Replicate ECG Averages with QTcF Corrected per ECG

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

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

1# Reference solution for the yamaa benchmark adam-adeg-replicate-qtc-average (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)910eg <- read_csv(11  "/app/input/eg.csv",12  col_types = cols(13    EGSTRESN = col_double(),14    EGTPTNUM = col_double(),15    .default = col_character()16  )17)1819qt <- eg |> filter(EGTESTCD == "QTAG")20rr <- eg |> filter(EGTESTCD == "RRAG")2122# One ECG is one replicate number at a time point: its QT pairs with the RR23# of the same replicate number, never by collection time.24pairs <- qt |>25  select(STUDYID, USUBJID, EGTPTNUM, EGTPT, EGREPNUM, QT = EGSTRESN) |>26  left_join(27    rr |> select(STUDYID, USUBJID, EGTPTNUM, EGREPNUM, RR = EGSTRESN),28    by = c("STUDYID", "USUBJID", "EGTPTNUM", "EGREPNUM")29  ) |>30  # Fridericia's correction of each ECG: QT over the cube root of RR in31  # seconds.32  mutate(QTCF = QT / (RR / 1000)^(1 / 3))3334# The mean over the ECGs that have a value; no value, no record.35averages <- function(data, value, paramcd, param) {36  data |>37    filter(!is.na(.data[[value]])) |>38    group_by(STUDYID, USUBJID, EGTPTNUM, EGTPT) |>39    summarise(AVAL = mean(.data[[value]]), .groups = "drop") |>40    mutate(PARAMCD = paramcd, PARAM = param)41}4243adeg <- bind_rows(44  averages(qt, "EGSTRESN", "QTAG", "QT Interval, Aggregate (msec)"),45  averages(rr, "EGSTRESN", "RRAG", "RR Interval, Aggregate (msec)"),46  averages(pairs, "QTCF", "QTCF", "QTcF Interval, Aggregate (msec)")47) |>48  mutate(ATPT = EGTPT, ATPTN = EGTPTNUM, DTYPE = "AVERAGE") |>49  arrange(STUDYID, USUBJID, PARAMCD, ATPTN) |>50  select(STUDYID, USUBJID, PARAMCD, PARAM, ATPT, ATPTN, DTYPE, AVAL)5152dir.create("/app/output", showWarnings = FALSE)53write_csv(adeg, "/app/output/adeg.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adeg-replicate-qtc-average (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 csv8from collections import OrderedDict910INPUT = "/app/input"11OUTPUT = "/app/output"1213PARAMS = [14    ("QTAG", "QT Interval, Aggregate (msec)"),15    ("RRAG", "RR Interval, Aggregate (msec)"),16    ("QTCF", "QTcF Interval, Aggregate (msec)"),17]181920def main():21    with open(f"{INPUT}/eg.csv", newline="") as f:22        rows = list(csv.DictReader(f))2324    # Group rows by subject and planned time point, preserving input order.25    groups = OrderedDict()26    for row in rows:27        key = (row["STUDYID"], row["USUBJID"], row["EGTPT"], row["EGTPTNUM"])28        groups.setdefault(key, []).append(row)2930    out = []31    for (studyid, usubjid, atpt, atptn), grows in groups.items():32        qt = {}  # EGREPNUM -> QT result (msec)33        rr = {}  # EGREPNUM -> RR result (msec)34        for row in grows:35            value = row["EGSTRESN"].strip()36            if value == "":37                # A test that was not done has no result.38                continue39            if row["EGTESTCD"] == "QTAG":40                qt[row["EGREPNUM"]] = float(value)41            elif row["EGTESTCD"] == "RRAG":42                rr[row["EGREPNUM"]] = float(value)4344        values = {}45        if qt:46            values["QTAG"] = sum(qt.values()) / len(qt)47        if rr:48            values["RRAG"] = sum(rr.values()) / len(rr)49        corrected = []50        for repnum, qtval in qt.items():51            if repnum in rr and rr[repnum] != 0:52                corrected.append(qtval / (rr[repnum] / 1000.0) ** (1.0 / 3.0))53        if corrected:54            values["QTCF"] = sum(corrected) / len(corrected)5556        for paramcd, param in PARAMS:57            if paramcd not in values:58                # A parameter with no value at a time point has no record.59                continue60            out.append(61                {62                    "STUDYID": studyid,63                    "USUBJID": usubjid,64                    "PARAMCD": paramcd,65                    "PARAM": param,66                    "ATPT": atpt,67                    "ATPTN": atptn,68                    "DTYPE": "AVERAGE",69                    "AVAL": repr(values[paramcd]),70                }71            )7273    columns = ["STUDYID", "USUBJID", "PARAMCD", "PARAM", "ATPT", "ATPTN",74               "DTYPE", "AVAL"]75    with open(f"{OUTPUT}/adeg.csv", "w", newline="") as f:76        writer = csv.DictWriter(f, fieldnames=columns)77        writer.writeheader()78        writer.writerows(out)798081if __name__ == "__main__":82    main()

