Placebo-Corrected ECG Change from Baseline

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

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

1# Reference solution for the yamaa benchmark adam-adeg-placebo-corrected-change (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)910adeg <- read_csv(11  "/app/input/adeg_raw.csv",12  col_types = cols(13    APERIOD = col_integer(), APERDAY = col_integer(),14    ATPTN = col_double(), AVAL = col_double(),15    BASE = col_double(), CHG = col_double(),16    .default = col_character()17  ),18  na = ""19)2021adeg <- adeg |>22  mutate(23    after_baseline = is.na(ABLFL) | ABLFL != "Y",24    ACOMPFL = if_else(after_baseline & TRTA == "Placebo", "Y", NA_character_)25  )2627# The placebo group: every comparator record of the same parameter and28# nominal time point, all cohorts together. Each mean skips missing values;29# a mean over no value has none.30mean_or_na <- function(x) if (all(is.na(x))) NA_real_ else mean(x, na.rm = TRUE)3132placebo <- adeg |>33  filter(ACOMPFL %in% "Y") |>34  group_by(PARAMCD, ATPTN) |>35  summarise(36    COMP = mean_or_na(AVAL),37    COMPBASE = mean_or_na(BASE),38    COMPCHG = mean_or_na(CHG),39    .groups = "drop"40  )4142adeg_out <- adeg |>43  left_join(placebo, by = c("PARAMCD", "ATPTN"),44            relationship = "many-to-one") |>45  mutate(46    # Baseline records carry no comparator; placebo records carry the47    # group's means like every other record after baseline.48    COMP = if_else(after_baseline, COMP, NA_real_),49    COMPBASE = if_else(after_baseline, COMPBASE, NA_real_),50    COMPCHG = if_else(after_baseline, COMPCHG, NA_real_),51    # The double delta, on drug records only.52    CCOMPCHG = if_else(after_baseline & is.na(ACOMPFL), CHG - COMPCHG,53                       NA_real_),54    COMPTYPE = if_else(after_baseline, paste0("Placebo group at ", ATPT),55                       NA_character_)56  ) |>57  select(58    STUDYID, USUBJID, COHORT, TRTA, PARAMCD, PARAM, APERIOD, APERDAY, ATPT,59    ATPTN, AVAL, AVALU, ABLFL, BASE, CHG, BASETYPE, ACOMPFL, COMP, COMPBASE,60    COMPCHG, CCOMPCHG, COMPTYPE61  )6263dir.create("/app/output", showWarnings = FALSE)64write_csv(adeg_out, "/app/output/adeg.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adeg-placebo-corrected-change (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 ADEG with placebo-corrected change columns from ADEG_RAW.89Reads /app/input/adeg_raw.csv and writes /app/output/adeg.csv.10"""1112import csv13from pathlib import Path1415INPUT = Path("/app/input/adeg_raw.csv")16OUTPUT = Path("/app/output/adeg.csv")1718COLUMNS = [19    "STUDYID", "USUBJID", "COHORT", "TRTA", "PARAMCD", "PARAM", "APERIOD",20    "APERDAY", "ATPT", "ATPTN", "AVAL", "AVALU", "ABLFL", "BASE", "CHG",21    "BASETYPE", "ACOMPFL", "COMP", "COMPBASE", "COMPCHG", "CCOMPCHG",22    "COMPTYPE",23]242526def to_float(text):27    """Parse a CSV cell as a float, returning None for a blank cell."""28    if text is None or text.strip() == "":29        return None30    return float(text)313233def fmt(value):34    """Format a computed float without rounding; blank for None."""35    if value is None:36        return ""37    return repr(value)383940def mean(values):41    vals = [v for v in values if v is not None]42    if not vals:43        return None44    return sum(vals) / len(vals)454647def main():48    with INPUT.open(newline="") as fh:49        rows = list(csv.DictReader(fh))5051    def is_placebo(row):52        return row["TRTA"] == "Placebo"5354    def is_baseline(row):55        return row["ABLFL"] == "Y"5657    # Placebo comparison groups: every placebo record after baseline with58    # the same PARAMCD and the same ATPTN, from all cohorts together.59    groups = {}60    for row in rows:61        if is_placebo(row) and not is_baseline(row):62            key = (row["PARAMCD"], row["ATPTN"])63            groups.setdefault(key, []).append(row)6465    stats = {}66    for key, members in groups.items():67        stats[key] = (68            mean([to_float(r["AVAL"]) for r in members]),69            mean([to_float(r["BASE"]) for r in members]),70            mean([to_float(r["CHG"]) for r in members]),71        )7273    out_rows = []74    for row in rows:75        out = {col: row.get(col, "") for col in COLUMNS[:16]}76        baseline = is_baseline(row)77        placebo = is_placebo(row)7879        acompfl = ""80        comp = compbase = compchg = None81        ccompchg = None82        comptype = ""83        if not baseline:84            key = (row["PARAMCD"], row["ATPTN"])85            comp, compbase, compchg = stats.get(key, (None, None, None))86            comptype = "Placebo group at " + row["ATPT"]87            if placebo:88                acompfl = "Y"89            else:90                chg = to_float(row["CHG"])91                if chg is not None and compchg is not None:92                    ccompchg = chg - compchg9394        out["ACOMPFL"] = acompfl95        out["COMP"] = fmt(comp)96        out["COMPBASE"] = fmt(compbase)97        out["COMPCHG"] = fmt(compchg)98        out["CCOMPCHG"] = fmt(ccompchg)99        out["COMPTYPE"] = comptype100        out_rows.append(out)101102    OUTPUT.parent.mkdir(parents=True, exist_ok=True)103    with OUTPUT.open("w", newline="") as fh:104        writer = csv.DictWriter(fh, fieldnames=COLUMNS)105        writer.writeheader()106        writer.writerows(out_rows)107108109if __name__ == "__main__":110    main()

