libname raw "/folders/myfolders/cliniops/REN002/tables" ;
%let outpath=/folders/myfolders/cliniops/REN002/tables ;
%let pgmname=t14_2_1 ;
* options byline ;
%let tst=* ;
proc format;
value visf -1='Screening'
0='Baseline'
2='02 hrs'
4='04 hrs'
8='08 hrs'
12='12 hrs'
18='18 hrs'
24='24 hrs'
48='48 hrs'
72='72 hrs'
96='96 hrs'
168='168 hrs' ;
value sumf 1='Visit Value'
2='Change'
3='% Change' ;
value $stf 'NV'='N'
'MV'='Mean'
'SV'='SD'
'DV'='Median'
'IV'='Min'
'AV'='Max' ;
value $st2f 'NV'='N'
'MV'='GeoMean[1]'
'SV'='GeoCV%[2]'
'DV'='Median'
'IV'='Min'
'AV'='Max' ;
run ;
proc import datafile = '/folders/myfolders/cliniops/excel data files/programs/subset1.csv'
out = raw.renibus
dbms = csv
replace;
run;
/*data cm ;
length SUBJECT $8 ;
set renibus ;
if CMTRT__CMD__CM__logs^='' ;
subject=put(subject_id,z3.) ;
rename CMDOCYN__CMD__CM__logs=CMDOCYN
CMDOSFRM__CMD__CM__logs=CMDOSFRM
CMDOSFRQ__CMD__CM__logs=CMDOSFRQ
CMENDAT__CMD__CM__logs=CMENDAT
CMINDC__CMD__CM__logs=CMINDC
CMONGO__CMD__CM__logs=CMONGO
CMPRIOR__CMD__CM__logs=CMPRIOR
CMROUTE__CMD__CM__logs=CMROUTE
CMSTDAT__CMD__CM__logs=CMSTDAT
CMTRT__CMD__CM__logs=CMTRT ;
keep subject CMDOCYN__CMD__CM__logs CMDOSFRM__CMD__CM__logs CMDOSFRQ__CMD__CM__logs CMENDAT__CMD__CM__logs CMINDC__CMD__CM__logs
CMONGO__CMD__CM__logs CMPRIOR__CMD__CM__logs CMROUTE__CMD__CM__logs CMSTDAT__CMD__CM__logs CMTRT__CMD__CM__logs ;
run ;*/
PROC IMPORT OUT= raw.lab
DATAFILE= "/folders/myfolders/cliniops/excel data files/programs/CliniOps-Renibus-Lab-REN-002-Jan-16-2019-1.xlsx"
DBMS=xlsx REPLACE;
RUN;
data adsl ;
length SUBJECT STRATUM $8 ;
set raw.renibus ;
if I_SCNNO__HEADER__CKDIE__ScrVST not in ('.','') then stratum='CKD' ;
if I_SCNNO__HEADER__HVIE__ScrVst not in ('.','') then stratum='HV' ;
if stratum='' then delete ;
subject=put(subject_id,z3.) ;
COHORT=strip(COHORT__COHORT__ALSUBJSCN_ScrVst) ;
TYPE=strip(INIE_COHORT_ALSUBJSCN_Screen); *1=HV, 2=CKD ;
keep subject stratum cohort type ;
run ;
data lb ;
length SUBJECT TESTCD $8 VISIT $24 ;
set raw.lab ;
subject=substr(subject_id,2,3) ;
if test in ('Ferritin','Haptoglobin','Plasma HO-1','Plasma Hemopexin','Plasma P21') ;* 'INTERLEUKIN10' ;
if test='Ferritin' then testcd='FE' ;
else if test='Haptoglobin' then testcd='HPG' ;
else if test='INTERLEUKIN10' then testcd='IL10' ;
else if test='Plasma HO-1' then testcd='PHO1' ;
else if test='Plasma Hemopexin' then testcd='PHPX' ;
else if test='Plasma P21' then testcd='PP21' ;
if index(visit,'Screening')>0 then visit='Screening Visit' ;
if visit='Study Day 1-2HR' then visit='Study Day 1, 02HR' ;
if visit='Study Day 1-4HR' then visit='Study Day 1, 04HR' ;
if visit='Study Day 1-8HR' then visit='Study Day 1, 08HR' ;
if visit='Study Day 1-12HR' then visit='Study Day 1, 12HR' ;
if visit='Study Day 1-18HR' then visit='Study Day 1, 18HR' ;
if visit='Study Day 1-Basel' then visit='Study Day 1' ;
if visit='Study Day 2-Basel' then visit='Study Day 2' ;
if visit='Study Day 3-Basel' then visit='Study Day 3' ;
if visit='Study Day 4-Basel' then visit='Study Day 4' ;
if visit='Study Day 5-Basel' then visit='Study Day 5' ;
if index(visit,'Screening')>0 then VISITN=-1 ;
if index(visit,'02HR')>0 then visitn=2 ;
if index(visit,'04HR')>0 then visitn=4 ;
if index(visit,'08HR')>0 then visitn=8 ;
if index(visit,'12HR')>0 then visitn=12 ;
if index(visit,'18HR')>0 then visitn=18 ;
if visit='Study Day 1' then visitn=0 ;
if visit='Study Day 2' then visitn=24 ;
if visit='Study Day 3' then visitn=48 ;
