libname asa_data 'C:\ASA_SAS';
ods trace on;
proc phreg data = asa_data.whas100;
model lenfol*fstat(0) = gender;
run;
ods trace off;
* Table 3.2;
ods output ParameterEstimates = temp1;
proc phreg data = asa_data.whas100;
model lenfol*fstat(0) = gender;
run;
libname asa_data 'C:\ASA_SAS';
ods trace on;
proc phreg data = asa_data.whas100;
model lenfol*fstat(0) = gender;
run;
ods trace off;
* Table 4.2;
ods output ParameterEstimates = temp1;
proc phreg data = asa_data.whas100;
model lenfol*fstat(0) = gender / ties = breslow;
run;
proc print data = temp1;run;
proc contents data = temp1;run;
data table4p2;
set temp1;
z = sqrt(ChiSq);
z2 = Estimate / StdErr;
lowerb = estimate - 1.96*stderr;
upperb = estimate + 1.96*stderr;
run;
proc print data = table4p2 label noobs;
var Parameter Estimate stderr z z2 Probchisq lowerb upperb;
format Estimate z z2 Probchisq lowerb upperb f8.3;
format stderr f8.4;
label Parameter = 'Variable'
Estimate = 'Coeff.'
stderr = 'Std.Err.'
Probchisq = 'p>|z|'
lowerb = 'Conf Lower'
upperb = 'Conf Upper';
run;
* Table 4.4;
data temp2;
set asa_data.whas100;
age_2 = 0;
age_3 = 0;
age_4 = 0;
if 60 <= age <= 69 then age_2 = 1;
else if 70 <= age <= 79 then age_3 = 1;
else if 80 <= age then age_4 = 1;
run;
* Table 4.5 & Table 4.7;
proc phreg data = temp2;
model lenfol*fstat(0) = age_2 age_3 age_4 / ties = breslow risklimits covb;
run;
data temp3;
set asa_data.whas100;
age_2 = 0;
age_3 = 0;
age_4 = 0;
if age < 60 then do;
age_2 = -1;
age_3 = -1;
age_4 = -1;
end;
if 60 <= age <= 69 then age_2 = 1;
if 60 <= age <= 69 then age_2 = 1;
else if 70 <= age <= 79 then age_3 = 1;
else if 80 <= age then age_4 = 1;
run;
* Table 4.8;
proc phreg data = temp3;
model lenfol*fstat(0) = age_2 age_3 age_4 / ties = breslow risklimits covb;
run;
* Table 4.13;
* Crude Model;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = gender/ risklimits;
run;
* Adjusted Model;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = gender age/ risklimits;
run;
* Interaction Model;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = gender age gender*age/ risklimits; *no hazard ratio in this case;
run;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = gender age ga/ risklimits;
ga = gender*age;
output out = temp4 xbeta = xbeta;
run;
proc print data = temp4; run;
proc gplot data = temp4;
plot xbeta*age = gender;
run;
* Figure 4.5;
data temp1;
set asa_data.gbcs;
time = rectime/30;
run;
proc phreg data = temp1;
model time*censrec(0) = hormone;
output out = temp2 survival = survival;
run;
proc sort data = temp2;
by hormone time;
run;
proc gplot data = temp2;
plot survival*time = hormone;
run;
quit;
libname asa_data 'C:\ASA_SAS';
* Figure 5.2a;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = age hr diasbp gender chf;
id id;
output out = fig52a resmart = mart;
run;
proc sort data = asa_data.whas500;
by id;
run;
proc sort data = fig52a;
by id;
run;
data fig52a;
merge fig52a asa_data.whas500;
by id;
run;
proc loess data = fig52a;
model mart = bmi;
ods output outputstatistics = temp1;
run;
proc sort data = temp1;
by bmi;
run;
proc contents data = temp1; run;
goptions reset = all;
symbol1 v = dot i = none;
symbol2 v = none i = join;
proc gplot data = temp1;
plot DepVar*bmi=1 pred*bmi=2 / overlay;
*plot pred*bmi=2;
run;
quit;
* Stepwise ;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = age chf hr diasbp bmi gender mitype miord sysbp cvd afb
/ selection = forward slentry = 0.25 slstay = 0.8;
run;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = age chf hr diasbp bmi gender mitype miord sysbp cvd afb
/ selection = stepwise slentry = 0.25 slstay = 0.8 details;
run;
* Best Subset;
