Derived ECG Intervals

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

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

1# Reference solution for the yamaa benchmark adam-adeg-derived-intervals (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)9library(tidyr)1011adeg <- read_csv(12  "/app/input/adeg.csv",13  col_types = cols(AVAL = col_double(), .default = col_character())14)1516wide <- adeg |>17  select(STUDYID, USUBJID, AVISIT, PARAMCD, AVAL) |>18  pivot_wider(names_from = PARAMCD, values_from = AVAL)1920# A QTc record needs both QT and RR; RR in seconds is RR in ms over 1000.21qtc <- wide |>22  filter(!is.na(QT), !is.na(RR)) |>23  mutate(24    RRSEC = RR / 1000,25    QTCBR = QT / sqrt(RRSEC),26    QTCFR = QT / (RRSEC^(1 / 3))27  )2829qtcbr <- qtc |>30  transmute(31    STUDYID, USUBJID, AVISIT,32    PARAMCD = "QTCBR",33    PARAM = "QTcB - Bazett's Correction Formula Rederived (ms)",34    AVAL = QTCBR,35    AVALU = "ms"36  )3738qtcfr <- qtc |>39  transmute(40    STUDYID, USUBJID, AVISIT,41    PARAMCD = "QTCFR",42    PARAM = "QTcF - Fridericia's Correction Formula Rederived (ms)",43    AVAL = QTCFR,44    AVALU = "ms"45  )4647# An RRR record needs a present, nonzero heart rate.48rrr <- wide |>49  filter(!is.na(HR), HR != 0) |>50  transmute(51    STUDYID, USUBJID, AVISIT,52    PARAMCD = "RRR",53    PARAM = "RR Duration Rederived (ms)",54    AVAL = 60000 / HR,55    AVALU = "ms"56  )5758adeg_out <- bind_rows(59  adeg |> select(STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, AVALU),60  qtcbr,61  qtcfr,62  rrr63) |>64  select(STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, AVALU)6566dir.create("/app/output", showWarnings = FALSE)67write_csv(adeg_out, "/app/output/adeg.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adeg-derived-intervals (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 derived QTcB, QTcF, and RR-rederived records.89Reads the collected ADEG dataset from /app/input, keeps every collected10record, and adds one record per subject and analysis visit for each11derived parameter whose source results are present:1213- QTCBR: QT / SQRT(RR / 1000)      (needs QT and RR)14- QTCFR: QT / POWER(RR / 1000, 1/3) (needs QT and RR)15- RRR:   60000 / heart rate       (needs heart rate present and nonzero)1617AVAL on the derived records is not rounded.18"""1920import csv21import math22from collections import OrderedDict2324INPUT_PATH = "/app/input/adeg.csv"25OUTPUT_PATH = "/app/output/adeg.csv"2627COLUMNS = ["STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVISIT", "AVAL", "AVALU"]2829DERIVED_PARAMS = {30    "QTCBR": "QTcB - Bazett's Correction Formula Rederived (ms)",31    "QTCFR": "QTcF - Fridericia's Correction Formula Rederived (ms)",32    "RRR": "RR Duration Rederived (ms)",33}343536def parse_number(text):37    """Return the float value of a cell, or None when it is empty."""38    if text is None:39        return None40    text = text.strip()41    if text == "":42        return None43    return float(text)444546def format_number(value):47    """Write a number without rounding; whole numbers without a fraction."""48    if value == int(value) and abs(value) < 1e15:49        return str(int(value))50    return repr(value)515253def main():54    with open(INPUT_PATH, newline="", encoding="utf-8") as handle:55        rows = list(csv.DictReader(handle))5657    # Group collected records by subject and analysis visit, keeping the58    # order in which each group first appears.59    groups = OrderedDict()60    for row in rows:61        key = (row["STUDYID"], row["USUBJID"], row["AVISIT"])62        groups.setdefault(key, []).append(row)6364    out_rows = []65    for (studyid, usubjid, avisit), group in groups.items():66        out_rows.extend(group)6768        # Source results for this subject and visit, by parameter.69        values = {}70        for row in group:71            number = parse_number(row["AVAL"])72            if number is not None:73                values[row["PARAMCD"]] = number7475        derived = []76        qt = values.get("QT")77        rr = values.get("RR")78        if qt is not None and rr is not None:79            rr_seconds = rr / 1000.080            derived.append(("QTCBR", qt / math.sqrt(rr_seconds)))81            derived.append(("QTCFR", qt / (rr_seconds ** (1.0 / 3.0))))82        hr = values.get("HR")83        if hr is not None and hr != 0:84            derived.append(("RRR", 60000.0 / hr))8586        for paramcd, aval in derived:87            out_rows.append(88                {89                    "STUDYID": studyid,90                    "USUBJID": usubjid,91                    "PARAMCD": paramcd,92                    "PARAM": DERIVED_PARAMS[paramcd],93                    "AVISIT": avisit,94                    "AVAL": format_number(aval),95                    "AVALU": "ms",96                }97            )9899    with open(OUTPUT_PATH, "w", newline="", encoding="utf-8") as handle:100        writer = csv.DictWriter(handle, fieldnames=COLUMNS)101        writer.writeheader()102        writer.writerows(out_rows)103104105if __name__ == "__main__":106    main()

1/* opensas reference solution for the yamaa benchmark adam-adeg-derived-intervals.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 PARAMCD PARAM AVISIT AVALU $1024;7  infile "/app/input/adeg.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. PARAM : $char1024. AVISIT : $char1024. AVAL AVALU : $char1024.;9run;1011proc sql;12  create table qt as select a.*,b.AVAL as RRVAL from adeg as a inner join adeg as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and a.AVISIT=b.AVISIT where a.PARAMCD='QT' and b.PARAMCD='RR' and not missing(a.AVAL) and not missing(b.AVAL);13quit;14data corrected;15  length PARAMCD PARAM AVALU $1024;16  set qt;17  QTVAL=AVAL; AVALU='ms';18  PARAMCD='QTCBR'; PARAM="QTcB - Bazett's Correction Formula Rederived (ms)"; AVAL=QTVAL/sqrt(RRVAL/1000); output;19  PARAMCD='QTCFR'; PARAM="QTcF - Fridericia's Correction Formula Rederived (ms)"; AVAL=QTVAL/(RRVAL/1000)**(1/3); output;20run;21data heart;22  length PARAMCD PARAM $1024;23  set adeg;24  if PARAMCD='HR' and not missing(AVAL) and AVAL ne 0;25  AVAL=60000/AVAL; PARAMCD='RRR'; PARAM='RR Duration Rederived (ms)'; AVALU='ms';26run;27data result; set adeg corrected heart; run;2829proc sql;30  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, AVALU from result;31quit;32proc export data=final outfile="/app/output/adeg.csv" dbms=csv replace; run;