbsnew) {
dev.new()
par.mar <- par("mar")
par.mar.adj <- par.mar - c(2,2,2,1)
par.mar.adj[par.mar.adj < 1] <- 1
par(mar = par.mar.adj)
on.exit(par(mar = par.mar), add=TRUE)
} else {
if (plotinf) {
par.ask <- par("ask")
par(ask=TRUE)
on.exit(par(ask = par.ask), add=TRUE)
}
}
par(mfrow=c(length(which.dfbs),1))
for (i in seq_len(length(which.dfbs))) {
zi <- x$dfbs[[which.dfbs[i]]]
not.na <- !is.na(zi)
if (na.act == "na.omit") {
zi <- zi[not.na]
len.ids <- length(x$ids)-sum(!not.na)
ids.infl <- x$is.infl[not.na]
lab.ids <- ids[not.na]
}
if (na.act == "na.exclude" || na.act == "na.pass") {
len.ids <- length(x$ids)
ids.infl <- x$is.infl
lab.ids <- ids
}
lplot(NA, NA, xlim=c(1,len.ids), ylim=range(zi,na.rm=TRUE), xaxt="n", main=paste("dfbs: ", names(x$dfbs)[which.dfbs[i]]), xlab="", ylab="", las=las, ...)
laxis(side=1, at=seq_len(len.ids), labels=lab.ids, xlab="", las=las, ...)
labline(h= 0, lty="dashed", ...)
labline(h= 1, lty="dotted", ...)
labline(h=-1, lty="dotted", ...)
if (na.act == "na.exclude" || na.act == "na.pass")
llines(seq_len(len.ids)[not.na], zi[not.na], col=col.na, ...)
llines(seq_len(len.ids), zi, ...)
lpoints(x=seq_len(len.ids), y=zi, bg=bg, pch=pch, ...)
lpoints(x=seq_len(len.ids)[ids.infl], y=zi[ids.infl], bg=bg.infl, pch=pch, ...)
}
}
#########################################################################
invisible()
}