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## event.chart.q: eventchart program 1.0 (creates function event.chart)
##
## last edited: 9-27-97
## last edited: 10-20-98, add pty='m' for the default plotting;
## one may change to pty='s' to get the 'square plot' for the Goldman's Event Chart
## FEH changes 9may02 for R
event.chart <-
function(data, subset.r = 1:dim(data)[1], subset.c = 1:dim(data)[2],
sort.by = NA, sort.ascending = TRUE,
sort.na.last = TRUE, sort.after.subset = TRUE,
y.var = NA, y.var.type = "n",
y.jitter = FALSE, y.jitter.factor = 1,
y.renum = FALSE, NA.rm = FALSE, x.reference = NA,
now = max(data[, subset.c], na.rm = TRUE),
now.line = FALSE, now.line.lty = 2,
now.line.lwd = 1, now.line.col = 1, pty = "m",
date.orig = c(1, 1, 1960), titl = "Event Chart",
y.idlabels = NA, y.axis = "auto",
y.axis.custom.at = NA, y.axis.custom.labels = NA,
y.julian = FALSE, y.lim.extend = c(0, 0),
y.lab = ifelse(is.na(y.idlabels), "", as.character(y.idlabels)),
x.axis.all = TRUE, x.axis = "auto",
x.axis.custom.at = NA, x.axis.custom.labels = NA,
x.julian = FALSE, x.lim.extend = c(0, 0), x.scale = 1,
x.lab = ifelse(x.julian, "Follow-up Time", "Study Date"),
line.by = NA, line.lty = 1, line.lwd = 1, line.col = 1,
line.add = NA, line.add.lty = NA,
line.add.lwd = NA, line.add.col = NA,
point.pch = 1:length(subset.c),
point.cex = rep(0.6, length(subset.c)),
point.col = rep(1, length(subset.c)),
point.cex.mult = 1., point.cex.mult.var = NA,
extra.points.no.mult = rep(NA, length(subset.c)),
legend.plot = FALSE, legend.location = "o", legend.titl = titl,
legend.titl.cex = 3, legend.titl.line = 1,
legend.point.at = list(x = c(5, 95), y = c(95, 30)),
legend.point.pch = point.pch,
legend.point.text = ifelse(rep(is.data.frame(data), length(subset.c)),
names(data[, subset.c]),
subset.c),
legend.cex = 2.5, legend.bty = "n",
legend.line.at = list(x = c(5, 95), y = c(20, 5)),
legend.line.text = names(table(as.character(data[, line.by]),
exclude = c("", "NA"))),
legend.line.lwd = line.lwd, legend.loc.num = 1,
...)
{
legnd <- function(..., pch) {
if(missing(pch)) legend(...)
else legend(..., pch = pch)
}
month.day.year <- function(jul, origin.) {
if (missing(origin.) || is.null(origin.)) {
origin. <- .Options$chron.origin
if (is.null(origin.))
origin. <- c(month = 1, day = 1, year = 1960)
}
shift <- if (all(origin. == 0)) 0 else julian(origin = origin.)
## relative origin
## "absolute" origin
j <- jul + shift
j <- j - 1721119
y <- (4 * j - 1) %/% 146097
j <- 4 * j - 1 - 146097 * y
d <- j %/% 4
j <- (4 * d + 3) %/% 1461
d <- 4 * d + 3 - 1461 * j
d <- (d + 4) %/% 4
m <- (5 * d - 3) %/% 153
d <- 5 * d - 3 - 153 * m
d <- (d + 5) %/% 5
y <- 100 * y + j
y <- y + ifelse(m < 10, 0, 1)
m <- m + ifelse(m < 10, 3, -9)
list(month = m, day = d, year = y)
}
## julian.r
## Convert between Julian and Calendar Dates
julian <- function(m, d, y, origin.) {
only.origin <- all(missing(m), missing(d), missing(y))
if (only.origin)
m <- d <- y <- NULL
## return days since origin
if (missing(origin.) || is.null(origin.)) {
origin. <- .Options$chron.origin
if (is.null(origin.))
