Nonparametric Survival Dialog Functions

DESCRIPTION:

These functions are used by the Nonparametric Survival dialog. menuSurvfit calls tabSummary.survfit and tabPlot.survfit if summary and plotting results are requested.

USAGE:

menuSurvfit(formula, data, weights, subset, na.omit.p, newdata,  
            individual, conf.int, se.fit, type, error, conf.type,  
            conf.lower, print.basic=T, print.summary=F, summary.times=NULL,  
            summary.censored=F, summary.scale=1, plot.fit, plot.conf.int,  
            mark.time, mark, col, lty, lwd, cex, log, yscale, xscale, xlab,  
            ylab, xaxs) 
tabSummary.survfit(fit, print.basic, print.summary, summary.times,  
            summary.censored, summary.scale) 
tabPlot.survfit(surv, plot.fit = T, plot.conf.int, mark.time, mark, col,  
            lty, lwd, cex, log, yscale, xscale, xlab, ylab, xaxs) 

REQUIRED ARGUMENTS:

formula
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.

SIDE EFFECTS:

Survival curves will be drawn if requested.

SEE ALSO:

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