Dose Reduction Flag

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

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

1# Reference solution for the yamaa benchmark adam-adex-dose-reduction (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)910ex <- read_csv(11  "/app/input/ex.csv",12  col_types = cols(EXSEQ = col_integer(), .default = col_character())13)1415adex <- ex |>16  mutate(17    EXSTDTM = if_else(18      !is.na(EXSTDTM) & nchar(EXSTDTM) == 16L, paste0(EXSTDTM, ":00"), EXSTDTM19    ),20    EXDOSE = suppressWarnings(as.numeric(EXDOSE))21  ) |>22  # Chronological treatment-start order within each subject, breaking23  # timestamp ties by sequence number.24  arrange(USUBJID, EXSTDTM, EXSEQ) |>25  group_by(USUBJID) |>26  mutate(27    PREVDOSE = lag(EXDOSE),28    # Y when the current dose is lower than the previous one; no value for29    # the first record and whenever either dose is zero or missing. The30    # previous dose is always the administration just before.31    DOSREDFL = if_else(32      !is.na(EXDOSE) & EXDOSE != 0 & !is.na(PREVDOSE) & PREVDOSE != 0 &33        EXDOSE < PREVDOSE,34      "Y",35      NA_character_36    )37  ) |>38  ungroup() |>39  select(STUDYID, USUBJID, EXSEQ, EXSTDTM, EXDOSE, DOSREDFL)4041dir.create("/app/output", showWarnings = FALSE)42write_csv(adex, "/app/output/adex.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adex-dose-reduction (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 ADEX from EX: flag administrations whose dose is lower than the8dose of the subject's immediately preceding administration."""910import csv1112INPUT = "/app/input/ex.csv"13OUTPUT = "/app/output/adex.csv"1415COLUMNS = ["STUDYID", "USUBJID", "EXSEQ", "EXSTDTM", "EXDOSE", "DOSREDFL"]161718def parse_dose(text):19    """Return the numeric dose, or None when the value is missing."""20    if text is None or text.strip() == "":21        return None22    return float(text)232425def main():26    with open(INPUT, newline="") as f:27        rows = list(csv.DictReader(f))2829    # Order administrations within each subject by start date/time,30    # breaking ties by sequence number.31    ordered = sorted(32        rows,33        key=lambda r: (r["USUBJID"], r["EXSTDTM"], int(r["EXSEQ"])),34    )3536    previous = {}  # subject -> numeric dose of the preceding administration37    for row in ordered:38        subject = row["USUBJID"]39        current = parse_dose(row["EXDOSE"])40        flag = ""41        if subject in previous:42            prev = previous[subject]43            if (44                current is not None45                and prev is not None46                and current != 047                and prev != 048                and current < prev49            ):50                flag = "Y"51        row["DOSREDFL"] = flag52        previous[subject] = current5354    with open(OUTPUT, "w", newline="") as f:55        writer = csv.DictWriter(f, fieldnames=COLUMNS)56        writer.writeheader()57        for row in ordered:58            writer.writerow({col: row[col] for col in COLUMNS})596061if __name__ == "__main__":62    main()

1/* opensas reference solution for the yamaa benchmark adam-adex-dose-reduction.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ex;6  length STUDYID USUBJID EXSTDTM $1024;7  infile "/app/input/ex.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. EXSEQ EXSTDTM : $char1024. EXDOSE;9run;1011proc sort data=ex out=ordered; by STUDYID USUBJID EXSTDTM EXSEQ; run;12data result;13  length DOSREDFL $1;14  retain previous;15  set ordered; by STUDYID USUBJID;16  if first.USUBJID then previous=.;17  if EXDOSE>0 and previous>0 and EXDOSE<previous then DOSREDFL='Y';18  previous=EXDOSE;19run;2021proc sql;22  create table final as select STUDYID, USUBJID, EXSEQ, EXSTDTM, EXDOSE, DOSREDFL from result;23quit;24proc export data=final outfile="/app/output/adex.csv" dbms=csv replace; run;