topic Re: To replace regimen line and regimen with standard format and fill up blanks accordingly in SAS Procedures

To replace regimen line and regimen with standard format and fill up blanks accordingly

Ken_nuga — Mon, 30 Jul 2018 15:50:44 GMT

Please, I need help ASAP.

I have tried this using SAS 9.4 but the blank spaces remain blank and only the formats changed. Thanks.

DATA FACNAME_MERGED;
set work.old_data;
run;
*/ /
/ To assign serial numbers to observations in a data set /
/ /;
DATA FACNAME_MERGED; SET FACNAME_MERGED; SN = _N_; RUN;


*/ TO REPLACE SEX RegLne_ArtStart Reg_ArtStart Curr_RegLine Curr_ART_Reg WITH CDC ACCEPTABLE FORMATS /;

PROC FORMAT;
value $SEX
Male = 'Male' Female = 'Female';

value $RegimenLine_start
"Adult.1st.line" = "Adult.1st.Line" "Adult.2nd.line" = "Adult.2nd.Line" "Peds.1st.line" = "Peds.1st.Line"
"Peds.2nd.line" = "Peds.2nd.Line" "Adult.3rd.line" = "Adult.3rd.Line" "Peds.3rd.line" = "Peds.3rd.Line" ;

value $RegimenLine_Current
"Adult.1st.line" = "Adult.1st.Line" "Adult.2nd.line" = "Adult.2nd.Line" "Peds.1st.line" = "Peds.1st.Line"
"Peds.2nd.line" = "Peds.2nd.Line" "1st Line" = "Peds.1st.Line" "2nd Line" = "Peds.2nd.Line"
"Adult.3rd.line" = "Adult.3rd.Line" "Peds.3rd.line" = "Peds.3rd.Line" ;

value $Regimen_start
"ZDV/3TC/NVP"="AZT-3TC-NVP" "AZT/3TC/NVP"="AZT-3TC-NVP" "NVP only"="AZT-3TC-NVP" "ZDV only"="AZT-3TC-NVP"
"ZDV/3TC"="AZT-3TC-NVP" "3TC/3TC/NVP"="AZT-3TC-NVP" "3TC/ZDV/NVP"="AZT-3TC-NVP" "AZT/3TC/EFV"="AZT-3TC-EFV"
"ZDV/3TC/EFV"="AZT-3TC-EFV" "3TC/3TC/EFV"="AZT-3TC-EFV" "3TC/ZDV/EFV"="AZT-3TC-EFV" "D4T/3TC/NVP"="D4T-3TC-NVP"
"D4T/3TC/EFV"="D4T-3TC-EFV" "TDF/3TC/NVP"="TDF-3TC-NVP" "TDF/3TC"="TDF-3TC-NVP" "TDF/3TC/EFV"="TDF-3TC-EFV"
"TDF/FTC/NVP"="TDF-FTC-NVP" "TDF/FTC/EFV"="TDF-FTC-EFV" "AZT/3TC/ABC"="AZT-3TC-ABC" "AZT/3TC/TDF"="AZT-3TC-TDF"
"TDF/FTC/LPVr"="TDF-FTC-LPV/r" "TDF/3TC/LPVr"="TDF-3TC-LPV/r" "ZDV/3TC/LPVr"="AZT-3TC-LPV/r"
"AZT/TDF/FTC/LPV/r"="AZT-TDF-FTC-LPV/r" "ABC/TDF/LPVr"="AZT-TDF-3TC-LPV/r" "TDF/FTC/ATV/r"="TDF-FTC-ATV/r"
"TDF/3TC/ATV/r"="TDF-3TC-ATV/r" "AZT/3TC/ATV/r"="AZT-3TC-ATV/r" "AZT/3TC/DRV/r"="AZT-3TC-DRV/r"
"TDF/3TC/DRV/r"="TDF-3TC-DRV/r" "DRVr/DTG±1/2NRTIs"="DRVr-DTG ± 1-2 NRTIs" "DRVr/2NRTIs±NNRTI"="DRVr-2NRTIs ± NNRTI"
"DRVr/RAL±1/2NRTIs"="DRVr-RAL ± 1-2NRTIs" "TDF/3TC/DTG"="TDF-3TC-DTG" "TDF/3TC/EFV400"="TDF-3TC-EFV400"
"ABC/3TC/DTG"="ABC-3TC-DTG" "ABC/3TC/NVP"="ABC-3TC-NVP" "ABC/3TC/EFV"="ABC-3TC-EFV"
"ABC/3TC/AZT"="ABC-3TC-AZT" "ABC/FTC/LPVr"="ABC-3TC-LPV/r" "ABC/3TC/LPVr"="ABC-3TC-LPV/r"
"AZT/3TC/LPV/r"="AZT-3TC-LPV/r" "ABC/DDI/LPVr"="ABC-DDI-LPV/r" "DDI/3TC/NVP"="DDI-3TC-NVP"
"ABC/3TC/DDI"="ABC-3TC-DDI" "TDF/3TC/RAL"="TDF-3TC-RAL" "d4T/3TC/LPVr"="D4T-3TC-LPV/r"
"AZT/3TC/RAL"="AZT-3TC-RAL" "DTG+2NRTIs"="DTG + 2 NRTIs" "DRVr+2NRTIs"="DRVr + 2 NRTIs";

