Adverse Event Incidence Results

1library(yamaa)23yamaa_spec("input/subjects.schema.yaml")$run()$save()4yamaa_spec("spec.yaml")$run()$output

1import yamaa23yamaa.spec("input/subjects.schema.yaml").run().save()4yamaa.spec("spec.yaml").run().output

1subjects <- read.csv("/app/input/adsl.csv", stringsAsFactors = FALSE)2events <- read.csv("/app/input/adae.csv", stringsAsFactors = FALSE)3subjects <- subjects[subjects$SAFFL == "Y", ]4events <- events[events$TRTEMFL == "Y", ]5subject_key <- paste(subjects$STUDYID, subjects$USUBJID, sep = "\r")6event_key <- paste(events$STUDYID, events$USUBJID, sep = "\r")7subjects$EVENTN <- as.integer(subject_key %in% event_key)8groups <- split(subjects, interaction(subjects$STUDYID, subjects$TRT01PN,9                                      subjects$TRT01P, drop = TRUE))10result <- do.call(rbind, lapply(groups, function(group) {11  count <- sum(group$EVENTN)12  data.frame(STUDYID = group$STUDYID[1], ANALYSISID = "AEINC",13    ANALYSISSETID = "SAFETY", DATASET = "ADAE", VARIABLE = "USUBJID",14    ANALYSISSET = "SAFFL = 'Y'", DATASUBSET = "TRTEMFL = 'Y'",15    GROUPINGID = "TRT01P", GROUPORDER = group$TRT01PN[1],16    GROUPLEVEL = group$TRT01P[1], METHODID = "AEINCIDENCE",17    OPERATIONID = c("COUNT", "PERCENT"),18    RESULT = c(count, 100 * count / nrow(group)))19}))20result <- result[order(result$STUDYID, result$GROUPORDER,21                       result$OPERATIONID), ]22write.csv(result, "/app/output/results.csv", row.names = FALSE, na = "")

1# Reference solution for the yamaa benchmark adam-results-ae-incidence (Python track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67"""Create the RESULTS dataset (AE incidence) from ADAE and ADSL.89One record per planned treatment group and operation (COUNT, PERCENT),10covering only safety subjects (SAFFL = 'Y' in ADSL).  A qualifying event11is an adverse event with TRTEMFL = 'Y'; a subject with at least one12qualifying event counts once.13"""1415import csv16from collections import OrderedDict1718INPUT_DIR = "/app/input"19OUTPUT_DIR = "/app/output"202122def read_csv(path):23    with open(path, newline="", encoding="utf-8") as fh:24        return list(csv.DictReader(fh))252627def main():28    adsl = read_csv(f"{INPUT_DIR}/adsl.csv")29    adae = read_csv(f"{INPUT_DIR}/adae.csv")3031    studyid = adsl[0]["STUDYID"] if adsl else ""3233    # Planned treatment groups, ordered by the planned treatment code34    # (TRT01PN); GROUPLEVEL is the planned treatment name (TRT01P).35    groups = OrderedDict()  # TRT01PN -> {"name": ..., "subjects": set}36    safety_subjects = set()37    for row in adsl:38        if row["SAFFL"] != "Y":39            continue40        safety_subjects.add(row["USUBJID"])41        code = row["TRT01PN"]42        group = groups.setdefault(code, {"name": row["TRT01P"], "subjects": set()})43        group["subjects"].add(row["USUBJID"])4445    # Safety subjects with at least one qualifying (TRTEMFL = 'Y') event.46    subjects_with_event = set()47    for row in adae:48        if row["TRTEMFL"] == "Y" and row["USUBJID"] in safety_subjects:49            subjects_with_event.add(row["USUBJID"])5051    columns = [52        "STUDYID", "ANALYSISID", "ANALYSISSETID", "DATASET", "VARIABLE",53        "ANALYSISSET", "DATASUBSET", "GROUPINGID", "GROUPORDER",54        "GROUPLEVEL", "METHODID", "OPERATIONID", "RESULT",55    ]5657    out_rows = []58    for code in sorted(groups, key=lambda c: (int(c) if c.lstrip("-").isdigit() else c, c)):59        group = groups[code]60        total = len(group["subjects"])61        count = len(group["subjects"] & subjects_with_event)62        percent = count / total * 100 if total else 0.063        base = {64            "STUDYID": studyid,65            "ANALYSISID": "AEINC",66            "ANALYSISSETID": "SAFETY",67            "DATASET": "ADAE",68            "VARIABLE": "USUBJID",69            "ANALYSISSET": "SAFFL = 'Y'",70            "DATASUBSET": "TRTEMFL = 'Y'",71            "GROUPINGID": "TRT01P",72            "GROUPORDER": code,73            "GROUPLEVEL": group["name"],74            "METHODID": "AEINCIDENCE",75        }76        count_row = dict(base, OPERATIONID="COUNT", RESULT=str(count))77        percent_row = dict(base, OPERATIONID="PERCENT", RESULT=repr(percent))78        out_rows.extend([count_row, percent_row])7980    with open(f"{OUTPUT_DIR}/results.csv", "w", newline="", encoding="utf-8") as fh:81        writer = csv.DictWriter(fh, fieldnames=columns)82        writer.writeheader()83        writer.writerows(out_rows)8485    print(f"Wrote {len(out_rows)} records to {OUTPUT_DIR}/results.csv")868788if __name__ == "__main__":89    main()

