Accumulation Ratios Between Day 1 and Steady State

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

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

1# Reference solution for the yamaa benchmark adam-adpp-accumulation-ratio (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)9library(tidyr)1011pp <- read_csv(12  "/app/input/pp.csv",13  col_types = cols(PPSTRESN = col_double(), .default = col_character())14)15adsl <- read_csv("/app/input/adsl.csv", col_types = cols(.default = col_character()))1617# Every PP record, a parameter that was not calculated included.18collected <- pp |>19  transmute(20    STUDYID, USUBJID,21    PARAMCD = PPTESTCD,22    PARAM = PPTEST,23    AVISIT = VISIT,24    AVAL = PPSTRESN,25    AVALU = PPSTRESU26  )2728# The steady-state profile is the last planned dosing day of the arm.29steady_state <- tibble(ARMCD = c("A", "B"), SSVISIT = c("DAY 7", "DAY 5"))3031subjects <- pp |>32  distinct(STUDYID, USUBJID) |>33  inner_join(select(adsl, STUDYID, USUBJID, ARMCD), by = c("STUDYID", "USUBJID")) |>34  inner_join(steady_state, by = "ARMCD")3536params <- tibble(37  PARAMCD = c("ARAUC", "ARCMAX"),38  PARAM = c("Accumulation Ratio AUCTAU", "Accumulation Ratio Cmax"),39  PPTESTCD = c("AUCTAU", "CMAX")40)4142steady <- pp |>43  select(STUDYID, USUBJID, PPTESTCD, VISIT, SSVALUE = PPSTRESN)44first <- pp |>45  filter(VISIT == "DAY 1") |>46  select(STUDYID, USUBJID, PPTESTCD, FIRSTVALUE = PPSTRESN)4748# A ratio needs both values; it sits at the steady-state visit.49ratios <- params |>50  cross_join(subjects) |>51  inner_join(52    steady,53    by = c("STUDYID", "USUBJID", "PPTESTCD", "SSVISIT" = "VISIT")54  ) |>55  inner_join(first, by = c("STUDYID", "USUBJID", "PPTESTCD")) |>56  filter(!is.na(SSVALUE), !is.na(FIRSTVALUE), FIRSTVALUE != 0) |>57  transmute(58    STUDYID, USUBJID, PARAMCD, PARAM,59    AVISIT = SSVISIT,60    AVAL = SSVALUE / FIRSTVALUE,61    AVALU = "RATIO"62  )6364adpp <- bind_rows(collected, ratios) |>65  select(STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, AVALU)6667dir.create("/app/output", showWarnings = FALSE)68write_csv(adpp, "/app/output/adpp.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adpp-accumulation-ratio (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 collections import OrderedDict910INPUT_DIR = "/app/input"11OUTPUT_DIR = "/app/output"1213STEADY_STATE_VISIT = {"A": "DAY 7", "B": "DAY 5"}14FIRST_DOSE_VISIT = "DAY 1"1516RATIO_PARAMS = [17    ("AUCTAU", "ARAUC", "Accumulation Ratio AUCTAU"),18    ("CMAX", "ARCMAX", "Accumulation Ratio Cmax"),19]202122def read_csv(path):23    with open(path, newline="") as f:24        return list(csv.DictReader(f))252627def main():28    adsl = read_csv(f"{INPUT_DIR}/adsl.csv")29    pp = read_csv(f"{INPUT_DIR}/pp.csv")3031    arm_by_subject = {row["USUBJID"]: row["ARMCD"] for row in adsl}3233    # Index collected values: (subject, testcd, visit) -> (value, studyid)34    values = {}35    for row in pp:36        raw = (row.get("PPSTRESN") or "").strip()37        value = float(raw) if raw else None38        values[(row["USUBJID"], row["PPTESTCD"], row["VISIT"])] = (39            value,40            row["STUDYID"],41        )4243    out_rows = []4445    # Collected records, one per PP record, in input order, grouped by46    # subject so each subject's ratio records can follow its own records.47    subjects_in_order = []48    for row in pp:49        if row["USUBJID"] not in subjects_in_order:50            subjects_in_order.append(row["USUBJID"])5152    pp_by_subject = OrderedDict()53    for row in pp:54        pp_by_subject.setdefault(row["USUBJID"], []).append(row)5556    for subject in subjects_in_order:57        for row in pp_by_subject[subject]:58            raw = (row.get("PPSTRESN") or "").strip()59            out_rows.append(60                {61                    "STUDYID": row["STUDYID"],62                    "USUBJID": subject,63                    "PARAMCD": row["PPTESTCD"],64                    "PARAM": row["PPTEST"],65                    "AVISIT": row["VISIT"],66                    "AVAL": raw if raw else "",67                    "AVALU": row["PPSTRESU"] if raw else row["PPSTRESU"],68                }69            )7071        # Ratio records for this subject.72        arm = arm_by_subject.get(subject)73        ss_visit = STEADY_STATE_VISIT.get(arm)74        if ss_visit is None:75            continue76        for testcd, ratio_cd, ratio_name in RATIO_PARAMS:77            ss = values.get((subject, testcd, ss_visit))78            d1 = values.get((subject, testcd, FIRST_DOSE_VISIT))79            if ss is None or d1 is None:80                continue81            ss_value, studyid = ss82            d1_value, _ = d183            if ss_value is None or d1_value is None:84                continue85            if d1_value == 0:86                continue87            ratio = ss_value / d1_value88            out_rows.append(89                {90                    "STUDYID": studyid,91                    "USUBJID": subject,92                    "PARAMCD": ratio_cd,93                    "PARAM": ratio_name,94                    "AVISIT": ss_visit,95                    "AVAL": repr(ratio),96                    "AVALU": "RATIO",97                }98            )99100    fieldnames = ["STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVISIT", "AVAL", "AVALU"]101    with open(f"{OUTPUT_DIR}/adpp.csv", "w", newline="") as f:102        writer = csv.DictWriter(f, fieldnames=fieldnames)103        writer.writeheader()104        writer.writerows(out_rows)105106107if __name__ == "__main__":108    main()