value $Regimen_Current
"ZDV/3TC/NVP"="AZT-3TC-NVP" "AZT/3TC/NVP"="AZT-3TC-NVP" "NVP only"="AZT-3TC-NVP" "ZDV only"="AZT-3TC-NVP"
"ZDV/3TC"="AZT-3TC-NVP" "3TC/3TC/NVP"="AZT-3TC-NVP" "3TC/ZDV/NVP"="AZT-3TC-NVP" "AZT/3TC/EFV"="AZT-3TC-EFV"
"ZDV/3TC/EFV"="AZT-3TC-EFV" "3TC/3TC/EFV"="AZT-3TC-EFV" "3TC/ZDV/EFV"="AZT-3TC-EFV" "D4T/3TC/NVP"="D4T-3TC-NVP"
"D4T/3TC/EFV"="D4T-3TC-EFV" "TDF/3TC/NVP"="TDF-3TC-NVP" "TDF/3TC"="TDF-3TC-NVP" "TDF/3TC/EFV"="TDF-3TC-EFV"
"TDF/FTC/NVP"="TDF-FTC-NVP" "TDF/FTC/EFV"="TDF-FTC-EFV" "AZT/3TC/ABC"="AZT-3TC-ABC" "AZT/3TC/TDF"="AZT-3TC-TDF"
"TDF/FTC/LPVr"="TDF-FTC-LPV/r" "TDF/3TC/LPVr"="TDF-3TC-LPV/r" "ZDV/3TC/LPVr"="AZT-3TC-LPV/r"
"AZT/TDF/FTC/LPV/r"="AZT-TDF-FTC-LPV/r" "ABC/TDF/LPVr"="AZT-TDF-3TC-LPV/r" "TDF/FTC/ATV/r"="TDF-FTC-ATV/r"
"TDF/3TC/ATV/r"="TDF-3TC-ATV/r" "AZT/3TC/ATV/r"="AZT-3TC-ATV/r" "AZT/3TC/DRV/r"="AZT-3TC-DRV/r"
"TDF/3TC/DRV/r"="TDF-3TC-DRV/r" "DRVr/DTG±1/2NRTIs"="DRVr-DTG ± 1-2 NRTIs" "DRVr/2NRTIs±NNRTI"="DRVr-2NRTIs ± NNRTI"
"DRVr/RAL±1/2NRTIs"="DRVr-RAL ± 1-2NRTIs" "TDF/3TC/DTG"="TDF-3TC-DTG" "TDF/3TC/EFV400"="TDF-3TC-EFV400"
"ABC/3TC/DTG"="ABC-3TC-DTG" "ABC/3TC/NVP"="ABC-3TC-NVP" "ABC/3TC/EFV"="ABC-3TC-EFV"
"ABC/3TC/AZT"="ABC-3TC-AZT" "ABC/FTC/LPVr"="ABC-3TC-LPV/r" "ABC/3TC/LPVr"="ABC-3TC-LPV/r"
"AZT/3TC/LPV/r"="AZT-3TC-LPV/r" "ABC/DDI/LPVr"="ABC-DDI-LPV/r" "DDI/3TC/NVP"="DDI-3TC-NVP"
"ABC/3TC/DDI"="ABC-3TC-DDI" "TDF/3TC/RAL"="TDF-3TC-RAL" "d4T/3TC/LPVr"="D4T-3TC-LPV/r"
"AZT/3TC/RAL"="AZT-3TC-RAL" "DTG+2NRTIs"="DTG + 2 NRTIs" "DRVr+2NRTIs"="DRVr + 2 NRTIs";
run;

