SAS Instructions Entering the data and plotting survival curves

Transcription

1 SAS Instructions Entering the data and plotting survival curves Entering the data The first part of most SAS programs consists in creating a dataset. This is done through the DATA statement. You can either read a text file that contains the dataset, or enter the data by typing them directly in the DATA statement. Typing the data in DATA dataset_name; INPUT var_1 var_2$ var_3... ; CARDS; value11 string21 value31 value12 string22 value32 etc. Reading data in from a text file DATA dataset_name; INFILE "full_file_name" FIRSTOBS=line_number_first_observ; INPUT var_1 var_2$ var_3... ; Plotting survival curves This is done with the PROC LIFETEST procedure. Here are some excerpts of the SAS help. To access the full documentation, do the following in SAS: 1. Click on Help on the toolbox of the program editor. 2. Click on Modeling & Analysis Tool ; 3. Click on Data Analysis. 4. Click on Lifetest in the Survival Analysis column. LIFETEST: Syntax PROC LIFETEST options; TIME variable<*censor(list)>; /* required */ STRATA variable <(list)><...variable<(list)>>; TEST variable-list; ID variable-list; FREQ variable; BY variable-list;

2 Options that can be used in the PROC LIFETEST statement: ALPHA= value ANNOTATE= SAS-data-set DESCRIPTION= 'string' GOUT= graphics catalog INTERVALS= value-list MAXTIME= value MISSING NOCENSPLOT NOTABLE OUTTEST OUTT= SAS-data-set REDUCEOUT TIMELIM= keyword value WIDTH= value ALPHAQT= value DATA= SAS-data-set FORMCHAR(1,2,7,9)= 'string' GRAPHICS LANNOTATE= SAS-data-set METHOD= PL KM LT LIFE ACT NINTERVAL= value NOPRINT OUTSURV OUTS= SAS-data-set PLOTS= (keyword <... keyword>) SINGULAR= value TIMELIST= value-list Syntax of most often used options ALPHA= value The ALPHA= option specifies a number between.0001 and.999 that sets the confidence level for the confidence intervals for the survival estimates. The confidence level is 1- ALPHA. For example, ALPHA= 0.05 results in the calculation of 95% confidence intervals. Default:.05 DATA= SAS-data-set The DATA= option specifies the input SAS data set. The most recently created SAS data set will be used if the DATA= option is omitted. GRAPHICS The GRAPHICS option creates plots specified by the PLOT= option for a graphics device. If you do not use this option, line printer plots are produced. METHOD= PL KM LT LIFE ACT The METHOD= option requests the method used to compute the survival distribution estimates. PL or KM specifies that product-limit (or Kaplan Meier) estimates be computed; LT, LIFE or ACT specifies that life table (or actuarial) estimates be computed. The default is to compute product limit estimates. OUTSURV OUTS= SAS-data-set The OUTSURV= option creates an output SAS data set containing the survival estimates and confidence limits for all strata.

3 PLOTS= (SURVIVAL S, LOGSURV LS, LOGLOGS LLS, HAZARD H, PDF P) The PLOTS option produces printer plots of the estimates against time or log(time). If the GRAPHICS option is also used, plots can be produced on graphics devices. Valid types are: SURVIVAL the estimated SDF versus time. LOGSURV -log (estimated SDF) versus time. LOGLOGS log(-log (estimated SDF)) versus log(time). HAZARD estimated hazard function versus time. PDF estimated probability density function versus time. required in specifying the printer plots. Parentheses are TIMELIST= value-list The TIMELIST= option specifies a list of time points at which the Kaplan-Meier estimates are printed. The values in the list appear in a column labelled by _TIME_. Since the survival curve is a decreasing step function, each listed value falls in an interval that has a constant time estimate. The event time that corresponds to the beginning of the interval is printed, along with its survival estimate.

4 ******************** TIME variable<*censor(list)>; The TIME statement is used to indicate the failure time variable and an optional censoring variable which must be numeric. time failure time variable censor censoring variable list numeric values corresponding to right-censoring ***************** STRATA variable <(list)> <...variable<(list)>>; The STRATA statement names the variables whose values are to determine the stratum levels. variable variable defining stratum levels list cutpoints used with a numeric STRATA variable ********************* TEST variable-list; The TEST statement lists the numeric variables whose association with the response survival time is to be tested. ******************** ID variable-list; The ID statement specifies the variables whose values are used to label observations of the product-limit survival function estimates. ******************* FREQ variable; The FREQ statement specifies the variable containing the frequency of occurrence of each observation. ********************

5 BY <DESCENDING> variables... <NOTSORTED>; A BY statement is used with a procedure to obtain separate analyses on observations in groups defined by the BY variables. The data set being processed need not have been previously sorted by the SORT procedure. However, the data set must be in the same order as though PROC SORT had sorted it unless NOTSORTED is specified. If you have used a FORMAT or ATTRIB statement to group a continuous variable into discrete groups, the BY statement creates BY groups based on the formatted values. You can also ensure that variables are processed in ascending order by creating an index for one or more variables in the SAS data set. The usages of the BY statement differ in each procedure. Please refer to the Users' Guide for the details.

6 Example ex1.sas, the file with the commands: DATA example1; INPUT name$ ti deltai; CARDS; joe 1 1 jim 2 1 jack 3 0 jill jd 4 1 jc 5 1 jb tj 7 1 tim 7 1 tom 8 1 PROC LIFETEST DATA=example1 PLOTS=(s); TIME ti*deltai(0);

7 ex1.lst, the file containing the output: PROC LIFETEST DATA=example1 PLOTS=(s); TIME ti*deltai(0); The SAS System 1 Product-Limit Survival Estimates Survival Standard Number Number TI Survival Failure Error Failed Left ^L * * * The SAS System 2 * Censored Observation ^L The SAS System 3 Summary Statistics for Time Variable TI Point 95% Confidence Interval Quantile Estimate [Lower, Upper) 75% % % Mean Standard Error Summary of the Number of Censored and Uncensored Values Total Failed Censored %Censored

8 ^L The SAS System 4 Survival Function Estimates S A------A u A------A r SDF A A v A------A i v A A a l A------A D i A s t TI ^L The SAS System 5 Censored Observations Strata A + A A A TI