Derive BMI

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-bmi (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)910vs <- read_csv(11  "/app/input/vs.csv",12  col_types = cols(VSSTRESN = col_double(), .default = col_character())13)14adsl <- read_csv(15  "/app/input/adsl.csv",16  col_types = cols(HEIGHTBL = col_double(), .default = col_character())17)1819# Every collected result stays in place.20collected <- vs |>21  select(STUDYID, USUBJID, AVISIT = VISIT, PARAMCD = VSTESTCD, PARAM = VSTEST, AVAL = VSSTRESN)2223# One BMI record for each weight with a result, using the subject's24# baseline height in metres. Without a usable height the record stays25# with no value.26weights <- vs |>27  filter(VSTESTCD %in% "WEIGHT", !is.na(VSSTRESN)) |>28  left_join(adsl |> select(USUBJID, HEIGHTBL), by = "USUBJID") |>29  mutate(30    BMI = if_else(31      !is.na(HEIGHTBL) & HEIGHTBL != 0,32      VSSTRESN / ((HEIGHTBL / 100) ^ 2),33      NA_real_34    )35  ) |>36  transmute(37    STUDYID, USUBJID, AVISIT = VISIT,38    PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)", AVAL = BMI39  )4041advs <- bind_rows(collected, weights) |>42  arrange(USUBJID, AVISIT, PARAMCD)4344dir.create("/app/output", showWarnings = FALSE)45write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-bmi (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 pl1011vs = pl.read_csv("/app/input/vs.csv", infer_schema=False).with_columns(12    pl.col("VSSTRESN").cast(pl.Float64, strict=False)13)14adsl = pl.read_csv("/app/input/adsl.csv", infer_schema=False).with_columns(15    pl.col("HEIGHTBL").cast(pl.Float64, strict=False)16)1718# Every collected result stays in place.19collected = vs.select(20    "STUDYID",21    "USUBJID",22    AVISIT="VISIT",23    PARAMCD="VSTESTCD",24    PARAM="VSTEST",25    AVAL="VSSTRESN",26)2728# One BMI record for each weight with a result, using the subject's29# baseline height in metres. Without a usable height the record stays30# with no value.31weights = (32    vs.filter(33        (pl.col("VSTESTCD") == "WEIGHT") & pl.col("VSSTRESN").is_not_null()34    )35    .join(adsl.select("USUBJID", "HEIGHTBL"), on="USUBJID", how="left")36    .with_columns(37        BMI=pl.when(38            pl.col("HEIGHTBL").is_not_null() & (pl.col("HEIGHTBL") != 0)39        )40        .then(pl.col("VSSTRESN") / ((pl.col("HEIGHTBL") / 100) ** 2))41        .otherwise(None)42    )43    .select(44        "STUDYID",45        "USUBJID",46        AVISIT="VISIT",47        PARAMCD=pl.lit("BMI"),48        PARAM=pl.lit("Body Mass Index (kg/m^2)"),49        AVAL="BMI",50    )51)5253advs = pl.concat([collected, weights], how="diagonal").sort(54    ["USUBJID", "AVISIT", "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-bmi.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. HEIGHTBL;9run;1011data vs;12  length STUDYID USUBJID VSTESTCD VSTEST VISIT $1024;13  infile "/app/input/vs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VSTESTCD : $char1024. VSTEST : $char1024. VSSTRESN VISIT : $char1024.;15run;1617proc sql; create table joined as select a.*,b.HEIGHTBL from vs as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data result;19  length AVISIT $1024 PARAMCD $16 PARAM $1024;20  set joined;21  AVISIT=VISIT; PARAMCD=VSTESTCD; PARAM=VSTEST; AVAL=VSSTRESN; output;22  if VSTESTCD='WEIGHT' and not missing(VSSTRESN) then do;23    PARAMCD='BMI'; PARAM='Body Mass Index (kg/m^2)'; AVAL=.;24    if not missing(HEIGHTBL) and HEIGHTBL ne 0 then AVAL=VSSTRESN/(HEIGHTBL/100)**2;25    output;26  end;27run;2829proc sql;30  create table final as select STUDYID, USUBJID, AVISIT, PARAMCD, PARAM, AVAL from result;31quit;32proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;