DATA SASUSER.FACNAME; Set FACNAME_MERGED;
format Sex $SEX. RegLne_ArtStart $RegimenLine_start. Curr_RegLine $RegimenLine_Current.
Reg_ArtStart $Regimen_start. Curr_ART_Reg $Regimen_Current.;
run;


DATA FACNAME_MERGED; set SASUSER.FACNAME;
IF (Age_ArtStaMnts_5_ ^=. OR Age_ArtStart_Yrs <=14) & /* peads 1st line drug class*/ (Reg_ArtStart = "AZT-3TC-NVP" 
| Reg_ArtStart = "AZT-3TC-EFV" | Reg_ArtStart = "D4T-3TC-NVP" | Reg_ArtStart = "D4T-3TC-EFV" 
| Reg_ArtStart = "ABC-3TC-NVP" | Reg_ArtStart = "ABC-3TC-EFV" | Reg_ArtStart = "ABC-3TC-AZT" 
| Reg_ArtStart = "TDF-3TC-EFV" | Reg_ArtStart = "TDF-3TC-DTG" | Reg_ArtStart = "TDF-3TC-EFV400" 
| Reg_ArtStart = "ABC-3TC-DTG") THEN RegLne_ArtStart = "Peds.1st.Line"; ELSE IF

(Age_ArtStaMnts_5_ ^=. OR Age_ArtStart_Yrs <=14) & /* peads 2nd line drug class*/ (Reg_ArtStart = "ABC-DDI-LPV/r" 
| Reg_ArtStart = "ABC-3TC-LPV/r" | Reg_ArtStart = "AZT-3TC-LPV/r" | Reg_ArtStart = "D4T-3TC-LPV/r" 
| Reg_ArtStart = "DDI-3TC-NVP" | Reg_ArtStart = "ABC-3TC-DDI" | Reg_ArtStart = "TDF-3TC-ATV/r" 
| Reg_ArtStart = "TDF-3TC-RAL" | Reg_ArtStart = "AZT-3TC-RAL") THEN RegLne_ArtStart = "Peds.2nd.Line"; ELSE IF

(Age_ArtStaMnts_5_ =. OR Age_ArtStart_Yrs >14) & /* adult 1st line drug class*/ (Reg_ArtStart = "AZT-3TC-NVP" 
| Reg_ArtStart = "AZT-3TC-EFV" | Reg_ArtStart = "D4T-3TC-NVP" | Reg_ArtStart = "D4T-3TC-EFV" 
| Reg_ArtStart = "TDF-3TC-NVP" | Reg_ArtStart = "TDF-3TC-EFV" | Reg_ArtStart = "TDF-FTC-NVP" 
| Reg_ArtStart = "TDF-FTC-EFV" | Reg_ArtStart = "AZT-3TC-ABC" | Reg_ArtStart = "AZT-3TC-TDF")
THEN RegLne_ArtStart = "Adult.1st.Line"; ELSE IF

