Help running Macro for Calculating Summary Stats using the Kaplan-Meier Method

rshaw1 — Thu, 13 Dec 2018 21:23:31 GMT

I am trying to run the following macro in SAS Enterprise Guide version 7.1 which I found in Paper SDA-09, "A Macro for Calculating Summary Statistics on Left Censored Environmental Data using the Kaplan-Meier Method" authored by Dennis Beal. When I run the macro using my own data I get the following error message: "ERROR: Variable popn_num is not on file WORK.PEST_2017_RESULT_FORPROGRAM.” I'm a relative beginner is SAS coding and have not worked with macros much. Why am I getting this error? Here is what the 1st few records in my data file look like:

SAMPLE_PK	COMMOD	COMMTYPE	PESTCODE	chemical	RESULTS	HIT	CONCEN	LOD	CONUNIT
1	HY	RE	011	Captan	0.5	0		0.5	M
1	HY	RE	024	Diazinon	0.05	0		0.05	M
1	HY	RE	032	Diuron	0.002	0		0.002	M
1	HY	RE	042	Azinphos methyl	0.5	0		0.5	M
1	HY	RE	052	Malathion	0.05	0		0.05	M
1	HY	RE	057	Parathion methyl	0.05	0		0.05	M

I would like to calculate the KM-mean for each chemical in this file.

Here is the code I am trying to run:

/*Before running the SAS code, some initial macros must be executed. The following macro OBSNVARS simply stores the number of records and variables in a data set into SAS macro variables.*/

%macro obsnvars(ds);

%* this macro returns the number of variables and observations from a data set;

%global dset nvars nobs;

%let dset=&ds;

%let dsid = %sysfunc(open(&dset));

%if &dsid %then %do;

%let nobs =%sysfunc(attrn(&dsid,NOBS));

%let nvars=%sysfunc(attrn(&dsid,NVARS));

%let rc = %sysfunc(close(&dsid));

%end;

%else

%put Open for data set &dset failed - %sysfunc(sysmsg());

%mend obsnvars;

/*The DS_NAMES2 macro sets a number of SAS data sets together.*/

%macro ds_names2(name, num);

%do zz = 1 %to &num;

&name&zz.

%end;

%mend ds_names2;

/*The following macro definitions are determining the number of chemicals that will be run and a SORTBY macro variable where additional variables can be added for sorting the data.*/

%let N_POPNS =1;

%let SORTBY = chemical;

/*The macro calc_km calculates the KM method using Eqns. 1 – 6. The data set b4 (I changed b4 to WORK.PEST_2017_RESULT_FORPROGRAM) contains the data, where the variable HIT = 0 for censored results (non-detects),

/*and HIT = 1 for uncensored detected results. The variable RESULTS is the reported measurement from the laboratory for detects or the reporting limit for non-detects.*/

%macro calc_km;

%do POPNUM = 1 %to &N_POPNS;

data one&POPNUM.;

set WORK.PEST_2017_RESULT_FORPROGRAM;

where popn_num = &POPNUM.; run;

%obsnvars(one&POPNUM.); %let TOTN = &nobs;

proc sort data=one&POPNUM.; by &SORTBY RESULTS;

proc summary data=one&POPNUM.;

var results;

where hit=0; ** nondetects only;

output out=nondets(drop=_type_ _freq_) n=nds; run;

%obsnvars(nondets); %let N_NONDETECTS = &nobs;

proc summary data=one&POPNUM.;

var results;

where HIT=1; ** detects only;

by &SORTBY results;

output out=distinct&POPNUM.(drop=_type_ _freq_) n=mi;

proc print data=distinct&POPNUM.; run;

%obsnvars(distinct&POPNUM.); %let N_DISTINCT_LEVELS = &nobs;

data hitsonly;

set one&POPNUM.;

where hit=1; run;

%obsnvars(hitsonly); %let N_DETECTS = &nobs;

%macro calc_ni;

proc transpose data=distinct&POPNUM. out=outt&POPNUM.; var results; run;

** detected distinct results only;

data a&POPNUM.;

set one&POPNUM.;

if _N_=1 then set outt&POPNUM.;