proc phreg data = asa_data.whas500;
model lenfol*fstat(0) = age chf hr diasbp bmi gender mitype miord sysbp cvd afb
/ selection = score best = 3 details;
run;
Wednesday, November 27, 2013
Monday, November 18, 2013
SAS Survival Analysis II: descriptive analysis
libname asa_data 'C:\ASA_SAS';
data toydata;
input subject time censor;
datalines;
1 6 1
2 44 1
3 21 0
4 14 1
5 62 1
;
run;
* Table 2.2, Figure 2.1;
proc lifetest data = toydata plots = s cs = none;
time time*censor(0);
run;
data whas100;
set asa_data.whas100;
year = lenfol/365.25;
run;
* Figure 2.2, Table 2.3;
proc lifetest data = whas100 plots = (s ls h) cs = none;
time year*fstat(0);
label year = 'Survival Time (Years)';
run;
ods trace on;
proc lifetest data = whas100 plots = (s ls h) cs = none;
time year*fstat(0);
label year = 'Survival Time (Years)';
run;
ods trace off;
ods select productlimitestimates;
proc lifetest data = whas100 plots = (s ls h) cs = none;
time year*fstat(0);
label year = 'Survival Time (Years)';
run;
* Table 2.4, Figure 2.4;
proc lifetest data = whas100 plots = s method = lt;
time year*fstat(0);
run;
proc lifetest data = whas100 plots = s conftype = loglog confband = hw
outs = conf_data;
time year*fstat(0);
run;
proc print;run;
* Figure 2.7;
goptions reset = all;
legend1 label=none value=(h=1.5 font=swiss 'Est. Surv. Pr.' 'Pointwise 95%' 'Hall & Wellner Band')
position=(bottom center inside) mode=protect down=3 across=1;
axis1 label=(a=90 'Estimated Survival Probability') order=(0 to 1 by 0.1) minor=none;
axis2 label=('Survival Time (Years)') order=(0 to 8 by 1) minor=none;
symbol1 i=steplj color=black line=1;
symbol2 i=steplj color=black line=14;
symbol3 i=steplj color=black line=46;
symbol4 i=steplj color=black line=14;
symbol5 i=steplj color=black line=46;
proc gplot data = conf_data;
plot (survival sdf_ucl hw_ucl)*year / overlay vaxis=axis1 haxis=axis2 legend=legend1;
plot2 (sdf_lcl hw_lcl)*year /overlay vaxis=axis1 noaxis nolegend;
run;
quit;
* Figure 2.7;
proc sort data = whas100;
by year;
run;
proc lifetest data = whas100 outs = loglogdata conftype = loglog;
time year*fstat(0);
run;
proc contents; run;
proc print;run;
data loglogdata;
set loglogdata;
rename SDF_LCL = lcl_loglog SDF_UCL = ucl_loglog;
drop _CENSOR_;
run;
proc lifetest data = whas100 outs = logdata conftype = log;
time year*fstat(0);
run;
data logdata;
set logdata;
rename SDF_LCL = lcl_log SDF_UCL = ucl_log;
drop _CENSOR_;
run;
proc lifetest data = whas100 outs = logitdata conftype = logit;
time year*fstat(0);
run;
data logitdata;
set logitdata;
rename SDF_LCL = lcl_logit SDF_UCL = ucl_logit;
drop _CENSOR_;
run;
proc lifetest data = whas100 outs = asindata conftype = asinsqrt noprint;
time year*fstat(0);
run;
data asindata;
set asindata;
rename SDF_LCL = lcl_asin SDF_UCL = ucl_asin;
drop _CENSOR_;
run;
data all;
merge loglogdata logdata logitdata asindata;
by year;
run;
goptions reset = all;
legend1 label=none value=(h=1.5 font=swiss 'Est. Surv. Pr.' 'Log' 'Log-Log' 'Logit' 'Arcsine'
'lower logit' 'upper logit' 'lower arcsine' 'upper arcsine')
position=(bottom left inside) mode=protect across=2;
axis1 label=(a=90 'Estimated Survival Probability') order=(0 to 1 by .2) minor=none ;
axis2 label=('Survival Time (Years)') order=(0 to 8 by 1) minor=none;
symbol1 i=steplj line=1 color=black;
symbol2 i=steplj line=4 color=black;
symbol3 i=steplj line=14 color=black;
symbol4 i=steplj line=46 color=black;
symbol5 i=steplj line=41 color=black;
symbol6 i=steplj line=4 color=black;
symbol7 i=steplj line=14 color=black;
symbol8 i=steplj line=46 color=black;
symbol9 i=steplj line=41 color=black;
proc gplot data = all;
