Derive log10 neutralizing antibody titers

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

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

1# Reference solution for the yamaa benchmark adam-adis-log-titer (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)910is_in <- read_csv(11  "/app/input/is.csv",12  col_types = cols(13    ISSTRESN = col_double(),14    ISLLOQ = col_double(),15    .default = col_character()16  )17)1819# A titer below the lower limit of quantitation gives no record; a record20# whose titer has no value stays.21adis <- is_in |>22  filter(is.na(ISSTRESN) | ISSTRESN >= ISLLOQ) |>23  mutate(24    PARAMCD = "NABLOG10",25    AVISIT = VISIT,26    AVAL = log10(ISSTRESN)27  ) |>28  select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL)2930dir.create("/app/output", showWarnings = FALSE)31write_csv(adis, "/app/output/adis.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adis-log-titer (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 1.67import csv8import math910INPUT_CSV = "/app/input/is.csv"11OUTPUT_CSV = "/app/output/adis.csv"121314def number(text):15    text = text.strip()16    return float(text) if text else None171819def main():20    with open(INPUT_CSV, newline="") as f:21        rows = list(csv.DictReader(f))2223    fieldnames = ["STUDYID", "USUBJID", "PARAMCD", "AVISIT", "AVAL"]24    with open(OUTPUT_CSV, "w", newline="") as f:25        writer = csv.DictWriter(f, fieldnames=fieldnames)26        writer.writeheader()27        for row in rows:28            titer = number(row["ISSTRESN"])29            # A titer below the lower limit of quantitation gives no record;30            # a record whose titer has no value stays.31            if titer is not None and titer < number(row["ISLLOQ"]):32                continue33            writer.writerow(34                {35                    "STUDYID": row["STUDYID"],36                    "USUBJID": row["USUBJID"],37                    "PARAMCD": "NABLOG10",38                    "AVISIT": row["VISIT"],39                    "AVAL": "" if titer is None else repr(math.log10(titer)),40                }41            )424344if __name__ == "__main__":45    main()

1/* opensas reference solution for the yamaa benchmark adam-adis-log-titer.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data is;6  length STUDYID USUBJID ISTESTCD $40 ISTEST $60 VISIT $40;7  infile "/app/input/is.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char40. USUBJID : $char40. ISTESTCD : $char40.9        ISTEST : $char60. VISITNUM VISIT : $char40. ISSTRESN ISLLOQ;10run;1112/* A titer below the lower limit of quantitation gives no record; a record13   whose titer has no value stays. */14data adis;15  set is;16  where missing(ISSTRESN) or ISSTRESN >= ISLLOQ;17  length PARAMCD $8 AVISIT $40;18  PARAMCD = 'NABLOG10';19  AVISIT = VISIT;20  if not missing(ISSTRESN) then AVAL = log10(ISSTRESN);21  keep STUDYID USUBJID PARAMCD AVISIT AVAL;22run;2324proc sql;25  create table final as26    select STUDYID, USUBJID, PARAMCD, AVISIT, AVAL from adis;27quit;28proc export data=final outfile="/app/output/adis.csv" dbms=csv replace; run;