origin. <- c(month = 1, day = 1, year = 1960)
}
nms <- names(d)
max.len <- max(length(m), length(d), length(y))
## prepend new origin value and rep out to common max. length:
m <- c(origin.[1], rep(m, length = max.len))
d <- c(origin.[2], rep(d, length = max.len))
y <- c(origin.[3], rep(y, length = max.len))
## code from julian date in the S book (p.269)
y <- y + ifelse(m > 2, 0, -1)
m <- m + ifelse(m > 2, -3, 9)
c <- y %/% 100
ya <- y - 100 * c
out <- (146097 * c) %/% 4 + (1461 * ya) %/% 4 + (153 * m + 2) %/% 5 +
d + 1721119
## now subtract the new origin from all dates
if (!only.origin) {
if (all(origin. == 0))
out <- out[-1]
else
out <- out[-1] - out[1]
}
names(out) <- nms
out
}
## stop function if unacceptable violations occur
## (other stops may occur later)
if (!is.matrix(data) && !is.data.frame(data))
stop("argument data must be a matrix or a data frame\n")
## section 1: do necessary subsetting and sorting of data
targodata <- apply(data[, subset.c, drop = FALSE], 2, as.numeric)
## targodata for target 'overall' data
if (!is.na(x.reference))
targodata <- apply(targodata - data[, x.reference], 2, as.numeric)
## start of sort routine
if (!is.na(sort.by[1])) {
if (sort.after.subset == TRUE)
data <- data[subset.r, ]
m <- dim(data)[1]
keys <- 1:m
rotate <- m:1
length.sort.by <- length(sort.by)
asc <- rep(sort.ascending, length.sort.by)
for (i in length.sort.by:1) {
if (asc[i])
keys[] <- keys[sort.list(data[, sort.by[[i]]][keys],
na.last = sort.na.last)]
else
keys[] <- keys[order(data[, sort.by[[i]]][keys],
rotate, na.last = sort.na.last)[rotate]]
}
data <- data[keys, ]
if (sort.after.subset == FALSE) {
subset.r <- (1:dim(data)[1])[subset.r]
targdata <- apply(data[subset.r, subset.c, drop = FALSE], 2, as.numeric)
} else if (sort.after.subset == TRUE) {
targdata <- apply(data[, subset.c, drop = FALSE], 2, as.numeric)
subset.ro <- (1:dim(data)[1])[subset.r]
subset.r <- seq(length(subset.ro))
}
} else if (is.na(sort.by[1])) {
subset.r <- (1:dim(data)[1])[subset.r]
targdata <- apply(data[subset.r, subset.c, drop = FALSE], 2, as.numeric)
}
## end of sort routine
## start to deal with missing values and renumbering y-axis
if (NA.rm == TRUE) {
whotoplot <- subset.r[!(apply(is.na(targdata), 1, all))]
## whotoplot is for use for data matrix(dataframe);
## essentially who will be plotted from data
t.whotoplot <- seq(dim(targdata)[1])[!(apply(is.na(targdata), 1, all))]
## t.whotoplot is for use for targdata matrix(dataframe);
## essentially, who will be plotted from targdata
if (y.renum == TRUE) {
whattoplot <- seq(subset.r[!(apply(is.na(targdata), 1, all))])
## whattoplot is what will be plotted on y-axis of event chart
} else if (y.renum == FALSE) {
if ((!is.na(sort.by[1]) & sort.after.subset == FALSE) | (is.na(sort.by[1])))
whattoplot <- subset.r[!(apply(is.na(targdata), 1, all))]
else if (!is.na(sort.by[1]) & sort.after.subset == TRUE)
whattoplot <- subset.ro[!(apply(is.na(targdata), 1, all))]
}
} else if (NA.rm == FALSE) {
whotoplot <- subset.r
t.whotoplot <- seq(dim(targdata)[1])
if (y.renum == TRUE)
whattoplot <- seq(subset.r)
else if (y.renum == FALSE) {
if ((!is.na(sort.by[1]) & sort.after.subset == FALSE) | (is.na(sort.by[1])))
whattoplot <- subset.r
else if (!is.na(sort.by[1]) & sort.after.subset == TRUE)
whattoplot <- subset.ro
}
}
## end of dealing with missing values and renumbering of y-axis
## section 2: perform necessary manipulations using x.reference and y.var
## deal with re-referencing x-axis with x.reference
if (!is.na(x.reference)) {