(Age_ArtStaMnts_5_ =. OR Age_ArtStart_Yrs >14) & /* adult 2nd line drug class*/ (Reg_ArtStart = "TDF-FTC-LPV/r" 
| Reg_ArtStart = "TDF-3TC-LPV/r" | Reg_ArtStart = "AZT-3TC-LPV/r" | Reg_ArtStart = "AZT-TDF-FTC-LPV/r" 
| Reg_ArtStart = "AZT-TDF-3TC-LPV/r" | Reg_ArtStart = "TDF-FTC-ATV/r" | Reg_ArtStart = "TDF-3TC-ATV/r" 
| Reg_ArtStart = "AZT-3TC-ATV/r" | Reg_ArtStart = "TDF-3TC-DRV/r" | Reg_ArtStart = "AZT-3TC-DRV/r")
THEN RegLne_ArtStart = "Adult.2nd.Line";


ELSE IF (Age_ArtStaMnts_5_ ^=. OR Age_ArtStart_Yrs <=14) & /* adult 1st line drug class*/ (Reg_ArtStart = "AZT-3TC-NVP" 
| Reg_ArtStart = "AZT-3TC-EFV" | Reg_ArtStart = "D4T-3TC-NVP" | Reg_ArtStart = "D4T-3TC-EFV" 
| Reg_ArtStart = "TDF-3TC-NVP" | Reg_ArtStart = "TDF-3TC-EFV" | Reg_ArtStart = "TDF-FTC-NVP" 
| Reg_ArtStart = "TDF-FTC-EFV" | Reg_ArtStart = "AZT-3TC-ABC" | Reg_ArtStart = "AZT-3TC-TDF")
THEN RegLne_ArtStart = "Peds.1st.Line" & Reg_ArtStart = "AZT-3TC-NVP"; ELSE IF

(Age_ArtStaMnts_5_ ^=. OR Age_ArtStart_Yrs <=14) & /* adult 2nd line drug class*/ (Reg_ArtStart = "TDF-FTC-LPV/r" 
| Reg_ArtStart = "TDF-3TC-LPV/r" | Reg_ArtStart = "AZT-3TC-LPV/r" | Reg_ArtStart = "AZT-TDF-FTC-LPV/r" 
| Reg_ArtStart = "AZT-TDF-3TC-LPV/r" | Reg_ArtStart = "TDF-FTC-ATV/r" | Reg_ArtStart = "TDF-3TC-ATV/r" 
| Reg_ArtStart = "AZT-3TC-ATV/r" | Reg_ArtStart = "TDF-3TC-DRV/r" | Reg_ArtStart = "AZT-3TC-DRV/r")
THEN RegLne_ArtStart = "Peds.2nd.Line" & Reg_ArtStart = "ABC-3TC-LPV/r"; ELSE IF

(Age_ArtStaMnts_5_ =. OR Age_ArtStart_Yrs >14) & /* peads 1st line drug class*/ (Reg_ArtStart = "AZT-3TC-NVP" 
| Reg_ArtStart = "AZT-3TC-EFV" | Reg_ArtStart = "D4T-3TC-NVP" | Reg_ArtStart = "D4T-3TC-EFV" 
| Reg_ArtStart = "ABC-3TC-NVP" | Reg_ArtStart = "ABC-3TC-EFV" | Reg_ArtStart = "ABC-3TC-AZT" 
| Reg_ArtStart = "TDF-3TC-EFV" | Reg_ArtStart = "TDF-3TC-DTG" | Reg_ArtStart = "TDF-3TC-EFV400" 
| Reg_ArtStart = "ABC-3TC-DTG") THEN RegLne_ArtStart = "Adult.1st.Line" & Reg_ArtStart = "AZT-3TC-NVP"; ELSE IF

