**Code of 0/1 data***
**Generate the data file with Table 8.2 book****
**gen var1=1,....,67, by hand

save "C:\My Documents\655LDA\DataLDA\cross2x2.dta"
 rename var1 id
 gen trt1=1
 replace trt1=0 in 35/67
 gen trt2=0
 replace trt2=1 in 34/67

gen per1=1
 replace per1=0 if res1==0&trt1==1
 replace per1=0 if res1==0&trt1==0

gen per2=1
 replace per2=0 if res2==0&trt2==1
 replace per2=0 if res2==0&trt2==0


save "C:\My Documents\655LDA\DataLDA\cross2x2.dta", replace
 reshape long trt res, i(id) j(visit)
label var res "Response 1=normal"
label var trt "TReatment 1=A"
 xi: xtgee  res i.trt*i.visit,  nolog f(bin) l(logit) corr(exch)
 xtgee res trt visit, nolog f(bin) l(logit) corr(ind) 
 xtgee res trt visit, nolog f(bin) l(logit) corr(ind) robust

***TRansitional Model***
***Look at the transitional probabilities first
xttrans res
dis log(79*83/17/21)
***A subject with an abnormal response at one time 
***has a 21% chance og getting a normal test at the next time
***The log odds ratio for a normal response for two sequantial observations is 2.9**
sort id
by id: gen resl1=res[_n-1]
logit res resl1
logit res resl1 trt, nolog  


**RE model ---See book pg 181***
**first, the marginal model
 xtlogit  res trt visit, nolog pa
**the RE model***
 xtlogit  res trt visit, nolog re 


outfile id visit trt res per using "C:\My Documents\655LDA\DataLDA\cross2x2SAS.txt"

***Now the SAS code***
data cross2x2;
infile 'C:\My Documents\655LDA\DataLDA\cross2x2SAS.txt';
input id visit trt res per;
run;

proc genmod data=cross2x2;
class id trt;
model res=trt visit trt*visit/type3 error=bin link=logit;
repeated subject=id/logor=exch;
run;

proc genmod data=cross2x2;
class id trt;
model res=trt visit/type3 error=bin link=logit;
repeated subject=id/logor=exch;
run;
proc genmod data=cross2x2;
class id trt;
model res=trt visit /type3 error=bin link=logit;
repeated subject=id/type=ind;
run;

title "Unstructured correlation"
proc genmod data=cross2x2 descending;
class id visit;
model res=trt visit trt*visit/dist=bin link=logit;
repeated subject=id/type=un corrw covb modelse within=visit;
run;


title "Exponential correlation"
proc genmod data=cross2x2 descending;
class id visit;
model res=trt visit trt*visit/dist=bin link=logit;
repeated subject=id/type=ar(1) corrw covb modelse within=visit;
run;

title "Exchangeable correlation"
proc genmod data=cross2x2 descending;
class id visit;
model res=trt visit trt*visit/dist=bin link=logit;
repeated subject=id/type=exch corrw covb modelse within=visit;
run;

*******Code for Bin/N data****
 glm rel trt visit, f(bin tot) l(logit) nolog
 outfile visit trt gr tot rel using "C:\My Documents\655LDA\DataLDA\cross22SAS.txt"
***SAS code***
data cross22;
infile 'C:\My Documents\655LDA\DataLDA\cross22SAS.txt';
input visit trt gr tot rel;
run;

proc genmod data=cross22;
model rel/tot=trt visit /dist=bin link=logit;
run;

proc genmod data=cross22;
class id trt;
model res=trt visit trt*visit/type3 error=bin link=logit;
repeated subject=id/logor=exch;
run;