These functions are used by the Nonparametric Survival dialog.
menuSurvfit
calls
tabSummary.survfit and
tabPlot.survfit
if summary and plotting results are requested.
a formula object or a
coxph object. If a formula object is supplied
it must have a
Surv object as the response on the left of a ~ operator,
and if desired, terms separated by
+ operators on the right. If there
are no terms on the right side of the formula, a standard Kaplan-Meier
survival curve will be generated.
fit
an object of class
survfit.
surv
an object of class
survfit.
OPTIONAL ARGUMENTS:
data
an optional data frame in which to interpret the variables occurring in the
formula.
weights
the optional case weights.
subset
an expression saying which subset of the rows of the data should be used
in the fit. This can be a logical vector (which is replicated to have
length equal to the number of observations), or a numeric vector indicating
which observation numbers are to be included, or a character vector of the
row names to be included. All observations are included by default.
na.omit.p
if
TRUE, then any observation with missing values are removed
from the analysis. If
FALSE and there are missing values then the
function will exit with a message that missing values are not allowed.
If
na.omit.p is
TRUE then
na.action is set to
na.omit in the
call to
survfit. If
na.omit.p is
FALSE then
na.action is set
to
na.fail in the call to
survfit.
newdata
a data frame with the same variable names as those that appear in
formula.
Only applicable when
formula is a
coxph object.
individual
if
TRUE, the data frame represents different time epochs for only one
individual. If
FALSE, multiple rows indicate multiple individuals.
Only applicable when
formula is a
coxph object.
conf.int
the level for a two-sided confidence interval on the survival curve(s).
se.fit
if
TRUE, standard errors will be computed.
type
a character string specifying the type of survival curve. Possible values
are
"kaplan-meier",
"fleming-harrington", or
"fh2".
error
a character string specifying the error. Possible values are
"greenwood"
for the Greenwood formula or
"tsiatis" for the Tsiatis formula.
conf.type
a character string specifying the confidence interval type. Possible values
are
"none" for no confidence intervals,
"plain" for standard intervals,
"log" for intervals based on the cumulative hazard, and
"log-log" for
intervals based on the log hazard.
conf.lower
a character string specifying modified lower limits to the curve. Possible
values are
"usual",
"peto", and
"modified".
print.basic
if
TRUE, a short summary of the nonparametric survival model is printed.
This output is from the function
print.survfit.
print.summary
if
TRUE, a long summary of the nonparametric survival model is printed.
This output is from the function
summary.survfit.
summary.times
a vector of times. This must be in increasing order and missing values
are not allowed.
summary.censored
if
TRUE, the censoring times are included in the output. This is
ignored if
summary.times is specified.
summary.scale
numeric value to rescale the survival time.
plot.fit
if
TRUE, a plot of the survival curves is created.
plot.conf.int
if
TRUE, confidence intervals are included on the plot.
mark.time
if
TRUE, curves are marked at each censoring time which is not also a
death time.
mark
a list of mark symbols, which will be used to label the curves. The list
is converted to a vector for the call to
survfit. Elements of the list
are reused cyclically if the length of the list is shorter than the number
of curves.
col
a list of integers specifying colors for each curve. The list
is converted to a vector for the call to
survfit. Elements of the list
are reused cyclically if the length of the list is shorter than the number
of curves.
lty
a list of integers specifying line types for each curve. The list
is converted to a vector for the call to
survfit. Elements of the list
are reused cyclically if the length of the list is shorter than the number
of curves.
lwd
a list of numeric values for line widths for each curve. The list
is converted to a vector for the call to
survfit. Elements of the list
are reused cyclically if the length of the list is shorter than the number
of curves.
cex
a numeric value specifying the size of the marks. Not a vector; all
marks have the same size.
log
if
TRUE, the y-axis will be on the log scale.
yscale
a numeric value used to multiply the labels on the y-axis.
xscale
a numeric value used like
yscale for labels on the x-axis.
xlab
a character string used to label the x-axis.
ylab
a character string used to label the y-axis.
xaxs
a character string denoting the x-axis style. Possible values are
"standard",
"tight", and
"extended". These values are converted to
NULL,
"i", and
"e", respectively, for the call to
plot.survfit.
VALUE:
an object of class
survfit. See the
survfit.object help file for details.