(Age_ArtStaMnts_5_ =. OR Age_ArtStart_Yrs >14) & /* peads 2nd line drug class*/ (Reg_ArtStart = "ABC-DDI-LPV/r" 
| Reg_ArtStart = "ABC-3TC-LPV/r" | Reg_ArtStart = "AZT-3TC-LPV/r" | Reg_ArtStart = "D4T-3TC-LPV/r" 
| Reg_ArtStart = "DDI-3TC-NVP" | Reg_ArtStart = "ABC-3TC-DDI" | Reg_ArtStart = "TDF-3TC-ATV/r" 
| Reg_ArtStart = "TDF-3TC-RAL" | Reg_ArtStart = "AZT-3TC-RAL") THEN RegLne_ArtStart = "Adult.2nd.Line" 
& Reg_ArtStart = "AZT-3TC-LPV/r";
run;

Re: To replace regimen line and regimen with standard format and fill up blanks accordingly

ballardw — Mon, 30 Jul 2018 16:38:42 GMT

@Ken_nuga wrote:

Please, I need help ASAP.

I have tried this using SAS 9.4 but the blank spaces remain blank and only the formats changed. Thanks.

You will likely get quicker help if you provide a description of what needs to be corrected and how to tell if the correction was the right one. I have no clue as to which "blank spaces" might be an issue.

Also your code is nearly useless without a data set to test.

First hint: Are you attempting to compare the FORMATTED values of your variables? Comparisons are done with the actual values not the format unless you do something that actually applies the format.

Second: if you want to test if a single variable has a value in a list of values the IN operator is much more compact and may execute quicker:

(Reg_ArtStart in ( "AZT-3TC-NVP"   "AZT-3TC-EFV"   "D4T-3TC-NVP"   "D4T-3TC-EFV" 
                   "ABC-3TC-NVP"   "ABC-3TC-EFV"   "ABC-3TC-AZT"   "TDF-3TC-EFV"   "TDF-3TC-DTG"   "TDF-3TC-EFV400" 
                   "ABC-3TC-DTG")
)

for instance.

Which if you need the formatted value of Reg_ArtStart for the comparison would look like:

(put(Reg_ArtStart,$Regimen_start.) in ( "AZT-3TC-NVP"   "AZT-3TC-EFV"   "D4T-3TC-NVP"   "D4T-3TC-EFV" 
                   "ABC-3TC-NVP"   "ABC-3TC-EFV"   "ABC-3TC-AZT"   "TDF-3TC-EFV"   "TDF-3TC-DTG"   "TDF-3TC-EFV400" 
                   "ABC-3TC-DTG")
)

maybe.

Re: To replace regimen line and regimen with standard format and fill up blanks accordingly

Ken_nuga — Thu, 02 Aug 2018 11:29:56 GMT

Thank you for your prompt response, sorry it`s been a busy reporting period for me. I have data pulled down from a patient-level DB and the format it has for regimen line and regimen (both at ART start and current) are not consistent with the CDC formats e.g. AZT/3TC/NVP or ZDV/3TC/NVP should both now be AZT-3TC-NVP. The formats actually applied successfully when I attempted to do so.

The next step will be to identify patient IDs with missing regimen line and fill up accordingly if the regimen is a 1st, 2nd or 3rd line drug based on age at ART start.

Then, should there be a unique ID where the age at ART start is that of a pediatric (0 to 14 years) but the regimen assigned is an adult drug at ART start (except D4T-3TC-NVP or D4T-3TC-EFV), such should be re-assigned AZT-3TC-NVP. Another scenario is where the patient is a paed and the regimen is a 1st line regimen but the regimen line is missing, such regimen line should be Peds.1st.Line.

