Track the Running Nadir Sum

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

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

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 1.67import csv8from datetime import date910INPUT = "/app/input/adtr_raw.csv"11OUTPUT = "/app/output/adtr.csv"1213COLUMNS = [14    "STUDYID", "USUBJID", "AVISIT", "AVISITN", "ADT", "PARAMCD", "PARAM",15    "AVAL", "NMEAS", "NTARGET", "ANL01FL", "NADIR",16]171819def parse_date(text):20    text = (text or "").strip()21    if not text:22        return None23    return date.fromisoformat(text)242526def fmt_num(value):27    if value is None:28        return ""29    if float(value).is_integer():30        return str(int(value))31    return str(value)323334with open(INPUT, newline="") as f:35    rows = list(csv.DictReader(f))3637# Complete assessments per subject: ANL01FL "Y" with a dated ADT.38complete = {}39for row in rows:40    if (row.get("ANL01FL") or "").strip() == "Y":41        adt = parse_date(row.get("ADT"))42        aval_text = (row.get("AVAL") or "").strip()43        if adt is not None and aval_text:44            complete.setdefault(row["USUBJID"], []).append((adt, float(aval_text)))4546for row in rows:47    adt = parse_date(row.get("ADT"))48    nadir = None49    if adt is not None:50        candidates = [aval for d, aval in complete.get(row["USUBJID"], [])51                      if d <= adt]52        if candidates:53            nadir = min(candidates)54    row["NADIR"] = fmt_num(nadir)5556with open(OUTPUT, "w", newline="") as f:57    writer = csv.DictWriter(f, fieldnames=COLUMNS)58    writer.writeheader()59    for row in rows:60        writer.writerow({c: row.get(c, "") for c in COLUMNS})

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;