plot (survival lcl_log lcl_loglog lcl_logit lcl_asin)*year / overlay vaxis=axis1 haxis=axis2 legend=legend1;
plot2 (ucl_log ucl_loglog ucl_logit ucl_asin)*year /overlay vaxis=axis1 noaxis nolegend;
run;
quit;
* Table 2.5;
ods select quartiles;
proc lifetest data = whas100 conftype = log;
time year*fstat(0);
run;
* Table 2.7;
proc lifetest data = toydata;
time time*censor(0);
run;
data toy_temp;
set toydata;
if subject = 5 then censor = 0;
run;
proc lifetest data = toy_temp;
time time*censor(0);
run;
* Figure 2.9, Table 2.12;
proc lifetest data = whas100 plots = s cs = none;
time lenfol*fstat(0);
strata gender / test = (logrank wilcoxon peto tarone);
run;
data toydata;
input subject time censor;
datalines;
1 6 1
2 44 1
3 21 0
4 14 1
5 62 1
;
run;
* Table 2.2, Figure 2.1;
proc lifetest data = toydata plots = s cs = none;
time time*censor(0);
run;
data whas100;
set asa_data.whas100;
year = lenfol/365.25;
run;
* Figure 2.2, Table 2.3;
proc lifetest data = whas100 plots = (s ls h) cs = none;
time year*fstat(0);
label year = 'Survival Time (Years)';
run;
ods trace on;
proc lifetest data = whas100 plots = (s ls h) cs = none;
time year*fstat(0);
label year = 'Survival Time (Years)';
run;
ods trace off;
ods select productlimitestimates;
proc lifetest data = whas100 plots = (s ls h) cs = none;
time year*fstat(0);
label year = 'Survival Time (Years)';
run;
* Table 2.4, Figure 2.4;
proc lifetest data = whas100 plots = s method = lt;
time year*fstat(0);
run;
proc lifetest data = whas100 plots = s conftype = loglog confband = hw
outs = conf_data;
time year*fstat(0);
run;
proc print;run;
* Figure 2.7;
goptions reset = all;
legend1 label=none value=(h=1.5 font=swiss 'Est. Surv. Pr.' 'Pointwise 95%' 'Hall & Wellner Band')
position=(bottom center inside) mode=protect down=3 across=1;
axis1 label=(a=90 'Estimated Survival Probability') order=(0 to 1 by 0.1) minor=none;
axis2 label=('Survival Time (Years)') order=(0 to 8 by 1) minor=none;
symbol1 i=steplj color=black line=1;
symbol2 i=steplj color=black line=14;
symbol3 i=steplj color=black line=46;
symbol4 i=steplj color=black line=14;
symbol5 i=steplj color=black line=46;
proc gplot data = conf_data;
plot (survival sdf_ucl hw_ucl)*year / overlay vaxis=axis1 haxis=axis2 legend=legend1;
plot2 (sdf_lcl hw_lcl)*year /overlay vaxis=axis1 noaxis nolegend;
run;
quit;
* Figure 2.7;
proc sort data = whas100;
by year;
run;
proc lifetest data = whas100 outs = loglogdata conftype = loglog;
time year*fstat(0);
run;
proc contents; run;
proc print;run;
data loglogdata;
set loglogdata;
rename SDF_LCL = lcl_loglog SDF_UCL = ucl_loglog;
drop _CENSOR_;
run;
proc lifetest data = whas100 outs = logdata conftype = log;
time year*fstat(0);
run;
data logdata;
set logdata;
rename SDF_LCL = lcl_log SDF_UCL = ucl_log;
drop _CENSOR_;
run;
proc lifetest data = whas100 outs = logitdata conftype = logit;
time year*fstat(0);
run;
data logitdata;
set logitdata;
rename SDF_LCL = lcl_logit SDF_UCL = ucl_logit;
drop _CENSOR_;
run;
proc lifetest data = whas100 outs = asindata conftype = asinsqrt noprint;
time year*fstat(0);
run;
data asindata;
set asindata;
rename SDF_LCL = lcl_asin SDF_UCL = ucl_asin;
drop _CENSOR_;
run;
data all;
merge loglogdata logdata logitdata asindata;
by year;
run;
goptions reset = all;
legend1 label=none value=(h=1.5 font=swiss 'Est. Surv. Pr.' 'Log' 'Log-Log' 'Logit' 'Arcsine'
'lower logit' 'upper logit' 'lower arcsine' 'upper arcsine')
position=(bottom left inside) mode=protect across=2;
axis1 label=(a=90 'Estimated Survival Probability') order=(0 to 1 by .2) minor=none ;
axis2 label=('Survival Time (Years)') order=(0 to 8 by 1) minor=none;
symbol1 i=steplj line=1 color=black;