if visit='Study Day 4' then visitn=72 ;
if visit='Study Day 5' then visitn=96 ;
if visit='Study Day 8' then visitn=168 ;
if value not in ('-','Plasma','Sample') then aval=input(value,best.) ;
format visit $char24. ;
run ;
proc sort data=lb ;
by subject testcd visitn ;
run ;
proc sort data=adsl ;
by subject ;
run ;
data lb2 ;
merge lb adsl ;
by subject ;
if testcd in ('FE','HPG','PHPX','PP21') ;
run ;
data base ;
set lb2 ;
where visitn=0 ;
rename aval=base ;
keep subject testcd aval ;
run ;
data lb3 ;
merge lb2(in=a where=(visitn>=0)) base(in=b) ;
by subject testcd ;
if a and b ;
/* if visitn>0 and aval>. then do ;*/
/* CHG=aval-base ;*/
/* PCHG=(aval-base)/base*100 ;*/
/* end ;*/
LOGBASE=log(base) ;
if aval>. then do ;
LOGAVAL=log(aval) ;
if visitn>0 then do ;
CHG=aval-base ;
CHGLOG=logaval-logbase ;
PCHG=(aval-base)/base*100 ;
end ;
end ;
output ;
stratum='HV+CKD' ;
output ;
run ;
/*
data lb3tmp ;
set lb3 ;
logaval=log(aval) ;
run ;
proc sort data=lb3tmp ;
by test ;
run ;
ods select histogram qqplot testsfornormality ;
proc univariate data=lb3tmp normal ;
var pchg ;* aval logaval ;
histogram ;
qqplot ;
by test ;
run ;
* USE LOG(FERRITIN), LOG(HAPTOGLOBIN) OR BAPTOGLOBIN, HO-1, LOG(PLASMA HEMOPEXIN), LOG(PLASMA P21) ;
*/
proc sort data=lb3 ;
WHERE STRATUM='HV' AND TESTCD='FE' ;
by stratum testcd visitn cohort ;
run ;
proc summary data=lb3 ;
var logaval ;
by stratum testcd test visitn cohort ;
output out=visval n=nv mean=mv std=sv median=dv min=iv max=av cv=cv ;
run ;
proc summary data=lb3 ;
where visitn>0 ;
var chglog ;
by stratum testcd test visitn cohort ;
output out=chg n=nv mean=mv std=sv median=dv min=iv max=av cv=cv ;
run ;
proc summary data=lb3 ;
where visitn>0 ;
var pchg ;
by stratum testcd test visitn cohort ;
output out=pchg n=nv mean=mv std=sv median=dv min=iv max=av ;
run ;
data summ ;
set visval(in=a) chg(in=b) pchg(in=c) ;
by stratum testcd visitn cohort ;
if a then sumtyp=1 ;
if b then sumtyp=2 ;
if c then sumtyp=3 ;
if a or b then do ;
mv=exp(mv) ; * CONVERT FROM LOG BACK TO ORIGINAL SCALE, THIS IS GEOMETRIC MEAN ;
sv=sqrt(exp(sv**2)-1)*100 ;* exp(sv) ;* COEFFICIENT OF VARIATION FOR GEOMETRIC MEAN ;
dv=exp(dv) ; * MEDIAN, MIN, MAX BACK TO ORIGINAL SCALE ;
iv=exp(iv) ;
av=exp(av) ;
end ;
run ;
proc sort data=summ ;
by stratum testcd visitn sumtyp cohort ;
run ;
proc transpose data=summ out=summ2 ;
var nv mv sv dv iv av ;
by stratum testcd test visitn ;
id cohort sumtyp ;
run ;
data summ3 ;
set summ2 ;
by stratum testcd test visitn ;
length STAT $44 ;
stat=put(_name_,$stf.) ;
array old cohort_11 cohort_12 cohort_13 cohort_21 cohort_22 cohort_23 cohort_31 cohort_32 cohort_33 ;
array new $20 c11 c12 c13 c21 c22 c23 c31 c32 c33 ;
do over old ;
if _name_='NV' then new=put(old,2.) ;
if _name_ in ('MV','DV') then new=put(old,8.3) ;
if _name_='SV' then new=put(old,8.4) ;
if _name_ in ('IV','AV') then new=put(old,8.2) ;
new=strip(new) ;
if new='.' then new='' ;
end ;
run ;
ods select none ;
ods output lsmeans=lsm_aval ;
proc mixed data=lb3 ;
where visit^='Study Day 1' ;
by stratum testcd test ;
class cohort visitn subject ;
model logaval = cohort visitn cohort*visitn logbase / ddfm=kr2 ;
repeated visitn / subject=subject type=cs ;* ar(1) ;
lsmeans cohort*visitn / slice=visitn cl ;
run ;
ods select all ; i am getting error work.lsm_aval does not exsist, though my code has ods output lsmeans=lsm_aval ; why the dataset lsm_aval is not getting created?
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