Fever Occurrence

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

1import yamaa23yamaa.spec("spec.yaml").run().output

1# Reference solution for the yamaa benchmark adam-adfa-fever (R 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 1.67library(dplyr, warn.conflicts = FALSE)8library(readr)910vs <- read_csv(11  "/app/input/vs.csv",12  col_types = cols(13    VSSEQ = col_integer(),14    VSSTRESN = col_double(),15    .default = col_character()16  )17)1819# Only temperature records in the reactogenicity category qualify.20adfa <- vs |>21  filter(VSTESTCD == "TEMP", VSCAT == "REACTOGENICITY") |>22  mutate(23    DOMAIN = "ADFA",24    PARAMCD = "FEVER",25    PARAM = "Fever Occurrence",26    # VSSTRESN is the standard result in C, even for a temperature27    # collected in Fahrenheit.28    AVALC = case_when(29      VSSTRESN >= 38 ~ "Y",30      VSSTRESN < 38 ~ "N"31    ),32    AVAL = case_when(33      AVALC == "Y" ~ 1,34      AVALC == "N" ~ 035    ),36    ADT = as.Date(substr(VSDTC, 1, 10)),37    SRCDOM = "VS",38    SRCVAR = "VSSTRESN",39    SRCSEQ = VSSEQ40  ) |>41  # Number each subject's records 1, 2, 3 ... in assessment-date order,42  # the collected sequence breaking ties on the same date.43  arrange(STUDYID, USUBJID, ADT, VSSEQ) |>44  group_by(STUDYID, USUBJID) |>45  mutate(ASEQ = row_number()) |>46  ungroup() |>47  arrange(USUBJID, ASEQ) |>48  select(49    DOMAIN, STUDYID, USUBJID, ASEQ, PARAMCD, PARAM,50    AVAL, AVALC, ADT, SRCDOM, SRCVAR, SRCSEQ51  )5253dir.create("/app/output", showWarnings = FALSE)54write_csv(adfa, "/app/output/adfa.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adfa-fever (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 ADFA (Fever Occurrence) from the VS dataset.89One record per qualifying temperature record: VSTESTCD "TEMP" in the10"REACTOGENICITY" category. AVALC is "Y" for a temperature of 38 C or11higher and "N" below that, judged on the standard result VSSTRESN, which12SDTM holds in "C" even when the collected result is in Fahrenheit; it has13no value when the result is missing. AVAL is 1 for "Y" and 0 for "N".14"""1516import csv1718INPUT_VS = "/app/input/vs.csv"19OUTPUT_ADFA = "/app/output/adfa.csv"2021COLUMNS = [22    "DOMAIN", "STUDYID", "USUBJID", "ASEQ", "PARAMCD", "PARAM",23    "AVAL", "AVALC", "ADT", "SRCDOM", "SRCVAR", "SRCSEQ",24]252627def main():28    with open(INPUT_VS, newline="", encoding="utf-8") as f:29        rows = list(csv.DictReader(f))3031    qualifying = [32        r for r in rows33        if r["VSTESTCD"] == "TEMP" and r["VSCAT"] == "REACTOGENICITY"34    ]3536    # Group by subject, keeping first-appearance order of subjects.37    subjects = []38    by_subject = {}39    for r in qualifying:40        key = (r["STUDYID"], r["USUBJID"])41        if key not in by_subject:42            by_subject[key] = []43            subjects.append(key)44        by_subject[key].append(r)4546    out = []47    for studyid, usubjid in subjects:48        recs = by_subject[(studyid, usubjid)]49        recs.sort(key=lambda r: (r["VSDTC"][:10], float(r["VSSEQ"])))50        for i, r in enumerate(recs, start=1):51            result = r["VSSTRESN"].strip()52            if result == "":53                avalc = ""54                aval = ""55            elif float(result) >= 38:56                avalc = "Y"57                aval = "1"58            else:59                avalc = "N"60                aval = "0"61            seq = r["VSSEQ"].strip()62            srcseq = str(int(float(seq))) if seq else ""63            out.append({64                "DOMAIN": "ADFA",65                "STUDYID": studyid,66                "USUBJID": usubjid,67                "ASEQ": str(i),68                "PARAMCD": "FEVER",69                "PARAM": "Fever Occurrence",70                "AVAL": aval,71                "AVALC": avalc,72                "ADT": r["VSDTC"][:10],73                "SRCDOM": "VS",74                "SRCVAR": "VSSTRESN",75                "SRCSEQ": srcseq,76            })7778    with open(OUTPUT_ADFA, "w", newline="", encoding="utf-8") as f:79        writer = csv.DictWriter(f, fieldnames=COLUMNS)80        writer.writeheader()81        writer.writerows(out)828384if __name__ == "__main__":85    main()

1/* opensas reference solution for the yamaa benchmark adam-adfa-fever.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data vs;6  length STUDYID USUBJID VSTESTCD VSCAT VSORRES VSORRESU VSSTRESU VSSTAT VSDTC $1024;7  infile "/app/input/vs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VSTESTCD : $char1024. VSCAT : $char1024. VSORRES : $char1024. VSORRESU : $char1024. VSSTRESN VSSTRESU : $char1024. VSSTAT : $char1024. VSDTC : $char1024.;9run;1011data dated; set vs; length ADT $10; ADT=substr(VSDTC,1,10); NODATE=missing(ADT); run;12proc sort data=dated(where=(VSTESTCD='TEMP' and VSCAT='REACTOGENICITY')) out=ordered; by STUDYID USUBJID NODATE ADT VSSEQ; run;13data result;14  length DOMAIN $4 PARAMCD $16 PARAM $40 AVALC $1 ADT $10 SRCDOM $2 SRCVAR $16;15  set ordered; by STUDYID USUBJID;16  if first.USUBJID then ASEQ=0; ASEQ+1;17  DOMAIN='ADFA'; PARAMCD='FEVER'; PARAM='Fever Occurrence'; ADT=substr(VSDTC,1,10);18  SRCDOM='VS'; SRCVAR='VSSTRESN'; SRCSEQ=VSSEQ;19  /* VSSTRESN is the standard result in C, even when collected in F. */20  if not missing(VSSTRESN) then do;21    if VSSTRESN>=38 then do; AVAL=1; AVALC='Y'; end;22    else do; AVAL=0; AVALC='N'; end;23  end;24run;2526proc sql;27  create table final as select DOMAIN, STUDYID, USUBJID, ASEQ, PARAMCD, PARAM, AVAL, AVALC, ADT, SRCDOM, SRCVAR, SRCSEQ from result;28quit;29proc export data=final outfile="/app/output/adfa.csv" dbms=csv replace; run;