targdata <- apply(targdata - data[subset.r, x.reference], 2, as.numeric)
if (NA.rm == TRUE) {
x.referencew <- data[whotoplot, x.reference]
whotoplot <- whotoplot[!is.na(x.referencew)]
t.whotoplot <- t.whotoplot[!is.na(x.referencew)]
whattoplot.ref <- whattoplot[!is.na(x.referencew)]
if (y.renum == FALSE) {
if ((!is.na(sort.by[1]) & sort.after.subset == FALSE) | (is.na(sort.by[1])))
whattoplot <- seq(subset.r[1],
subset.r[1] + length(whattoplot.ref) - 1)
else if (!is.na(sort.by[1]) & sort.after.subset == TRUE)
whattoplot <- seq(subset.ro[1],
subset.ro[1] + length(whattoplot.ref) - 1)
} else if (y.renum == TRUE)
whattoplot <- seq(length(whattoplot.ref))
}
}
## deal with using a data frame variable to place lines on y-axis
if (!is.na(y.var)) {
if (!is.na(sort.by[1]))
stop("cannot use sort.by and y.var simultaneously\n")
y.varw <- as.numeric(data[whotoplot, y.var])
whotoplot <- whotoplot[!is.na(y.varw)]
t.whotoplot <- t.whotoplot[!is.na(y.varw)]
whattoplot <- y.varw[!is.na(y.varw)]
if (y.jitter == TRUE) {
range.data <- diff(range(whattoplot))
range.unif <- y.jitter.factor *
(range.data / (2 * (length(whattoplot) - 1)))
whattoplot <- whattoplot +
runif(length(whattoplot), -(range.unif), range.unif)
}
}
sort.what <- sort(whattoplot)
length.what <- length(whattoplot)
## section 3: perform all plotting
## first, make sure length of point.pch, cex, col is same as subset.c
len.c <- length(subset.c)
if (length(point.pch) < len.c) {
warning("length(point.pch) < length(subset.c)")
point.pch <- rep(point.pch, len.c)[1:len.c]
}
if (length(point.cex) < len.c) {
warning("length(point.cex) < length(subset.c)")
point.cex <- rep(point.cex, len.c)[1:len.c]
}
if (length(point.col) < len.c) {
warning("length(point.col) < length(subset.c)")
point.col <- rep(point.col, len.c)[1:len.c]
}
## set default of par(new = FALSE)
par(new = FALSE)
## plot external legend (if requested)
if (legend.plot == TRUE && legend.location == "o") {
plot(1, 1, type = "n", xlim = c(0, 100), ylim = c(0, 100),
axes = FALSE, xlab = "", ylab = "")
mtext(legend.titl, line = legend.titl.line, outer = FALSE,
cex = legend.titl.cex)
legnd(legend.point.at[[1]], legend.point.at[[2]],
leg = legend.point.text,
pch = legend.point.pch, cex = legend.cex,
col = point.col, bty = legend.bty)
if (!is.na(line.by)) {
par(new = TRUE)
legnd(legend.line.at[[1]], legend.line.at[[2]],
leg = legend.line.text, cex = legend.cex,
lty = line.lty, lwd = legend.line.lwd,
col = line.col, bty = legend.bty)
}
invisible(par(ask = TRUE))
}
## start creating objects to be used in determining plot region
targdata <- targdata / x.scale
targodata <- targodata / x.scale
minvec <- apply(targdata[t.whotoplot,, drop = FALSE], 1, min, na.rm = TRUE)
minotime <- ifelse(x.axis.all,
min(apply(targodata, 1, min, na.rm = TRUE), na.rm = TRUE),
min(minvec, na.rm = TRUE))
maxvec <- apply(targdata[t.whotoplot,, drop = FALSE], 1, max, na.rm = TRUE)
maxotime <- ifelse(x.axis.all,
max(apply(targodata, 1, max, na.rm = TRUE), na.rm = TRUE),
max(maxvec, na.rm = TRUE))
## determine par parameters and plot graphical region based
## on request of y.var and, subsequently, y.var.type and now.line
y.axis.top <- sort.what[length.what] + y.lim.extend[2]
y.axis.bottom <- sort.what[1] - y.lim.extend[1]
x.axis.right <- maxotime + x.lim.extend[2]
x.axis.left <- minotime - x.lim.extend[1]
if (!is.na(y.var) & y.var.type == "d") {
oldpar <- par(omi = rep(0, 4), lwd = 0.6,
mgp = c(3.05, 1.1, 0), tck = -0.006, ...)
