01/20151 EPI 5344: Survival Analysis in Epidemiology SAS code and output February 24, 2015 Dr. N....
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Transcript of 01/20151 EPI 5344: Survival Analysis in Epidemiology SAS code and output February 24, 2015 Dr. N....
![Page 1: 01/20151 EPI 5344: Survival Analysis in Epidemiology SAS code and output February 24, 2015 Dr. N. Birkett, School of Epidemiology, Public Health & Preventive.](https://reader033.fdocuments.us/reader033/viewer/2022042822/56649edd5503460f94bede00/html5/thumbnails/1.jpg)
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EPI 5344:Survival Analysis in
EpidemiologySAS code and output
February 24, 2015
Dr. N. Birkett,School of Epidemiology, Public Health &
Preventive Medicine,University of Ottawa
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SAS Output Delivery System (ODS)
• Default method for getting output from SAS procedures
• Can produce:– printed results– graphics (hi-res)– Data tables for use in future procs
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SAS Output Delivery System (ODS)
• Output formats include:– HTML
– RTF
• Provides extensive control of output format,
colors, etc.– 1500 page ‘basic manual’.
– more manuals for graphics01/2015 3
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SAS Output Delivery System (ODS)
• Basic use is relatively simple– 80/20 rule
– add on features as you get better at it
• By default, ALL SAS output is prepared as
HTML– Presented in the Results Window
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ODS produces output which has two components
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To change type of output:
ODS HTML close;
ODS PDF;
To save output to a file:
ODS HTML file = ‘file_name.html’;
- Can define the filename in a ‘filename’ statement and put the
reference here:
filename f1 ‘C:/home/EPI5344.html’;
ODS HTML file=f1;
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To change the style of output:
ODS HTML style=beige;
When ready to actually save your output file, place
this statement at the end of your code:
ODS HTML close;
Place an ‘ODS HTML’ at the start of
your file to re-open output stream.
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ODS pdf style=Normal
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ODS pdf style=Torn
ODS pdf style=Journal
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HTML Output
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RTF Output- displayed in Word
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PDF Output
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Graphicsexample
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Graphicsexample
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Some ODS code
ODS HTMLfile ‘C:/mysas.html’;ods pdf file=‘C:/mysas.pdf’;ods rtf file=‘C:/mysas.rtf’;ods ps file=‘C:/mysas.ps’;
proc print data=employee_data (obs=12); id idnumber; title ‘Personnel data’;run;
ods _all_ close;ods listing;01/2015 14
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2 other ODS commands
Get a list of the tables created by a Proc. Use to link data into subsequent Procs. Result is placed in ‘LOG FILE’.
ODS trace on; proc freq data=t1; run;ODS trace off;
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2280 ods trace on;2281 proc lifetest data=njb1;2282 time ftime*vstatus(0);2283 run;
Output Added:-------------Name: ProductLimitEstimatesLabel: Product-Limit EstimatesTemplate: Stat.Lifetest.ProductLimitEstimatesPath: Lifetest.Stratum1.ProductLimitEstimates-------------
Output Added:-------------Name: QuartilesLabel: Quartiles of the Survival DistributionTemplate: Stat.Lifetest.QuartilesPath: Lifetest.Stratum1.TimeSummary.Quartiles-------------01/2015 16
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Output Added:-------------Name: MeansLabel: MeanTemplate: Stat.Lifetest.MeansPath: Lifetest.Stratum1.TimeSummary.Means-------------
Output Added:-------------Name: SurvivalPlotLabel: Survival CurveTemplate: Stat.Lifetest.Graphics.ProductLimitSurvivalPath: Lifetest.Stratum1.SurvivalPlot-------------
Output Added:-------------Name: CensoredSummaryLabel: Censored SummaryTemplate: Stat.Lifetest.CensoredSummaryPath: Lifetest.CensoredSummary-------------01/2015 17
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2 other ODS commands
Produce graphical output. Output varies depending the Proc.
