Derive Body Surface Area

1library(yamaa)23advs <- yamaa_domain("spec.yaml")$output4advs

1import yamaa23advs = yamaa.yamaa_domain("spec.yaml").output4advs

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 1.67from pathlib import Path89import polars as pl1011raw = pl.read_csv("/app/input/advs.csv", infer_schema=False).with_columns(12    pl.col("AVAL").cast(pl.Float64, strict=False)13)1415# Every collected record stays in place.16collected = raw.select(17    "STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVAL", "VISIT",18    DTYPE=pl.lit(None, dtype=pl.String),19)2021# The visit's height and weight results; a zero result still counts.22heights = (23    raw.filter(24        (pl.col("PARAMCD") == "HEIGHT") & pl.col("AVAL").is_not_null()25    )26    .group_by(["STUDYID", "USUBJID", "VISIT"])27    .agg(HEIGHT_VAL=pl.col("AVAL").first())28)29weights = (30    raw.filter(31        (pl.col("PARAMCD") == "WEIGHT") & pl.col("AVAL").is_not_null()32    )33    .group_by(["STUDYID", "USUBJID", "VISIT"])34    .agg(WEIGHT_VAL=pl.col("AVAL").first())35)3637# One body surface area record for each visit with both results.38bsa = (39    heights.join(weights, on=["STUDYID", "USUBJID", "VISIT"], how="inner")40    .with_columns(AVAL=(pl.col("HEIGHT_VAL") * pl.col("WEIGHT_VAL") / 3600).sqrt())41    .select(42        "STUDYID",43        "USUBJID",44        "AVAL",45        "VISIT",46        PARAMCD=pl.lit("BSA"),47        PARAM=pl.lit("Body Surface Area (m^2)"),48        DTYPE=pl.lit("CALCULATION"),49    )50    .select("STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVAL", "VISIT", "DTYPE")51)5253advs = pl.concat([collected, bsa], how="diagonal").sort(54    ["USUBJID", "VISIT", "PARAMCD"]55)5657Path("/app/output").mkdir(parents=True, exist_ok=True)58advs.write_csv("/app/output/advs.csv")

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;