1/* opensas reference solution for the yamaa benchmark adam-adeg-replicate-qtc-average.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data eg;6  length STUDYID DOMAIN USUBJID EGTESTCD EGTEST EGSTAT EGSTRESU EGTPT EGDTC $1024;7  infile "/app/input/eg.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. DOMAIN : $char1024. USUBJID : $char1024. EGSEQ9        EGTESTCD : $char1024. EGTEST : $char1024. EGREPNUM EGSTAT : $char1024.10        EGSTRESN EGSTRESU : $char1024. EGTPT : $char1024. EGTPTNUM11        EGDTC : $char1024.;12run;1314/* The QT records, and the RR records under their own column names. */15data qt;16  set eg;17  if EGTESTCD='QTAG';18  QT=EGSTRESN;19  keep STUDYID USUBJID EGTPT EGTPTNUM EGREPNUM QT;20run;21data rr;22  length R_STUDYID R_USUBJID R_TPT $1024;23  set eg;24  if EGTESTCD='RRAG';25  R_STUDYID=STUDYID; R_USUBJID=USUBJID; R_TPT=EGTPT;26  R_TPTNUM=EGTPTNUM; R_REPNUM=EGREPNUM;27  RR=EGSTRESN;28  keep R_STUDYID R_USUBJID R_TPT R_TPTNUM R_REPNUM RR;29run;3031/* One ECG is one replicate number at a time point: its QT pairs with the32   RR of the same replicate number, never by collection time. */33proc sql;34  create table pairs as35    select a.STUDYID, a.USUBJID, a.EGTPT, a.EGTPTNUM, a.QT, b.RR36    from qt as a left join rr as b37      on a.STUDYID=b.R_STUDYID and a.USUBJID=b.R_USUBJID38         and a.EGTPTNUM=b.R_TPTNUM and a.EGREPNUM=b.R_REPNUM;39quit;4041/* Fridericia's correction of each ECG: QT over the cube root of RR in42   seconds; an ECG without both results has no corrected value. */43data pairs;44  set pairs;45  if not missing(QT) and not missing(RR) then QTCF=QT/(RR/1000)**(1/3);46  else QTCF=.;47run;4849/* The mean over the ECGs that have a value; no value, no record. */50proc sql;51  create table qtavg as52    select STUDYID, USUBJID, EGTPT, EGTPTNUM, mean(QT) as AVAL53    from qt where QT is not missing54    group by STUDYID, USUBJID, EGTPTNUM, EGTPT;55  create table rravg as56    select R_STUDYID as STUDYID, R_USUBJID as USUBJID, R_TPT as EGTPT,57           R_TPTNUM as EGTPTNUM, mean(RR) as AVAL58    from rr where RR is not missing59    group by R_STUDYID, R_USUBJID, R_TPTNUM, R_TPT;60  create table qtcfavg as61    select STUDYID, USUBJID, EGTPT, EGTPTNUM, mean(QTCF) as AVAL62    from pairs where QTCF is not missing63    group by STUDYID, USUBJID, EGTPTNUM, EGTPT;64quit;6566data result;67  length PARAMCD PARAM ATPT DTYPE $1024;68  set qtavg(in=inqt) rravg(in=inrr) qtcfavg(in=inqtcf);69  if inqt then do; PARAMCD='QTAG'; PARAM='QT Interval, Aggregate (msec)'; end;70  else if inrr then do; PARAMCD='RRAG'; PARAM='RR Interval, Aggregate (msec)'; end;71  else do; PARAMCD='QTCF'; PARAM='QTcF Interval, Aggregate (msec)'; end;72  ATPT=EGTPT; ATPTN=EGTPTNUM; DTYPE='AVERAGE';73run;7475proc sort data=result; by STUDYID USUBJID PARAMCD ATPTN; run;7677proc sql;78  create table final as79    select STUDYID, USUBJID, PARAMCD, PARAM, ATPT, ATPTN, DTYPE, AVAL80    from result;81quit;82proc export data=final outfile="/app/output/adeg.csv" dbms=csv replace; run;