Below is a sample data:

PUID_ART	Sex	DOB	Age_ArtStart_Yrs	Age_ArtStaMnts_5@	ArtStart_Datdmy	RegLne_ArtStart	Reg_ArtStart	Curr_RegLine	Curr_ART_Reg
179	Female	01-Nov-97	20		10-Jan-18		ABC/FTC/LPVr	Adult.1st.line	TDF/3TC/EFV
36	Male	01-Jan-82	35		14-Feb-17	Adult.1st.line	TDF/3TC/EFV	Adult.1st.line	TDF/3TC/EFV
39	Male	01-Jan-88	29		24-Feb-15	Adult.1st.line	TDF/3TC/EFV		ABC/FTC/LPVr
55	Female	05-Jul-77	37		24-Jan-15	Adult.1st.line	TDF/3TC/EFV		ABC/FTC/LPVr
58	Female	18-Jun-56	58		12-Mar-15		ABC/FTC/LPVr		ABC/FTC/LPVr
66	Male	11-May-82	33		15-May-15	Adult.1st.line	TDF/3TC/EFV	Adult.1st.line	TDF/3TC/EFV
69	Female	01-Jan-79	36		02-Jul-15		ABC/FTC/LPVr		ABC/FTC/LPVr
74	Female	01-Jan-76	39		31-Jul-15	Adult.1st.line	TDF/3TC/EFV	Adult.1st.line	TDF/3TC/EFV
75	Male	01-Jan-88	29		01-Aug-15		ABC/FTC/LPVr	Adult.1st.line	TDF/3TC/EFV
77	Female	03-Oct-85	29		14-Aug-15		ABC/FTC/LPVr		ABC/FTC/LPVr
79	Male	01-Jan-82	35		10-Aug-15		ABC/FTC/LPVr		ABC/FTC/LPVr
84	Female	26-Feb-84	31		11-Nov-15	Adult.1st.line	TDF/3TC/EFV		ABC/FTC/LPVr
91	Female	01-Jun-74	41		26-Nov-15	Adult.1st.line	TDF/3TC/EFV	Adult.1st.line	TDF/3TC/EFV
99	Female	21-Sep-86	29		02-Nov-15	Adult.1st.line	TDF/3TC/EFV	Adult.1st.line	TDF/3TC/EFV
116	Female	05-Mar-95	18		12-Feb-13		ABC/DDI/LPVr	Adult.1st.line	TDF/3TC/EFV
135	Female	04-Mar-96	18		25-Jun-14	Adult.1st.line	TDF/3TC/EFV	Adult.1st.line	TDF/3TC/EFV
137	Female	14-Nov-96	17		16-Apr-14		ABC/DDI/LPVr	Adult.2nd.line	ABC/FTC/LPVr
157	Female	31-Aug-13		9	02-Apr-14		ABC/DDI/LPVr	Adult.1st.line	TDF/3TC/EFV
159	Female	16-Jul-99	15		23-Jul-14	Adult.2nd.line	ABC/DDI/LPVr	Adult.2nd.line	ABC/DDI/LPVr
163	Female	17-Jul-04	9		31-Jul-13		ZDV/3TC/NVP	Peds.1st.line	ZDV/3TC/NVP
164	Male	04-Mar-04	11		18-Sep-13		ZDV/3TC/NVP	1st Line	ZDV/3TC/NVP
177	Male	10-Jun-11	5		03-Feb-16		ZDV/3TC/NVP	1st Line	ZDV/3TC/NVP
187	Male	06-Jun-05	8		01-Oct-13		ZDV/3TC/NVP	1st Line	ZDV/3TC/NVP
2318	Female	17-Jul-13		3	27-Oct-13	Adult.1st.line	ZDV/3TC/NVP	Adult.1st.line	ZDV/3TC/NVP
5	Female	08-Apr-08	8		11-Jan-17	Adult.1st.line	D4T/3TC/NVP	1st Line	D4T/3TC/NVP
60	Female	04-Oct-96	16		11-Sep-13		ABC/DDI/LPVr	Adult.2nd.line	ABC/FTC/LPVr
96	Male	10-Oct-13		14	17-Dec-14	Adult.1st.line	ZDV/3TC/NVP	Adult.1st.line	ZDV/3TC/NVP
102	Male	05-Jun-14		15	16-Sep-15	Adult.1st.line	ZDV/3TC/NVP	Adult.1st.line	ZDV/3TC/NVP

Regards.