## set pty
par(pty = pty)
plot(whattoplot, type = "n",
xlim = c(x.axis.left,
ifelse(now.line,
(now - (min(data[, subset.c], na.rm = TRUE))) / x.scale,
x.axis.right)),
ylim = c(y.axis.bottom,
ifelse(pty == "s",
now,
y.axis.top)),
xlab = x.lab, ylab = y.lab, axes = FALSE)
if (now.line == TRUE)
abline(now, ((sort.what[1] - now) /
(((now - min(data[, subset.c], na.rm = TRUE)) / x.scale) - minotime)),
lty = now.line.lty, lwd = now.line.lwd, col = now.line.col)
} else if (is.na(y.var) | (!is.na(y.var) & y.var.type == "n")) {
if (now.line == TRUE)
stop("with now.line == TRUE, y.var & y.var.type == 'd' must be specified\n")
oldpar <- par(omi = rep(0, 4), lwd = 0.6,
mgp = c(2.8, 1.1, 0), tck = -0.006, ...)
plot(whattoplot, type = "n",
xlim = c(x.axis.left, x.axis.right),
ylim = c(y.axis.bottom - 1, y.axis.top + 1),
xlab = x.lab, ylab = y.lab, axes = FALSE)
}
## plot y-axis labels
if (!is.na(y.idlabels)) {
if (!is.na(y.var)) {
warning("y.idlabels not used when y.var has been specified\n")
axis(side = 2)
} else if (is.na(y.var))
axis(side = 2, at = whattoplot,
labels = as.vector(data[whotoplot, y.idlabels]))
} else if (is.na(y.idlabels)) {
if (y.axis == "auto") {
if (is.na(y.var) | (!is.na(y.var) & y.var.type == "n"))
axis(side = 2)
else if (!is.na(y.var) & y.var.type == "d") {
if (y.julian == FALSE) {
y.axis.auto.now.bottom <- ifelse(now.line, sort.what[1],
y.axis.bottom)
## marked by JJL, disable square plot
##y.axis.auto.now.top <- ifelse(now.line, now, y.axis.top)
y.axis.auto.now.top <- ifelse(now.line, y.axis.top, y.axis.top)
y.axis.auto.at <- round(seq(y.axis.auto.now.bottom,
y.axis.auto.now.top, length = 5))
y.axis.auto.labels <-
paste(month.day.year(y.axis.auto.at, origin = date.orig)$month, "/",
month.day.year(y.axis.auto.at, origin = date.orig)$day, "/",
substring(month.day.year(y.axis.auto.at,
origin = date.orig)$year, 3, 4),
sep = "")
axis(side = 2, at = y.axis.auto.at, labels = y.axis.auto.labels)
} else if (y.julian == TRUE)
axis(side = 2)
}
} else if (y.axis == "custom") {
if (is.na(y.axis.custom.at[1]) || is.na(y.axis.custom.labels[1]))
stop("with y.axis == 'custom', must specify y.axis.custom.at and y.axis.custom.labels\n")
axis(side = 2, at = y.axis.custom.at, labels = y.axis.custom.labels)
}
}
## plot x-axis labels
if (x.axis == "auto") {
if (x.julian == FALSE) {
x.axis.auto.at <-
round(seq(x.axis.left, x.axis.right, length = 5))
x.axis.auto.labels <-
paste(month.day.year(x.axis.auto.at, origin = date.orig)$month, "/",
month.day.year(x.axis.auto.at, origin = date.orig)$day, "/",
substring(month.day.year(x.axis.auto.at,
origin = date.orig)$year, 3, 4),
sep = "")
axis(side = 1, at = x.axis.auto.at, labels = x.axis.auto.labels)
} else if (x.julian == TRUE)
axis(side = 1)
} else if (x.axis == "custom") {
if (is.na(x.axis.custom.at[1]) || is.na(x.axis.custom.labels[1]))
stop("with x.axis = 'custom', user must specify x.axis.custom.at and x.axis.custom.labels\n")
axis(side = 1, at = x.axis.custom.at, labels = x.axis.custom.labels)
}
if (!is.na(titl)) {
title(titl)
}
## plot lines and points
if (!is.na(line.by)) {
