Lag a Result Across Visits While Constructing Change Parameters

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

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

1# Reference solution for the yamaa benchmark adam-adlbc-row-window (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# Build the change parameters from albumin and bilirubin; any other test20# produces no rows. A record with no numeric result gets no row.21adbc <- lb |>22  filter(LBTESTCD %in% c("ALB", "BILI"), !is.na(LBSTRESN), !is.na(VISITNUM)) |>23  mutate(24    PARAMCD = case_when(25      LBTESTCD == "ALB" ~ "_ALB",26      LBTESTCD == "BILI" ~ "_BILI"27    ),28    AVISITN = VISITNUM,29    AVAL = LBSTRESN30  ) |>31  arrange(USUBJID, PARAMCD, AVISITN) |>32  group_by(USUBJID, PARAMCD) |>33  mutate(34    PREV_AVAL = lag(AVAL),35    CHG = AVAL - PREV_AVAL36  ) |>37  ungroup() |>38  select(STUDYID, USUBJID, PARAMCD, AVISITN, AVAL, PREV_AVAL, CHG)3940dir.create("/app/output", showWarnings = FALSE)41write_csv(adbc, "/app/output/adlbc.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adlbc-row-window (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 ADLBC from LB: one record per subject per parameter per visit,8with the previous visit's result and the change since the previous visit."""910import csv11from decimal import Decimal, InvalidOperation1213INPUT_CSV = "/app/input/lb.csv"14OUTPUT_CSV = "/app/output/adlbc.csv"1516PARAM_BY_TEST = {"ALB": "_ALB", "BILI": "_BILI"}171819def parse_number(text):20    """Return the Decimal value of a collected result, or None."""21    if text is None:22        return None23    text = text.strip()24    if not text:25        return None26    try:27        return Decimal(text)28    except InvalidOperation:29        return None303132def fmt(value):33    """Render a Decimal without exponent notation, or blank for None."""34    if value is None:35        return ""36    return format(value, "f")373839def main():40    with open(INPUT_CSV, newline="") as handle:41        rows = list(csv.DictReader(handle))4243    # Keep only ALB/BILI records with a numeric result.44    kept = []45    for row in rows:46        testcd = (row.get("LBTESTCD") or "").strip()47        if testcd not in PARAM_BY_TEST:48            continue49        aval = parse_number(row.get("LBSTRESN"))50        if aval is None:51            continue52        kept.append(53            {54                "STUDYID": row["STUDYID"],55                "USUBJID": row["USUBJID"],56                "PARAMCD": PARAM_BY_TEST[testcd],57                "AVISITN": int(row["VISITNUM"]),58                "AVAL": aval,59            }60        )6162    # Order by subject, parameter, then visit number so each row's63    # previous value is the latest earlier visit for the same64    # subject and parameter.65    kept.sort(key=lambda r: (r["STUDYID"], r["USUBJID"], r["PARAMCD"], r["AVISITN"]))6667    previous = {}68    out_rows = []69    for record in kept:70        key = (record["STUDYID"], record["USUBJID"], record["PARAMCD"])71        prev = previous.get(key)72        chg = record["AVAL"] - prev if prev is not None else None73        out_rows.append(74            [75                record["STUDYID"],76                record["USUBJID"],77                record["PARAMCD"],78                str(record["AVISITN"]),79                fmt(record["AVAL"]),80                fmt(prev),81                fmt(chg),82            ]83        )84        previous[key] = record["AVAL"]8586    with open(OUTPUT_CSV, "w", newline="") as handle:87        writer = csv.writer(handle)88        writer.writerow(89            ["STUDYID", "USUBJID", "PARAMCD", "AVISITN", "AVAL", "PREV_AVAL", "CHG"]90        )91        writer.writerows(out_rows)929394if __name__ == "__main__":95    main()

1/* opensas reference solution for the yamaa benchmark adam-adlbc-row-window.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','BILI') 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 from result;27quit;28proc export data=final outfile="/app/output/adlbc.csv" dbms=csv replace; run;