Carry a Previous Visit's Change

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

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

1# Reference solution for the yamaa benchmark adam-adlbc-window-chain (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)910lb <- read_csv(11  "/app/input/lb.csv",12  col_types = cols(13    LBSTRESN = col_double(),14    VISITNUM = col_integer(),15    .default = col_character()16  )17)1819# Albumin results with a numeric value; a record without one gets no row,20# so the lag compares against the latest earlier visit with a result.21alb <- lb |>22  filter(LBTESTCD %in% "ALB", !is.na(LBSTRESN)) |>23  mutate(PARAMCD = "_ALB", AVISITN = VISITNUM, AVAL = LBSTRESN) |>24  arrange(STUDYID, USUBJID, AVISITN)2526# The change since the previous visit with a result, and its lag: the27# previous visit's change. A zero change is a real value.28adlbc <- alb |>29  group_by(STUDYID, USUBJID) |>30  mutate(31    PREV_AVAL = lag(AVAL),32    CHG = AVAL - PREV_AVAL,33    PREV2 = lag(CHG)34  ) |>35  ungroup() |>36  select(STUDYID, USUBJID, PARAMCD, AVISITN, AVAL, PREV_AVAL, CHG, PREV2) |>37  arrange(STUDYID, USUBJID, AVISITN)3839dir.create("/app/output", showWarnings = FALSE)40write_csv(adlbc, "/app/output/adlbc.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adlbc-window-chain (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 csv89INPUT_DIR = "/app/input"10OUTPUT_DIR = "/app/output"111213def fmt(value):14    if value is None:15        return ""16    return repr(float(value))171819def main():20    with open(f"{INPUT_DIR}/lb.csv", newline="") as f:21        rows = list(csv.DictReader(f))2223    # Keep only albumin records with a numeric result.24    records = []25    for row in rows:26        if row["LBTESTCD"] != "ALB":27            continue28        raw = (row["LBSTRESN"] or "").strip()29        if raw == "":30            continue31        try:32            aval = float(raw)33        except ValueError:34            continue35        records.append(36            {37                "STUDYID": row["STUDYID"],38                "USUBJID": row["USUBJID"],39                "AVISITN": int(row["VISITNUM"]),40                "AVAL": aval,41            }42        )4344    # Order by subject (first appearance) then visit number.45    subject_order = {}46    for rec in records:47        if rec["USUBJID"] not in subject_order:48            subject_order[rec["USUBJID"]] = len(subject_order)49    records.sort(key=lambda r: (subject_order[r["USUBJID"]], r["AVISITN"]))5051    out = []52    prev_aval = {}53    prev_chg = {}54    for rec in records:55        subj = rec["USUBJID"]56        p_aval = prev_aval.get(subj)57        chg = None if p_aval is None else rec["AVAL"] - p_aval58        p_chg = prev_chg.get(subj)59        out.append(60            {61                "STUDYID": rec["STUDYID"],62                "USUBJID": subj,63                "PARAMCD": "_ALB",64                "AVISITN": rec["AVISITN"],65                "AVAL": rec["AVAL"],66                "PREV_AVAL": p_aval,67                "CHG": chg,68                "PREV2": p_chg,69            }70        )71        prev_aval[subj] = rec["AVAL"]72        prev_chg[subj] = chg7374    fieldnames = ["STUDYID", "USUBJID", "PARAMCD", "AVISITN", "AVAL",75                  "PREV_AVAL", "CHG", "PREV2"]76    with open(f"{OUTPUT_DIR}/adlbc.csv", "w", newline="") as f:77        writer = csv.DictWriter(f, fieldnames=fieldnames)78        writer.writeheader()79        for row in out:80            writer.writerow(81                {82                    "STUDYID": row["STUDYID"],83                    "USUBJID": row["USUBJID"],84                    "PARAMCD": row["PARAMCD"],85                    "AVISITN": row["AVISITN"],86                    "AVAL": fmt(row["AVAL"]),87                    "PREV_AVAL": fmt(row["PREV_AVAL"]),88                    "CHG": fmt(row["CHG"]),89                    "PREV2": fmt(row["PREV2"]),90                }91            )929394if __name__ == "__main__":95    main()

1/* opensas reference solution for the yamaa benchmark adam-adlbc-window-chain.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data lb;6  length STUDYID USUBJID LBTESTCD $1024;7  infile "/app/input/lb.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. LBTESTCD : $char1024. LBSTRESN VISITNUM;9run;1011data collected;12  length PARAMCD $8;13  set lb; if LBTESTCD in ('ALB') and not missing(LBSTRESN);14  PARAMCD=cats('_',LBTESTCD); AVISITN=VISITNUM; AVAL=LBSTRESN;15run;16proc sort data=collected; by STUDYID USUBJID PARAMCD AVISITN; run;17data result;18  retain previous priorchange;19  set collected; by STUDYID USUBJID PARAMCD;20  if first.PARAMCD then do; previous=.; priorchange=.; end;21  PREV_AVAL=previous; CHG=AVAL-PREV_AVAL; PREV2=priorchange;22  previous=AVAL; priorchange=CHG;23run;2425proc sql;26  create table final as select STUDYID, USUBJID, PARAMCD, AVISITN, AVAL, PREV_AVAL, CHG, PREV2 from result;27quit;28proc export data=final outfile="/app/output/adlbc.csv" dbms=csv replace; run;