Derive mean arterial pressure records

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-map (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 systolic and diastolic results.20sysbp <- raw |>21  filter(PARAMCD %in% "SYSBP", !is.na(AVAL)) |>22  group_by(STUDYID, USUBJID, VISIT) |>23  summarise(SYSBP_VAL = first(AVAL), .groups = "drop")2425diabp <- raw |>26  filter(PARAMCD %in% "DIABP", !is.na(AVAL)) |>27  group_by(STUDYID, USUBJID, VISIT) |>28  summarise(DIABP_VAL = first(AVAL), .groups = "drop")2930# One mean arterial pressure record for each visit with both results,31# counting the diastolic pressure twice.32map_records <- sysbp |>33  inner_join(diabp, by = c("STUDYID", "USUBJID", "VISIT")) |>34  transmute(35    STUDYID, USUBJID,36    PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)",37    AVAL = (SYSBP_VAL + 2 * DIABP_VAL) / 3,38    VISIT, DTYPE = "CALCULATION"39  )4041advs <- bind_rows(collected, map_records) |>42  arrange(USUBJID, VISIT, PARAMCD)4344dir.create("/app/output", showWarnings = FALSE)45write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-map (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 systolic and diastolic results.22sysbp = (23    raw.filter(24        (pl.col("PARAMCD") == "SYSBP") & pl.col("AVAL").is_not_null()25    )26    .group_by(["STUDYID", "USUBJID", "VISIT"])27    .agg(SYSBP_VAL=pl.col("AVAL").first())28)29diabp = (30    raw.filter(31        (pl.col("PARAMCD") == "DIABP") & pl.col("AVAL").is_not_null()32    )33    .group_by(["STUDYID", "USUBJID", "VISIT"])34    .agg(DIABP_VAL=pl.col("AVAL").first())35)3637# One mean arterial pressure record for each visit with both results,38# counting the diastolic pressure twice.39map_records = (40    sysbp.join(diabp, on=["STUDYID", "USUBJID", "VISIT"], how="inner")41    .with_columns(AVAL=(pl.col("SYSBP_VAL") + 2 * pl.col("DIABP_VAL")) / 3)42    .select(43        "STUDYID",44        "USUBJID",45        "AVAL",46        "VISIT",47        PARAMCD=pl.lit("MAP"),48        PARAM=pl.lit("Mean Arterial Pressure (mmHg)"),49        DTYPE=pl.lit("CALCULATION"),50    )51    .select("STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVAL", "VISIT", "DTYPE")52)5354advs = pl.concat([collected, map_records], how="diagonal").sort(55    ["USUBJID", "VISIT", "PARAMCD"]56)5758Path("/app/output").mkdir(parents=True, exist_ok=True)59advs.write_csv("/app/output/advs.csv")

1/* opensas reference solution for the yamaa benchmark adam-advs-map.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,'MAP' as PARAMCD,'Mean Arterial Pressure (mmHg)' as PARAM,(a.AVAL+2*b.AVAL)/3 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='SYSBP' and b.PARAMCD='DIABP' 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;