ODS GRAPHICS ON; PROC LIFETEST DATA=allison.myel PLOTS=S; TIME dur*status(0); RUN;ODS GRAPHICS OFF;
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8 1 1 1 180 1 2 0 632 1 2 0 852 0 1 0 52 1 1 12240 0 2 0 220 1 1 0 63 1 1 1 195 1 2 0 76 1 2 0 70 1 2 0 8 1 1 0 13 1 2 11990 0 2 01976 0 1 0 18 1 2 1 700 1 2 01296 0 1 01460 0 1 0 210 1 2 0 63 1 1 11328 0 1 01296 1 2 0 365 0 1 0 23 1 2 1
Data for the Myelomatous data set, Allison
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DATA myel; INPUT dur status treat renal; DATALINES; 8 1 1 1 180 1 2 0 632 1 2 0 852 0 1 0 52 1 1 12240 0 2 0 220 1 1 0 63 1 1 1 195 1 2 0 76 1 2 0 70 1 2 0 8 1 1 0 13 1 2 11990 0 2 01976 0 1 0 18 1 2 1 700 1 2 01296 0 1 01460 0 1 0 210 1 2 0 63 1 1 11328 0 1 01296 1 2 0 365 0 1 0 23 1 2 1;run;
SAS programme to read the Data for the Myelomatous data set, Allison
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PROC LIFETEST DATA=myel;
TIME dur*status(0);
RUN;
Proc Lifetest <options>;
Some Important Options
DATA = SAS-data-set
OUTSURV = data set containing survival estimates
METHOD = KM/PL (Kaplan-Meier);
LIFE (actuarial)
PLOTS = S (survival);
LS (log-survival);
LLS (log-log survival);
H (hazard)
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libname allison 'C:/allison_2010/data_sets';
ODS GRAPHICS ON;ODS HTML style=statistical;
PROC LIFETEST DATA=allison.myel PLOTS=S; TIME dur*status(0);RUN;
ODS HTML close;ODS GRAPHICS OFF;
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Aside re: ‘plots’
• To get more than one plot, place the request in brackets:
proc lifetest data=allison.myel plots=(s,h,lls)
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libname allison 'C:/allison_2010/data_sets';
ODS GRAPHICS ON;ODS HTML style=statistical;
PROC LIFETEST DATA=allison.myel PLOTS=S(NOCENSOR ATRISK CL); TIME dur*status(0);RUN;
ODS HTML close;ODS GRAPHICS OFF;
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libname allison 'C:/allison_2010/data_sets';
ODS GRAPHICS ON;ODS HTML style=statistical;
PROC LIFETEST DATA=allison.myel PLOTS=S(NOCENSOR ATRISK CL CB=EP); TIME dur*status(0);RUN;
ODS HTML close;ODS GRAPHICS OFF;
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libname allison 'C:/allison_2010/data_sets';
PROC LIFETEST DATA=allison.myel OUTSURV=a; TIME dur*status(0);RUN;
Proc Print data=a;Run;
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libname allison 'C:/allison_2010/data_sets';
ODS OUTPUT ProductLimitEstimates=a;
PROC LIFETEST DATA=allison.myel; TIME dur*status(0);RUN;
Proc Print data=a;Run;
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Obs STRATUM dur Censor Survival Failure StdErr Failed Left
1 1 0.00 . 1.0000 0 0 0 25
2 1 8.00 0 . . . 1 24
3 1 8.00 0 0.9200 0.0800 0.0543 2 23
4 1 13.00 0 0.8800 0.1200 0.0650 3 22
5 1 18.00 0 0.8400 0.1600 0.0733 4 21
6 1 23.00 0 0.8000 0.2000 0.0800 5 20
7 1 52.00 0 0.7600 0.2400 0.0854 6 19
8 1 63.00 0 . . . 7 18
9 1 63.00 0 0.6800 0.3200 0.0933 8 17
10 1 70.00 0 0.6400 0.3600 0.0960 9 16
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• Reading data from a text file into SAS
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Sample Data (as given in file to be read)
1 56 0
2 7 1
3 21 0
4 62 0
5 38 0
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Sample Data (showing columns)
123456789012345
1 56 0
2 7 1
3 21 0
4 62 0
5 38 0
Formats for data• Col 1, F2.0• Col 4, F2.0• Col 7, F1.0
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Code to read in data.
filename in ‘C:\data\sample1.txt’;
data njb1; infile in; input @1 ID 2. @4 survtime 2. @7 status 1. ;run;
proc print data=njb1 (obs=20);run;
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