Nonparametric Survival

Nonparametric survival computes an estimate of a survival curve for censored data using either the Kaplan-Meier or the Fleming-Herrington method. This method is used in situations such as medical trials where the response is time to failure, usually with some times lost to censoring. The dialog fits a variety of nonparametric survival curves and allows the inclusion of grouping variables.

To perform nonparametric survival modeling

Choose Statistics __image\ebd_ebd60.gif Survival __image\ebd_ebd61.gif Nonparametric Survival. The dialog shown below appears.

Model page

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In the Nonparametric Survival dialog, the Model page has the following options:

Data

Data Set

Select a data set from the dropdown list or type the name of a data set. You can also type into the Data Set edit field any expression that evaluates to a data set.

Weights

Enter the column that specifies weights to be applied to all observations used in the analysis. To weight all rows equally, leave this blank.

Subset Rows

Enter an S-PLUS expression that identifies the rows to use in the analysis. To use all the rows in the data set, leave this field blank.

Omit Rows with Missing Values

Select this box to omit from the analysis any rows in the data set that contain missing values for any of the variables in the model.

Formula

Formula

In the Formula field, enter a formula specifying the desired model. In its simplest form a formula consists of the response variable, a tilde (~), and a list of predictor variables separated by "+"s. An intercept is automatically included by default.

Create Formula

Click the Create Formula button to open a formula builder dialog used to construct a formula specifying the desired model. See the online Help section Building Formulas for more information.

Model

Curve Type

Choose a type of survival curve: kaplan-meier, fleming-harrington, or fh2. The default is kaplan-meier.

Save Model Object

Save Model Object

In the Save As field, enter the name for the object in which to save the results of the analysis. If an object with this name already exists, its contents are overwritten. The model object can be used in later functions such as plotting.

Options page

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In the Nonparametric Survival dialog, the Options page has the following options:

Confidence Limits

Compute Standard Errors

Select this to compute standard errors.

Confidence Interval Level

Enter a number between 0 and 1 to specify the confidence interval level.

Standard Error Formula

Select the error formula: greenwood for the Greenwood formula or tsiatis for the Tsiatis formula.

Confidence Interval Type

Select a confidence interval type.

. log: for intervals based on the cumulative hazard or log(survival). This is the default.

. plain: for standard intervals.

. log-log: for intervals based on the log hazard or log(-log(survival)).

Lower Limits

Select a specification for the modified lower limits to the curves: usual, peto, or modified. The upper limits remain unchanged.

Results page

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In the Nonparametric Survival dialog, the Results page has the following options:

Printed Results

Short Output for Nonparametric Survival

Select this to print a short summary of the model results in the designated output window. This includes the number of observations, number of events, the mean survival and its standard error, and the median survival with confidence limits for the median.

Long Output for Nonparametric Survival

Select this to print a long summary of the model results in the designated output window. This produces tabled output including columns for the survival estimates, the standard errors of the estimates and confidence bounds for the estimates.

Summary Options

The following options are available if Long Output is selected:

Include Censoring Times Select this to include censoring times in the output. This field is ignored if a vector is specified in New Times.

New Times Enter a vector of times, listed in increasing order and having no missing values. If Include Censoring Times is selected, the default is the vector of all unique times in the fitted model. Otherwise, the default is the vector of event (death) times.

Scaling Factor Enter a number used to rescale the survival time. For example, if the input data is in days, enter 365.25 to rescale to years.

Plot page

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In the Nonparametric Survival dialog, the Plot page has the following options:

Survival Curves

Select this to plot survival curves for the current survival model.

Show Confidence Intervals

Select this to plot two-sided confidence intervals. For Nonparametric Survival the confidence interval level can be set on the Options page.

Curve Options

Line Colors Enter a list of integers using either the name of an existing S-PLUS vector or a comma-delimited list. If the number of curves to be plotted is greater than the length of the list, the line colors cycle through the list.

Line Types Enter a list of integers using either the name of an existing S-PLUS vector or a comma-delimited list. If the number of curves to be plotted is greater than the length of the list, the line types cycle through the list.

Line Widths Enter a list of integers using either the name of an existing S-PLUS vector or a comma-delimited list. If the number of curves to be plotted is greater than the length of the list, the line widths cycle through the list.

Censoring Marks

Mark Censoring Times Select this to mark curves at the censoring times.

Censoring Mark Symbol Enter a list of characters or integers specifying special symbols used to mark the curves. Use either the name of an existing S-PLUS vector or a comma delimited list such as 1, 2, 3 or "+", "*". The default is to use "+" at the censored values.

Size of Marks Enter a positive number used to control the character size of the censor marks. Values less than 1 produce smaller marks, while values greater than 1 result in larger marks.

Axis Options

Log Axis for Y Select this to plot the y-axis on the log scale.

X-Axis Style Select the x-axis style.

standard scale or extend the maximum survival time, creating an axis with extended labels on the right side of the plot. This is the default.

tight create an axis labeled internal to the data values.

extended create an axis whose numeric labels are more extreme than any data values.

Scale Factor for X-Axis Tick Labels Enter a number used to multiply the labels on the x-axis. For example, a value of 365.25 gives labels in years instead of the original days.

Scale Factor for Y-Axis Tick Labels Enter a number used to multiply the labels on the y-axis. For example a value of 100 yields a percent scale.

X-Axis Label Enter a label for the x-axis.

Y-Axis Label Enter a label for the y-axis.

Related S-Plus language functions for Nonparametric Survival

survfit, print.survfit, plot.survfit, points.survfit, lines.survfit, summary.survfit, survfit.km

Other related S-Plus language functions

coxph, Surv, strata