1/* opensas reference solution for the yamaa benchmark adam-adeg-placebo-corrected-change.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adeg;6  length STUDYID USUBJID COHORT TRTA PARAMCD PARAM ATPT AVALU ABLFL BASETYPE $1024;7  infile "/app/input/adeg_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. COHORT : $char1024. TRTA : $char1024. PARAMCD : $char1024. PARAM : $char1024. APERIOD APERDAY ATPT : $char1024. ATPTN AVAL AVALU : $char1024. ABLFL : $char1024. BASE CHG BASETYPE : $char1024.;9run;1011/* The comparator records: placebo records that are not baseline records. */12data flagged;13  length ACOMPFL $1;14  set adeg;15  if ABLFL ne 'Y' then AFTER = 1;16  else AFTER = 0;17  if AFTER = 1 and TRTA = 'Placebo' then ACOMPFL = 'Y';18  else ACOMPFL = '';19run;2021/* The placebo group: every comparator record of the same parameter and22   nominal time point, all cohorts together; each mean skips missing values. */23data comparator;24  length G_PARAMCD $1024;25  set flagged;26  if ACOMPFL = 'Y';27  G_PARAMCD = PARAMCD; G_ATPTN = ATPTN;28  keep G_PARAMCD G_ATPTN AVAL BASE CHG;29run;3031proc sql;32  create table groups as33    select G_PARAMCD, G_ATPTN, mean(AVAL) as G_COMP, mean(BASE) as G_COMPBASE,34           mean(CHG) as G_COMPCHG35    from comparator36    group by G_PARAMCD, G_ATPTN;37  create table matched as38    select a.*, b.G_COMP, b.G_COMPBASE, b.G_COMPCHG39    from flagged as a left join groups as b40      on a.PARAMCD = b.G_PARAMCD and a.ATPTN = b.G_ATPTN;41quit;4243/* Placebo records carry the group's means like every other record after44   baseline; the double delta is on drug records only. */45data final;46  length COMPTYPE $1024;47  set matched;48  if AFTER = 1 then do;49    COMP = G_COMP; COMPBASE = G_COMPBASE; COMPCHG = G_COMPCHG;50    COMPTYPE = 'Placebo group at ' || strip(ATPT);51  end;52  else do;53    COMP = .; COMPBASE = .; COMPCHG = .;54    COMPTYPE = '';55  end;56  if AFTER = 1 and ACOMPFL ne 'Y' and not missing(CHG) and not missing(COMPCHG)57    then CCOMPCHG = CHG - COMPCHG;58  else CCOMPCHG = .;59run;6061proc sql;62  create table out as63    select STUDYID, USUBJID, COHORT, TRTA, PARAMCD, PARAM, APERIOD, APERDAY,64           ATPT, ATPTN, AVAL, AVALU, ABLFL, BASE, CHG, BASETYPE, ACOMPFL,65           COMP, COMPBASE, COMPCHG, CCOMPCHG, COMPTYPE66    from final;67quit;68proc export data=out outfile="/app/output/adeg.csv" dbms=csv replace; run;