%do i = 1 %to &N_DISTINCT_LEVELS;

if results <= col&i. then N&i.=1; else N&i.=0;

if results = col&i. and hit=1 then M&i.=1; else M&i.=0;

%end; run;

proc summary data=a&POPNUM.;

var N1-N&N_DISTINCT_LEVELS. M1-M&N_DISTINCT_LEVELS.;

by &SORTBY col1-col&N_DISTINCT_LEVELS;

output out=calc_ni_out&POPNUM.(drop=_type_ _freq_)

sum=N1-N&N_DISTINCT_LEVELS. M1-M&N_DISTINCT_LEVELS.;

proc print data=calc_ni_out&POPNUM.; run;

proc summary data=a&POPNUM.;

var hit;

output out=hitsum&POPNUM.(drop=_type_ _freq_) sum=N_DETECTS;

data calc_cdf&POPNUM.;

set calc_ni_out&POPNUM.;

if _N_=1 then set hitsum&POPNUM.;

N_DISTINCT_DETECT_LEVELS = &N_DISTINCT_LEVELS;

CDF&N_DISTINCT_LEVELS = 1;

CDF0 = 0;

%do i = &N_DISTINCT_LEVELS %to 2 %by -1;

%let N_DISTINCT_LEVELS_M1 = %eval(&i. - 1);

CDF&N_DISTINCT_LEVELS_M1 = cdf&i. * (n&i. - m&i.) / n&i.;

%end;

KM_MEAN=0;

%do i = 1 %to &N_DISTINCT_LEVELS; ** calculate KM mean ;

%let im1 = %eval(&i. - 1);

KM_MEAN = KM_MEAN + col&i. * (cdf&i. - cdf&im1.);

%end;

KM_VAR=0;

%do i = 1 %to &N_DISTINCT_LEVELS; ** calculate KM standard deviation;

%let im1 = %eval(&i. - 1);

KM_VAR = KM_VAR + (col&i. - km_mean)**2 * (cdf&i. - cdf&im1.);

%end;

KM_STD = sqrt(km_var);

%do j = 1 %to &N_DISTINCT_LEVELS - 1; ** calculate KM SE of the mean;

a&j. = 0;

%do i = 1 %to &j;

%let ip1 = %eval(&i. + 1);

a&j. = a&j. + (col&ip1. - col&i.) * cdf&i.;

%end;

sum = 0;

%do i = 1 %to &N_DISTINCT_LEVELS - 1;

%let ip1 = %eval(&i. + 1);

sum = sum + a&i.**2 * m&ip1. / (n&ip1. * (n&ip1. - m&ip1.));

%end;

if n_detects > 1 then KM_STDERR2 = n_detects * sum / (n_detects - 1);

KM_STDERR = sqrt(km_stderr2);

drop sum; run;

%mend calc_ni;

%if &N_DISTINCT_LEVELS > 1 and &N_NONDETECTS > 0 %then %do;

%calc_ni

%end;

data allkm;

set %ds_names2(calc_cdf, &N_POPNS);

keep &SORTBY n_distinct_detect_levels km_mean km_var km_std km_stderr; run;

proc print data=allkm; run;

%mend calc_km;

%calc_km

Re: Help running Macro for Calculating Summary Stats using the Kaplan-Meier Method

PaigeMiller — Thu, 13 Dec 2018 23:05:02 GMT

The error message is relatively clear. The variable is not in the dataset. SAS expects it to be in there. Yoou need to figure out why this is happening by examining the code and your input data. Actually look in the data set mentioned. Actually look in your input data set. Do you find it?

Re: Help running Macro for Calculating Summary Stats using the Kaplan-Meier Method

rshaw1 — Thu, 13 Dec 2018 23:42:13 GMT

It's not in my data set. I don't know what this variable is supposed to be. Unfortunately, I don't have access to the data that was used in the paper, I can only go off of the variables they defined in the text and comments within the code. This variable (popn_num) looks like it should be defined by some of the macro variables - it's right at the beginning of the code:

%macro calc_km;

%do POPNUM = 1 %to &N_POPNS;

data one&POPNUM.;

set WORK.PEST_2017_RESULT_FORPROGRAM;

where popn_num = &POPNUM.; run;

Thank you for your help!

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Help running Macro for Calculating Summary Stats using the Kaplan-Meier Method

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