Derive Body Surface Area

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

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

1# Reference solution for the yamaa benchmark adam-advs-bsa (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/advs.csv",12  col_types = cols(AVAL = col_double(), .default = col_character())13)1415# Every collected record stays in place.16collected <- raw |>17  transmute(STUDYID, USUBJID, PARAMCD, PARAM, AVAL, VISIT, DTYPE = NA_character_)1819# The visit's height and weight results; a zero result still counts.20heights <- raw |>21  filter(PARAMCD %in% "HEIGHT", !is.na(AVAL)) |>22  group_by(STUDYID, USUBJID, VISIT) |>23  summarise(HEIGHT_VAL = first(AVAL), .groups = "drop")2425weights <- raw |>26  filter(PARAMCD %in% "WEIGHT", !is.na(AVAL)) |>27  group_by(STUDYID, USUBJID, VISIT) |>28  summarise(WEIGHT_VAL = first(AVAL), .groups = "drop")2930# One body surface area record for each visit with both results.31bsa <- heights |>32  inner_join(weights, by = c("STUDYID", "USUBJID", "VISIT")) |>33  transmute(34    STUDYID, USUBJID,35    PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)",36    AVAL = sqrt(HEIGHT_VAL * WEIGHT_VAL / 3600),37    VISIT, DTYPE = "CALCULATION"38  )3940advs <- bind_rows(collected, bsa) |>41  arrange(USUBJID, VISIT, PARAMCD)4243dir.create("/app/output", showWarnings = FALSE)44write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-bsa (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 an ADVS dataset with derived body surface area records.89Reads the collected ADVS dataset from /app/input, keeps every collected10record, and adds one body surface area (BSA) record for each subject and11visit that has both a height result (PARAMCD "HEIGHT") and a weight12result (PARAMCD "WEIGHT") with a value. BSA uses the Mosteller formula,13sqrt(height in cm * weight in kg / 3600), and is not rounded. A BSA14record carries DTYPE "CALCULATION"; collected records have no DTYPE.15"""1617import csv18import math19import os2021INPUT_PATH = "/app/input/advs.csv"22OUTPUT_PATH = "/app/output/advs.csv"2324COLUMNS = ["STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVAL", "VISIT", "DTYPE"]252627def main():28    with open(INPUT_PATH, newline="") as f:29        collected = list(csv.DictReader(f))3031    # Index height and weight results by study, subject and visit.32    heights = {}33    weights = {}34    for row in collected:35        aval = (row.get("AVAL") or "").strip()36        if not aval:37            continue38        key = (row["STUDYID"], row["USUBJID"], row["VISIT"])39        if row["PARAMCD"] == "HEIGHT":40            heights[key] = float(aval)41        elif row["PARAMCD"] == "WEIGHT":42            weights[key] = float(aval)4344    # Position of the last collected record of each subject and visit,45    # so a derived BSA record follows its source records.46    last_index = {}47    for i, row in enumerate(collected):48        key = (row["STUDYID"], row["USUBJID"], row["VISIT"])49        last_index[key] = i5051    out_rows = []52    for i, row in enumerate(collected):53        out = {c: row.get(c, "") for c in COLUMNS}54        out["DTYPE"] = ""55        out_rows.append(out)56        key = (row["STUDYID"], row["USUBJID"], row["VISIT"])57        if last_index[key] == i and key in heights and key in weights:58            bsa = math.sqrt(heights[key] * weights[key] / 3600.0)59            out_rows.append(60                {61                    "STUDYID": key[0],62                    "USUBJID": key[1],63                    "PARAMCD": "BSA",64                    "PARAM": "Body Surface Area (m^2)",65                    "AVAL": repr(bsa),66                    "VISIT": key[2],67                    "DTYPE": "CALCULATION",68                }69            )7071    os.makedirs(os.path.dirname(OUTPUT_PATH), exist_ok=True)72    with open(OUTPUT_PATH, "w", newline="") as f:73        writer = csv.DictWriter(f, fieldnames=COLUMNS)74        writer.writeheader()75        writer.writerows(out_rows)767778if __name__ == "__main__":79    main()

1/* opensas reference solution for the yamaa benchmark adam-advs-bsa.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data advs;6  length STUDYID USUBJID PARAMCD PARAM VISIT $1024;7  infile "/app/input/advs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. PARAM : $char1024. AVAL VISIT : $char1024.;9run;1011proc sql;12  create table computed as select a.STUDYID,a.USUBJID,'BSA' as PARAMCD,'Body Surface Area (m^2)' as PARAM,sqrt(a.AVAL*b.AVAL/3600) as AVAL,a.VISIT,'CALCULATION' as DTYPE from advs as a inner join advs as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and a.VISIT=b.VISIT13  where a.PARAMCD='HEIGHT' and b.PARAMCD='WEIGHT' and not missing(a.AVAL) and not missing(b.AVAL);14quit;15data collected; length DTYPE $11; set advs; run;16data result; set collected computed; run;1718proc sql;19  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVAL, VISIT, DTYPE from result;20quit;21proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;