symbol2 i=steplj line=4 color=black;
symbol3 i=steplj line=14 color=black;
symbol4 i=steplj line=46 color=black;
symbol5 i=steplj line=41 color=black;
symbol6 i=steplj line=4 color=black;
symbol7 i=steplj line=14 color=black;
symbol8 i=steplj line=46 color=black;
symbol9 i=steplj line=41 color=black;
proc gplot data = all;
plot (survival lcl_log lcl_loglog lcl_logit lcl_asin)*year / overlay vaxis=axis1 haxis=axis2 legend=legend1;
plot2 (ucl_log ucl_loglog ucl_logit ucl_asin)*year /overlay vaxis=axis1 noaxis nolegend;
run;
quit;
* Table 2.5;
ods select quartiles;
proc lifetest data = whas100 conftype = log;
time year*fstat(0);
run;
* Table 2.7;
proc lifetest data = toydata;
time time*censor(0);
run;
data toy_temp;
set toydata;
if subject = 5 then censor = 0;
run;
proc lifetest data = toy_temp;
time time*censor(0);
run;
* Figure 2.9, Table 2.12;
proc lifetest data = whas100 plots = s cs = none;
time lenfol*fstat(0);
strata gender / test = (logrank wilcoxon peto tarone);
run;
SAS Survival Analysis I: data input
libname asa_data 'C:\ASA_SAS';
data asa_data.whas100;
infile 'C:\Applied_Survival_Analysis_Data\whas100.dat';
input id 1-5 +2 admitdate mmddyy10. +2 foldate mmddyy10. los lenfol fstat age gender bmi;
run;
/*
proc print data = asa_data.whas100;
title 'WHAS100';
format admitdate date9. foldate date11.;
run;
*/
data asa_data.actg320;
infile 'C:\Applied_Survival_Analysis_Data\actg320.dat';
input id time censor time_d tx txgrp strat2 sex raceth ivdrug hemophil
karnof cd4 priorzdv age;
run;
data asa_data.actg320ncc;
infile 'C:\Applied_Survival_Analysis_Data\actg320ncc.dat';
input set case id time tx age cd4;
run;
data asa_data.bpd;
infile 'C:\Applied_Survival_Analysis_Data\bpd.dat';
input id surfact ondays censor;
run;
data asa_data.comprisk;
infile 'C:\Applied_Survival_Analysis_Data\comprisk.dat';
input id age gender bmi time ev_typ;
run;
data asa_data.cvdrisk;
infile 'C:\Applied_Survival_Analysis_Data\cvdrisk.dat';
input id age bmi gender time ev_typ;
run;
data asa_data.FRTCS;
infile 'C:\Applied_Survival_Analysis_Data\FRTCS.dat';
input id age sex date0 date9. sbp0 dbp0 antihyp0 date1 date9. sbp1
dbp1 antihyp1 date2 date9. sbp2 dbp2 antihyp2 date_event date9. censor;
run;
/*
proc print data = asa_data.FRTCS;
format date0 date9. date1 date9. date_event date9.;
run;
*/
data asa_data.gbcs;
infile 'C:\Applied_Survival_Analysis_Data\gbcs.dat';
input id diagdate date11. recdate date11. deathdate date11. age menopause
hormone size grade nodes prog_recp estrg_recp rectime censrec
survtime censdead;
run;
/*
proc print data = asa_data.gbcs (obs = 5);
format diagdate date9. recdate date11. deathdate date11.;
run;
*/
data asa_data.GRACE1000;
infile 'C:\Applied_Survival_Analysis_Data\GRACE1000.dat';
input id days death revasc revascdays los age sysbp stchange;
run;
data asa_data.recur;
infile 'C:\Applied_Survival_Analysis_Data\recur.dat';
input id age treat time0 time1 censor event;
run;
data asa_data.uis;
infile 'C:\Applied_Survival_Analysis_Data\uis.dat';
input id age beck hercoc ivhx ndrugtx race treat site los time censor;
run;
data asa_data.whas500;
infile 'C:\Applied_Survival_Analysis_Data\whas500.dat';
input id age gender hr sysbp diasbp bmi cvd afb sho chf av3 miord mitype year
admitdate mmddyy12. disdate mmddyy12. fdate mmddyy12. los dstat lenfol fstat;
run;
/*
proc print data = asa_data.whas500;
format admitdate date9. disdate date9. fdate date9.;
run;
*/
data asa_data.whasncc;
infile 'C:\Applied_Survival_Analysis_Data\whasncc.dat';
input set case t lenfol fstat age sex bmi chf miord nr;
run;
libname asa_data 'C:\ASA_SAS';
proc format;
value status 1 = 'Dead'
