Nothing
print.psm <- function(x, correlation = FALSE, digits=4, r2=c(0, 2, 4),
coefs=TRUE, pg=FALSE, title, ...)
{
k <- 0
z <- list()
dist <- x$dist
name <- survreg.distributions[[dist]]$name
if(missing(title))
title <- paste("Parametric Survival Model:", name, "Distribution")
stats <- x$stats
ci <- x$clusterInfo
counts <- reListclean(Obs = stats['Obs'],
Events = stats['Events'],
'Cluster on' = ci$name,
Clusters = ci$n,
'Sum of Weights' = stats['Sum of Weights'],
sigma = if(length(x$scale) == 1) x$scale,
dec = c(NA, NA, NA, NA, NA, 4))
lr <- reListclean('LR chi2' = stats['Model L.R.'],
'd.f.' = stats['d.f.'],
'Pr(> chi2)' = stats['P'],
dec = c(2,NA,-4))
newr2 <- grep('R2\\(', names(stats))
nnr <- length(newr2)
if(nnr %nin% c(0, 4)) stop('MCS R^2 did not compute 4 indexes')
disc <- reListclean(R2 = if(0 %in% r2) stats['R2'],
namesFrom = if(nnr > 0) stats[newr2][setdiff(r2, 0)],
Dxy = stats['Dxy'],
g = if(pg) stats['g'],
gr = if(pg) stats['gr'],
dec = 3)
headings <- c('',
'Model Likelihood\nRatio Test',
'Discrimination\nIndexes')
data <- list(counts, lr, disc)
k <- k + 1
z[[k]] <- list(type='stats', list(headings=headings, data=data))
summary.survreg <- getS3method('summary', 'survreg')
if(!x$fail) x$fail <- NULL # summary.survreg uses NULL for OK
s <- summary.survreg(x, correlation=correlation)
k <- k + 1
z[[k]] <- list(type='coefmatrix',
list(coef = s$table[,'Value'],
se = s$table[,'Std. Error']))
if (correlation && length(correl <- s$correlation)) {
p <- ncol(correl)
if (p > 1) {
cat("\nCorrelation of Coefficients:\n")
ll <- lower.tri(correl)
correl[ll] <- format(round(correl[ll], digits = digits))
correl[!ll] <- ""
k <- k + 1
z[[k]] <- list(type='print',
list(correl[-1, -p, drop = FALSE], quote = FALSE),
title='Correlation of Coefficients')
}
}
prModFit(x, title=title, z, digits=digits, coefs=coefs, ...)
}
# wt <- x$weights
# fparms <- x$fixed
# coef <- c(x$coef, x$parms[!fparms])
# resid <- x$residuals
# dresid <- x$dresiduals
# n <- length(resid)
# p <- x$rank
# if(!length(p)) p <- sum(!is.na(coef))
# if(!p)
# {
# warning("This model has zero rank --- no summary is provided")
# return(x)
# }
# nsingular <- length(coef) - p
# rdf <- x$df.resid
# if(!length(rdf))
# rdf <- n - p
# R <- x$R #check for rank deficiencies
# if(p < max(dim(R)))
# R <- R[1:p, #coded by pivoting
# 1:p]
# if(length(wt))
# {
# wt <- wt^0.5
# resid <- resid * wt
# excl <- wt == 0
# if(any(excl))
# {
# warning(paste(sum(excl),
# "rows with zero weights not counted"))
# resid <- resid[!excl]
# if(!length(x$df.residual))
# rdf <- rdf - sum(excl)
# }
# }
# famname <- x$family["name"]
# if(!length(famname)) famname <- "Gaussian"
# scale <- x$fparms
# nas <- is.na(coef)
# cnames <- names(coef[!nas])
# coef <- matrix(rep(coef[!nas], 4), ncol = 4)
# dimnames(coef) <- list(cnames, c("Value", "Std. Error", "z value", "p"))
# stds <- sqrt(diag(x$var[!nas,!nas,drop=FALSE]))
# coef[, 2] <- stds
# coef[, 3] <- coef[, 1]/stds
# coef[, 4] <- 2*pnorm(-abs(coef[,3]))
# if(correlation)
# {
# if(sum(nas)==1) ss <- 1/stds else ss <- diag(1/stds)
# correl <- ss %*% x$var[!nas, !nas, drop=FALSE] %*% ss
# dimnames(correl) <- list(cnames, cnames)
# }
# else
# correl <- NULL
# ocall <- x$call
# if(length(form <- x$formula))
# {
# if(!length(ocall$formula))
# ocall <- match.call(get("survreg"), ocall)
# ocall$formula <- form
# }
# dig <- .Options$digits
# survival:::print.summary.survreg(
# list(call = ocall, terms = x$terms, coefficients = coef#,
# df = c(p, rdf), deviance.resid = dresid,
# var=x$var, correlation = correl, deviance = devian#ce(x),
# null.deviance = x$null.deviance, loglik=x$loglik,
# iter = x$iter,
# nas = nas))
# options(digits=dig) #recovers from bug in print.summary.survreg
# invisible()
#}
## Mod of print.summary.survreg from survival5 - suppresses printing a
## few things, added correlation arg
print.summary.survreg2 <-
function (x, digits = max(options()$digits - 4, 3),
correlation=FALSE, ...)
{
correl <- x$correl
n <- x$n
if (is.null(digits))
digits <- options()$digits
print(x$table, digits = digits)
if (nrow(x$var) == length(x$coefficients))
cat("\nScale fixed at", format(x$scale, digits = digits),
"\n")
else
if (length(x$scale) == 1)
cat("\nScale=", format(x$scale, digits = digits), "\n")
else {
cat("\nScale:\n")
print(x$scale, digits = digits, ...)
}
if (correlation && length(correl)) {
p <- dim(correl)[2]
if (p > 1) {
cat("\nCorrelation of Coefficients:\n")
ll <- lower.tri(correl)
correl[ll] <- format(round(correl[ll], digits = digits))
correl[!ll] <- ""
print(correl[-1, -p, drop = FALSE], quote = FALSE)
}
}
cat("\n")
invisible(NULL)
}
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