Track the Running Nadir Sum

1library(yamaa)23adtr <- yamaa_domain("spec.yaml")$output4adtr

1import yamaa23adtr = yamaa.yamaa_domain("spec.yaml").output4adtr

1# Reference solution for the yamaa benchmark adam-adtr-nadir (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/adtr_raw.csv",12  col_types = cols(13    AVISITN = col_integer(), ADT = col_date(), AVAL = col_double(),14    NMEAS = col_integer(), NTARGET = col_integer(),15    .default = col_character()16  )17)1819# Complete dated assessments carry the nadir candidates; a complete20# assessment with no date never counts toward any nadir, its own21# included.22complete <- raw |>23  filter(ANL01FL == "Y", !is.na(ADT), !is.na(AVAL)) |>24  select(USUBJID, ADT, AVAL)2526# An incomplete current assessment keeps the nadir set by an earlier27# complete one, while a current record with no date has none.28adtr <- raw |>29  rowwise() |>30  mutate(31    NADIR = {32      cands <- complete$AVAL[complete$USUBJID == USUBJID & complete$ADT <= ADT]33      if (is.na(ADT) || length(cands) == 0L) NA_real_ else min(cands)34    }35  ) |>36  ungroup() |>37  select(38    STUDYID, USUBJID, AVISIT, AVISITN, ADT, PARAMCD, PARAM,39    AVAL, NMEAS, NTARGET, ANL01FL, NADIR40  ) |>41  arrange(USUBJID, AVISITN)4243dir.create("/app/output", showWarnings = FALSE)44write_csv(adtr, "/app/output/adtr.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adtr-nadir (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/adtr_raw.csv", infer_schema=False, null_values="").with_columns(12    pl.col("AVISITN").cast(pl.Int64, strict=False),13    pl.col("ADT").str.to_date(strict=False),14    pl.col("AVAL").cast(pl.Float64, strict=False),15    pl.col("NMEAS").cast(pl.Int64, strict=False),16    pl.col("NTARGET").cast(pl.Int64, strict=False),17)1819# Complete dated assessments carry the nadir candidates; a complete20# assessment with no date never counts toward any nadir, its own21# included. An incomplete current assessment keeps the nadir set by an22# earlier complete one, while a current record with no date has none.23complete = [24    (r["USUBJID"], r["ADT"], r["AVAL"])25    for r in raw.to_dicts()26    if r["ANL01FL"] == "Y" and r["ADT"] is not None and r["AVAL"] is not None27]2829nadirs = []30for r in raw.to_dicts():31    if r["ADT"] is None:32        nadirs.append(None)33        continue34    cands = [v for (u, d, v) in complete if u == r["USUBJID"] and d <= r["ADT"]]35    nadirs.append(min(cands) if cands else None)3637adtr = (38    raw.with_columns(NADIR=pl.Series(nadirs, dtype=pl.Float64))39    .select(40        "STUDYID",41        "USUBJID",42        "AVISIT",43        "AVISITN",44        "ADT",45        "PARAMCD",46        "PARAM",47        "AVAL",48        "NMEAS",49        "NTARGET",50        "ANL01FL",51        "NADIR",52    )53    .sort(["USUBJID", "AVISITN"])54)5556Path("/app/output").mkdir(parents=True, exist_ok=True)57adtr.write_csv("/app/output/adtr.csv", null_value="")

1/* opensas reference solution for the yamaa benchmark adam-adtr-nadir.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adtr_raw;6  length STUDYID USUBJID AVISIT ADT PARAMCD PARAM ANL01FL $1024;7  infile "/app/input/adtr_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AVISIT : $char1024. AVISITN ADT : $char1024. PARAMCD : $char1024. PARAM : $char1024. AVAL NMEAS NTARGET ANL01FL : $char1024.;9run;1011data history; set adtr_raw; PRIORDATE=ADT; PRIORVALUE=AVAL; PRIORFLAG=ANL01FL; keep STUDYID USUBJID PRIORDATE PRIORVALUE PRIORFLAG; run;12proc sql;13create table nadirs as select a.STUDYID,a.USUBJID,a.AVISIT,min(b.PRIORVALUE) as NADIR from adtr_raw a left join history b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and not missing(a.ADT) and not missing(b.PRIORDATE) and b.PRIORDATE<=a.ADT and b.PRIORFLAG='Y' group by a.STUDYID,a.USUBJID,a.AVISIT;14create table result as select a.*,b.NADIR from adtr_raw a left join nadirs b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and a.AVISIT=b.AVISIT; quit;15proc sql;16  create table final as select STUDYID, USUBJID, AVISIT, AVISITN, ADT, PARAMCD, PARAM, AVAL, NMEAS, NTARGET, ANL01FL, NADIR from result;17quit;18proc export data=final outfile="/app/output/adtr.csv" dbms=csv replace; run;