line.byw <- data[whotoplot, line.by]
table.by <- table(as.character(line.byw), exclude = c("", "NA"))
names.by <- names(table.by)
len.by <- length(table.by)
if (length(line.lty) < len.by)
warning("user provided length(line.lty) < num. of line.by categories")
if (length(line.lwd) < len.by)
warning("user provided length(line.lwd) < num. of line.by categories")
if (length(line.col) < len.by)
warning("user provided length(line.col) < num. of line.by categories")
line.lty <- rep(line.lty, len = len.by)
line.lwd <- rep(line.lwd, len = len.by)
line.col <- rep(line.col, len = len.by)
lbt.whotoplot <-
(1:(length(t.whotoplot)))[as.character(line.byw) != "" &
as.character(line.byw) != "NA"]
for (i in lbt.whotoplot) {
lines(c(minvec[i], maxvec[i]), rep(whattoplot[i], 2),
lty = as.vector(line.lty[names.by == line.byw[i]]),
lwd = as.vector(line.lwd[names.by == line.byw[i]]),
col = as.vector(line.col[names.by == line.byw[i]]))
}
} else if (is.na(line.by)) {
for (i in 1:length(t.whotoplot))
lines(c(minvec[i], maxvec[i]), rep(whattoplot[i], 2),
lty = line.lty[1], lwd = line.lwd[1], col = line.col[1])
}
if(is.na(point.cex.mult.var[1]))
for(j in 1:dim(targdata)[2])
points(as.vector(unlist(targdata[t.whotoplot, j])), whattoplot,
pch = point.pch[j], cex = point.cex[j], col = point.col[j])
else {
## loop only for extra points
for(j in which(!is.na(extra.points.no.mult)))
points(as.vector(unlist(targdata[t.whotoplot, j])), whattoplot,
pch = point.pch[j], cex = point.cex[j], col = point.col[j])
## loop for points to magnify based on level of covariates
for(i in 1:length(t.whotoplot)) {
k <- 0
for(j in which(is.na(extra.points.no.mult))) {
k <- k + 1
points(as.vector(unlist(targdata[t.whotoplot[i], j])),
whattoplot[i], pch = point.pch[j],
cex = ifelse(is.na(data[whotoplot[i], point.cex.mult.var[k]]),
point.cex[j],
point.cex.mult * data[whotoplot[i], point.cex.mult.var[k]] * point.cex[j]),
col = point.col[j])
}
}
}
## add line.add segments (if requested)
if (!is.na(as.vector(line.add)[1])) {
if (any(is.na(line.add.lty)))
stop("line.add.lty can not have missing value(s) with non-missing line.add\n")
if (any(is.na(line.add.lwd)))
stop("line.add.lwd can not have missing value(s) with non-missing line.add\n")
if (any(is.na(line.add.col)))
stop("line.add.col can not have missing value(s) with non-missing line.add\n")
line.add.m <- as.matrix(line.add)
dim.m <- dim(line.add.m)
if (dim.m[1] != 2)
stop("line.add must be a matrix with two rows\n")
if (length(line.add.lty) != dim.m[2])
stop("length of line.add.lty must be the same as number of columns in line.add\n")
if (length(line.add.lwd) != dim.m[2])
stop("length of line.add.lwd must be the same as number of columns in line.add\n")
if (length(line.add.col) != dim.m[2])
stop("length of line.add.col must be the same as number of columns in line.add\n")
for (j in (1:dim.m[2])) {
for (i in (1:length(t.whotoplot))) {
add.var1 <- subset.c == line.add.m[1, j]
if (!any(add.var1))
stop("variables chosen in line.add must also be in subset.c\n")
add.var2 <- subset.c == line.add.m[2, j]
