Nothing
latex.cph <-
function(object, title,
file='',
append=FALSE, surv=TRUE, maxt=FALSE, which=NULL, varnames,
columns=65, inline=FALSE,
before=if(inline)"" else "& &", after="",
dec=3, pretrans=TRUE,
caption=NULL, digits=.Options$digits, size='', ...)
{
md <- prType() %in% c('html', 'md', 'markdown')
filegiven <- file != ''
f <- object
whichThere <- length(which)
atr <- f$Design
lev <- names(f$freq)
Intercept <- -f$center
strata <- levels(f$strata) ## was f$strata
w <- if(length(caption)) {
if(md) paste('<div align=center><strong>', caption,
'</strong></div>')
else
paste('\\begin{center} \\bf',caption,'\\end{center}')
}
if(! length(which) & !inline) {
if(length(strata)==0)
w <- c(w, paste("$$\\Pr(T\\geq t~|~X) = S_{0}(t)^{\\mathrm{e}^{X\\beta}},~~ \\mathrm{where}$$",sep=""))
else {
sname <- atr$name[atr$assume.code==8]
strata.sub <- letters[8 + (1 : length(sname))]
s <- paste("\\mathrm{",sname,"}=",strata.sub,sep="")
s <- paste(s, collapse=",")
w <- c(w,paste("$$\\Pr(T\\geq t~|~X,",s,")=S_{",
paste(strata.sub,collapse=""),
"}(t)^{\\mathrm{e}^{X\\beta}},~~\\mathrm{where}$$", sep=""))
}
}
if(!length(which)) which <- 1:length(atr$name)
if(missing(varnames)) varnames <- atr$name[atr$assume.code!=9]
ltx <-
latexrms(f, file='', append=TRUE, which=which, varnames=varnames,
columns=columns,
before=before, after=after,
prefix=if(!whichThere)"X\\hat{\\beta}" else NULL,
intercept=Intercept, inline=inline,
pretrans=pretrans, digits=digits, size=size)
if(inline) return(ltx)
w <- c(w, ltx)
htmlTab <- function(s) {
s <- cbind('$t$'= as.numeric(rownames(s)), s)
for(j in 1 : ncol(s)) s[, j] <- round(s[, j], dec)
if (requireNamespace("kableExtra", quietly=TRUE)) {
as.character(
knitr::kable(s, format='html',
align='r', row.names=FALSE) |>
kableExtra::kable_styling(full_width=FALSE) )
} else {
as.character(
knitr::kable(s, format='html',
align='r', row.names=FALSE) )
}
}
ss <- f$surv.summary
if(surv && length(ss)) {
tf <- tempfile()
fs <- levels(f$strata)
nstrat <- 0; if(length(fs)) nstrat <- length(fs)
times <- as.numeric(dimnames(ss)[[1]])
maxtime <- f$maxtime
if(max(times) >= maxtime) maxt <- FALSE
if(nstrat == 0) {
s <- matrix(ss[, , 1], ncol=1)
if(maxt) {
s <- cbind(s, f$surv[L <- length(f$surv)])
times <- c(times, f$time[L])
}
dimnames(s) <- list(t=format(times), "$S_{0}(t)$")
if(md) {
# z <- htmlTable::txtRound(s, digits=dec)
# z <- htmlTable::htmlTable(z, rowlabel='$t$', escape.html=FALSE,
# css.cell='min-width: 9em;')
w <- c(w, htmlTab(s))
} else {
latex(s, file=tf, append=TRUE, rowlabel="$t$",
rowlabel.just="r",
dec=dec, table.env=FALSE)
w <- c(w, readLines(tf))
}
} else {
## Change . to ,blank
n <- sedit(paste(fs,',',sep=''), '.', ', ')
## Change sname=*, to *,
n <- sedit(n, paste(sname,'=*,',sep=''), rep('*, ', length(sname)))
n <- substring(n, 1, nchar(n) - sum(atr$assume.code == 8) - 1)
s <- ss[, , 1]
if(maxt) {
smax <- rep(NA, nstrat)
for(i in 1 : nstrat)
smax[i] <- f$surv[[i]][abs(f$time[[i]]-maxtime) < 0.001]
s <- rbind(s, smax)
times <- c(times, maxtime)
}
dimnames(s) <- list(t=format(times),
paste("$S_{", n, "}(t)$", sep=""))
if(md) {
# z <- htmlTable::txtRound(s, digits=dec)
# z <- htmlTable::htmlTable(z, rowlabel='$t$',
# escape.html=FALSE,
# css.cell='min-width: 9em;')
w <- c(w, htmlTab(s))
}
else {
ltx < latex(s, file=tf, append=TRUE,
rowlabel="$t$", rowlabel.just="r",
dec=dec, table.env=FALSE)
w <- c(w, readLines(tf))
}
}
}
if(filegiven || prType() == 'plain') {
cat('\n', w, sep='\n', file=file, append=append)
return(invisible())
}
rendHTML(w, html=FALSE)
}
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