1/* opensas reference: long-format operations from the safety population. */2data subjects;3  length STUDYID USUBJID $80 TRT01P $20 SAFFL $1;4  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover;5  input STUDYID : $80. USUBJID : $80. TRT01P : $20. TRT01PN SAFFL : $1.;6  if SAFFL='Y';7run;8data events;9  length STUDYID USUBJID $80 TRTEMFL $1;10  infile "/app/input/adae.csv" dsd dlm="," firstobs=2 truncover;11  input STUDYID : $80. USUBJID : $80. ASEQ TRTEMFL : $1.;12  if TRTEMFL='Y';13run;14proc sql;15  create table qualifying as select distinct STUDYID, USUBJID from events;16  create table counted as select s.STUDYID, s.USUBJID, s.TRT01P, s.TRT01PN,17    case when e.USUBJID is not null then 1 else 0 end as EVENTN18  from subjects s left join qualifying e19    on s.STUDYID=e.STUDYID and s.USUBJID=e.USUBJID;20  create table totals as select STUDYID, TRT01P, TRT01PN,21    sum(EVENTN) as NSUBJ, count(USUBJID) as DENOM22  from counted group by STUDYID, TRT01P, TRT01PN;23quit;24data results;25  length ANALYSISID $8 ANALYSISSETID $8 DATASET $8 VARIABLE $826    ANALYSISSET DATASUBSET $24 GROUPINGID $8 GROUPLEVEL $2027    METHODID $16 OPERATIONID $8;28  set totals;29  ANALYSISID='AEINC'; ANALYSISSETID='SAFETY'; DATASET='ADAE';30  VARIABLE='USUBJID'; ANALYSISSET="SAFFL = 'Y'";31  DATASUBSET="TRTEMFL = 'Y'"; GROUPINGID='TRT01P';32  GROUPORDER=TRT01PN; GROUPLEVEL=TRT01P; METHODID='AEINCIDENCE';33  OPERATIONID='COUNT'; RESULT=NSUBJ; output;34  OPERATIONID='PERCENT'; RESULT=100*NSUBJ/DENOM; output;35run;36proc sql;37  create table final as select STUDYID, ANALYSISID, ANALYSISSETID,38    DATASET, VARIABLE, ANALYSISSET, DATASUBSET, GROUPINGID, GROUPORDER,39    GROUPLEVEL, METHODID, OPERATIONID, RESULT from results40  order by STUDYID, GROUPORDER, OPERATIONID;41quit;42proc export data=final outfile="/app/output/results.csv" dbms=csv replace;43run;