if (!any(add.var2))
stop("variables chosen in line.add must also be in subset.c\n")
segments(targdata[i, (1:len.c)[add.var1]], whattoplot[i],
targdata[i, (1:len.c)[add.var2]], whattoplot[i],
lty = line.add.lty[j], lwd = line.add.lwd[j],
col = line.add.col[j])
}
}
}
## plot internal legend (if requested)
if (legend.plot == TRUE & legend.location != "o") {
if (legend.location == "i") {
legnd(legend.point.at[[1]], legend.point.at[[2]],
leg = legend.point.text,
pch = legend.point.pch, cex = legend.cex,
col = point.col, bty = legend.bty)
if (!is.na(line.by))
legnd(legend.line.at[[1]], legend.line.at[[2]],
leg = legend.line.text, cex = legend.cex,
lty = line.lty, lwd = legend.line.lwd,
col = line.col, bty = legend.bty)
} else if (legend.location == "l") {
cat("Please click at desired location to place legend for points.\n")
legnd(locator(legend.loc.num), leg = legend.point.text,
pch = legend.point.pch, cex = legend.cex,
col = point.col, bty = legend.bty)
if (!is.na(line.by)) {
cat("Please click at desired location to place legend for lines.\n")
legnd(locator(legend.loc.num), leg = legend.line.text,
cex = legend.cex, lty = line.lty,
lwd = legend.line.lwd, col = line.col, bty = legend.bty)
}
}
}
## add box to main plot and clean up
invisible(box())
invisible(par(ask = FALSE))
par(oldpar)
}
## event.convert.s
## convert 2-column coded events to multiple event time for event.chart()
## input: a matrix or dataframe with at least 2 columns
## by default, the first column contains the event time and
## the second column contains the k event codes (e.g. 1=dead, 0=censord)
## ouput: a matrix of k columns, each column contains the time of kth coded event
##
event.convert <- function(data2, event.time = 1, event.code = 2)
{
dim.d <- dim(data2)
len.t <- length(event.time)
if(len.t != length(event.code))
stop("length of event.time and event.code must be the same")
if(any(event.time > dim.d[2]))
stop(paste("Column(s) in event.time cannot be greater than ", dim.d[2]))
if(any(event.code > dim.d[2]))
stop(paste("Column(s) in event.code cannot be greater than ",
dim.d[2]))
name.data <- names(data2)[event.time]
if(is.null(name.data)) {
name.data <- paste("V", event.time, sep = "")
}
n.level <- rep(NA, len.t)
for (i in (1:len.t)) {
n.level[i] <- length(table(data2[, event.code[i]]))
}
tot.col <- sum(n.level)
data.out <- matrix(NA, dim.d[1], tot.col)
name.col <- rep(NA, tot.col)
n.col <- 1
for (i in (1:len.t)) {
tab.d <- table(data2[, event.code[i]])
if(is.null(class(data2[, event.code[i]])))
level.value <- as.numeric(names(tab.d))
else
level.value <- names(tab.d)
for (j in (1:length(tab.d))) {
data.out[, n.col] <- rep(NA, dim.d[1])
check <- data2[, event.code[i]] == level.value[j]
check[is.na(check)] <- FALSE
data.out[, n.col][data2[, event.code[i]] == level.value[j]] <-
data2[, event.time[i]][check]
name.col[n.col] <-
paste(name.data[i], ".", names(tab.d)[j], sep = "")
n.col <- n.col + 1
}
}
dimnames(data.out) <- list(1:dim.d[1], name.col)
return(as.matrix(data.out))
}
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