0 = 'Alive';
value gender 0 = 'Male'
1 = 'Female';
run;
title '100 Subjects in the Worcester Heart Attack Study (WHAS100)';
proc print data = asa_data.whas100 label;
id id;
var admitdate foldate los lenfol fstat age gender bmi;
format admitdate mmddyy8. foldate mmddyy8. fstat status. gender gender.;
label id = 'ID'
admitdate = 'Admission Date'
foldate = 'Follow Up Date'
los = 'Length of Stay'
lenfol = 'Follow Up Time'
fstat = 'Vital Status'
age = 'Age at Admission'
gender = 'Gender'
bmi = 'BMI';
run;
data asa_data.whas100;
infile 'C:\Applied_Survival_Analysis_Data\whas100.dat';
input id 1-5 +2 admitdate mmddyy10. +2 foldate mmddyy10. los lenfol fstat age gender bmi;
run;
/*
proc print data = asa_data.whas100;
title 'WHAS100';
format admitdate date9. foldate date11.;
run;
*/
data asa_data.actg320;
infile 'C:\Applied_Survival_Analysis_Data\actg320.dat';
input id time censor time_d tx txgrp strat2 sex raceth ivdrug hemophil
karnof cd4 priorzdv age;
run;
data asa_data.actg320ncc;
infile 'C:\Applied_Survival_Analysis_Data\actg320ncc.dat';
input set case id time tx age cd4;
run;
data asa_data.bpd;
infile 'C:\Applied_Survival_Analysis_Data\bpd.dat';
input id surfact ondays censor;
run;
data asa_data.comprisk;
infile 'C:\Applied_Survival_Analysis_Data\comprisk.dat';
input id age gender bmi time ev_typ;
run;
data asa_data.cvdrisk;
infile 'C:\Applied_Survival_Analysis_Data\cvdrisk.dat';
input id age bmi gender time ev_typ;
run;
data asa_data.FRTCS;
infile 'C:\Applied_Survival_Analysis_Data\FRTCS.dat';
input id age sex date0 date9. sbp0 dbp0 antihyp0 date1 date9. sbp1
dbp1 antihyp1 date2 date9. sbp2 dbp2 antihyp2 date_event date9. censor;
run;
/*
proc print data = asa_data.FRTCS;
format date0 date9. date1 date9. date_event date9.;
run;
*/
data asa_data.gbcs;
infile 'C:\Applied_Survival_Analysis_Data\gbcs.dat';
input id diagdate date11. recdate date11. deathdate date11. age menopause
hormone size grade nodes prog_recp estrg_recp rectime censrec
survtime censdead;
run;
/*
proc print data = asa_data.gbcs (obs = 5);
format diagdate date9. recdate date11. deathdate date11.;
run;
*/
data asa_data.GRACE1000;
infile 'C:\Applied_Survival_Analysis_Data\GRACE1000.dat';
input id days death revasc revascdays los age sysbp stchange;
run;
data asa_data.recur;
infile 'C:\Applied_Survival_Analysis_Data\recur.dat';
input id age treat time0 time1 censor event;
run;
data asa_data.uis;
infile 'C:\Applied_Survival_Analysis_Data\uis.dat';
input id age beck hercoc ivhx ndrugtx race treat site los time censor;
run;
data asa_data.whas500;
infile 'C:\Applied_Survival_Analysis_Data\whas500.dat';
input id age gender hr sysbp diasbp bmi cvd afb sho chf av3 miord mitype year
admitdate mmddyy12. disdate mmddyy12. fdate mmddyy12. los dstat lenfol fstat;
run;
/*
proc print data = asa_data.whas500;
format admitdate date9. disdate date9. fdate date9.;
run;
*/
data asa_data.whasncc;
infile 'C:\Applied_Survival_Analysis_Data\whasncc.dat';
input set case t lenfol fstat age sex bmi chf miord nr;
run;
libname asa_data 'C:\ASA_SAS';
proc format;
value status 1 = 'Dead'
0 = 'Alive';
value gender 0 = 'Male'
1 = 'Female';
run;
title '100 Subjects in the Worcester Heart Attack Study (WHAS100)';
proc print data = asa_data.whas100 label;
id id;
var admitdate foldate los lenfol fstat age gender bmi;
format admitdate mmddyy8. foldate mmddyy8. fstat status. gender gender.;
label id = 'ID'
admitdate = 'Admission Date'
foldate = 'Follow Up Date'
los = 'Length of Stay'
lenfol = 'Follow Up Time'
fstat = 'Vital Status'
age = 'Age at Admission'
gender = 'Gender'
bmi = 'BMI';
run;
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