Flag QTcF Values and Increases Beyond Categorical Limits

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

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

1# Reference solution for the yamaa benchmark adam-adeg-qtc-flags (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)910raw <- read_csv(11  "/app/input/adeg_raw.csv",12  col_types = cols(13    AVAL = col_double(),14    BASE = col_double(),15    CHG = col_double(),16    .default = col_character()17  )18)1920# Only on-treatment QTcF records are assessed, and values are compared21# unrounded, strictly above each limit: exactly at a limit reads N.22absolute <- function(data) {23  data$PARAMCD %in% "QTCF" & data$ONTRTFL %in% "Y" & !is.na(data$AVAL)24}25change <- function(data) {26  data$PARAMCD %in% "QTCF" & data$ONTRTFL %in% "Y" & !is.na(data$CHG)27}2829adeg <- raw |>30  mutate(31    CRIT1 = if_else(absolute(raw), "QTcF > 450 ms", NA_character_),32    CRIT1FL = case_when(33      !absolute(raw) ~ NA_character_,34      AVAL > 450 ~ "Y",35      .default = "N"36    ),37    CRIT2 = if_else(absolute(raw), "QTcF > 480 ms", NA_character_),38    CRIT2FL = case_when(39      !absolute(raw) ~ NA_character_,40      AVAL > 480 ~ "Y",41      .default = "N"42    ),43    CRIT3 = if_else(absolute(raw), "QTcF > 500 ms", NA_character_),44    CRIT3FL = case_when(45      !absolute(raw) ~ NA_character_,46      AVAL > 500 ~ "Y",47      .default = "N"48    ),49    CRIT4 = if_else(50      change(raw), "QTcF increase from baseline > 30 ms", NA_character_51    ),52    CRIT4FL = case_when(53      !change(raw) ~ NA_character_,54      CHG > 30 ~ "Y",55      .default = "N"56    ),57    CRIT5 = if_else(58      change(raw), "QTcF increase from baseline > 60 ms", NA_character_59    ),60    CRIT5FL = case_when(61      !change(raw) ~ NA_character_,62      CHG > 60 ~ "Y",63      .default = "N"64    )65  ) |>66  select(67    STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, ABLFL, ONTRTFL,68    BASE, CHG, CRIT1, CRIT1FL, CRIT2, CRIT2FL, CRIT3, CRIT3FL, CRIT4,69    CRIT4FL, CRIT5, CRIT5FL70  )7172dir.create("/app/output", showWarnings = FALSE)73write_csv(adeg, "/app/output/adeg.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adeg-qtc-flags (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 the ADEG dataset with QTcF criterion flags from ADEG_RAW.89Only records with PARAMCD "QTCF" and ONTRTFL "Y" are assessed. The10absolute criteria compare AVAL against 450, 480 and 500 ms; the11increase criteria compare CHG against 30 and 60 ms. A flag is Y only12when the value is strictly above its limit, N otherwise, and each13criterion and flag has no value when the record is not assessed or14the compared value has no value. Values are compared as they stand,15without rounding.16"""1718import csv1920INPUT_PATH = "/app/input/adeg_raw.csv"21OUTPUT_PATH = "/app/output/adeg.csv"2223COLUMNS = [24    "STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVISIT", "AVAL",25    "ABLFL", "ONTRTFL", "BASE", "CHG",26    "CRIT1", "CRIT1FL", "CRIT2", "CRIT2FL", "CRIT3", "CRIT3FL",27    "CRIT4", "CRIT4FL", "CRIT5", "CRIT5FL",28]2930ABSOLUTE = [31    ("CRIT1", "CRIT1FL", "QTcF > 450 ms", 450.0),32    ("CRIT2", "CRIT2FL", "QTcF > 480 ms", 480.0),33    ("CRIT3", "CRIT3FL", "QTcF > 500 ms", 500.0),34]3536INCREASE = [37    ("CRIT4", "CRIT4FL", "QTcF increase from baseline > 30 ms", 30.0),38    ("CRIT5", "CRIT5FL", "QTcF increase from baseline > 60 ms", 60.0),39]404142def number(text):43    """The numeric value of a cell, or None when it has no value."""44    if text is None or text.strip() == "":45        return None46    return float(text)474849def main():50    with open(INPUT_PATH, newline="") as handle:51        rows = list(csv.DictReader(handle))5253    out_rows = []54    for row in rows:55        out = {column: row.get(column, "") for column in COLUMNS[:10]}56        assessed = row.get("PARAMCD") == "QTCF" and row.get("ONTRTFL") == "Y"57        aval = number(row.get("AVAL"))58        chg = number(row.get("CHG"))59        for crit, flag, label, limit in ABSOLUTE:60            if assessed and aval is not None:61                out[crit] = label62                out[flag] = "Y" if aval > limit else "N"63            else:64                out[crit] = ""65                out[flag] = ""66        for crit, flag, label, limit in INCREASE:67            if assessed and chg is not None:68                out[crit] = label69                out[flag] = "Y" if chg > limit else "N"70            else:71                out[crit] = ""72                out[flag] = ""73        out_rows.append(out)7475    with open(OUTPUT_PATH, "w", newline="") as handle:76        writer = csv.DictWriter(handle, fieldnames=COLUMNS)77        writer.writeheader()78        writer.writerows(out_rows)798081if __name__ == "__main__":82    main()

1/* opensas reference solution for the yamaa benchmark adam-adeg-qtc-flags.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 ABLFL ONTRTFL $1024;7  infile "/app/input/adeg_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. PARAM : $char1024. AVISIT : $char1024. AVAL ABLFL : $char1024. ONTRTFL : $char1024. BASE CHG;9run;1011data result;12  length CRIT1 CRIT2 CRIT3 CRIT4 CRIT5 $1024 CRIT1FL CRIT2FL CRIT3FL CRIT4FL CRIT5FL $1;13  set adeg;14  CRIT1=''; CRIT1FL=''; CRIT2=''; CRIT2FL=''; CRIT3=''; CRIT3FL='';15  CRIT4=''; CRIT4FL=''; CRIT5=''; CRIT5FL='';16  /* Only on-treatment QTcF records are assessed, and values are compared17     unrounded, strictly above each limit: exactly at a limit reads N. */18  if PARAMCD='QTCF' and ONTRTFL='Y' and not missing(AVAL) then do;19    CRIT1='QTcF > 450 ms'; CRIT1FL=ifc(AVAL>450,'Y','N');20    CRIT2='QTcF > 480 ms'; CRIT2FL=ifc(AVAL>480,'Y','N');21    CRIT3='QTcF > 500 ms'; CRIT3FL=ifc(AVAL>500,'Y','N');22  end;23  if PARAMCD='QTCF' and ONTRTFL='Y' and not missing(CHG) then do;24    CRIT4='QTcF increase from baseline > 30 ms'; CRIT4FL=ifc(CHG>30,'Y','N');25    CRIT5='QTcF increase from baseline > 60 ms'; CRIT5FL=ifc(CHG>60,'Y','N');26  end;27run;2829proc sql;30  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, ABLFL, ONTRTFL, BASE, CHG, CRIT1, CRIT1FL, CRIT2, CRIT2FL, CRIT3, CRIT3FL, CRIT4, CRIT4FL, CRIT5, CRIT5FL from result;31quit;32proc export data=final outfile="/app/output/adeg.csv" dbms=csv replace; run;