1/* opensas reference solution for the yamaa benchmark adam-adpp-accumulation-ratio.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data pp;6  length STUDYID DOMAIN USUBJID PPSEQ PPTESTCD PPTEST PPSTRESU PPSTAT PPREASND VISITNUM VISIT $1024;7  infile "/app/input/pp.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. DOMAIN : $char1024. USUBJID : $char1024. PPSEQ : $char1024.9        PPTESTCD : $char1024. PPTEST : $char1024. PPSTRESN PPSTRESU : $char1024.10        PPSTAT : $char1024. PPREASND : $char1024. VISITNUM : $char1024. VISIT : $char1024.;11  ORD = _n_;12run;1314data adsl;15  length STUDYID USUBJID ARMCD ARM SSVISIT $1024;16  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;17  input STUDYID : $char1024. USUBJID : $char1024. ARMCD : $char1024. ARM : $char1024.;18  /* The steady-state profile is the last planned dosing day of the arm. */19  if ARMCD = 'A' then SSVISIT = 'DAY 7';20  else if ARMCD = 'B' then SSVISIT = 'DAY 5';21  else SSVISIT = '';22run;2324/* Every PP record, a parameter that was not calculated included. */25data collected;26  length STUDYID USUBJID PARAMCD PARAM AVISIT AVALU $1024;27  set pp;28  PARAMCD = PPTESTCD; PARAM = PPTEST; AVISIT = VISIT; AVAL = PPSTRESN; AVALU = PPSTRESU;29  keep STUDYID USUBJID PARAMCD PARAM AVISIT AVAL AVALU ORD;30run;3132data firstdose;33  set pp;34  if VISIT = 'DAY 1';35  FIRSTVAL = PPSTRESN;36  keep STUDYID USUBJID PPTESTCD FIRSTVAL;37run;3839proc sql;40  create table steady as41    select p.STUDYID, p.USUBJID, p.PPTESTCD, p.VISIT, p.PPSTRESN as SSVAL, p.ORD42    from pp as p inner join adsl as a43      on p.STUDYID = a.STUDYID and p.USUBJID = a.USUBJID and p.VISIT = a.SSVISIT;44  create table pairs as45    select s.STUDYID, s.USUBJID, s.PPTESTCD, s.VISIT, s.SSVAL, f.FIRSTVAL, s.ORD46    from steady as s inner join firstdose as f47      on s.STUDYID = f.STUDYID and s.USUBJID = f.USUBJID and s.PPTESTCD = f.PPTESTCD;48quit;4950/* A ratio needs both values; it sits at the steady-state visit. */51data ratios;52  length STUDYID USUBJID PARAMCD PARAM AVISIT AVALU $1024;53  set pairs;54  if not missing(SSVAL) and not missing(FIRSTVAL) and FIRSTVAL ne 0;55  if PPTESTCD = 'AUCTAU' then do; PARAMCD = 'ARAUC'; PARAM = 'Accumulation Ratio AUCTAU'; end;56  else if PPTESTCD = 'CMAX' then do; PARAMCD = 'ARCMAX'; PARAM = 'Accumulation Ratio Cmax'; end;57  else delete;58  AVISIT = VISIT; AVAL = SSVAL / FIRSTVAL; AVALU = 'RATIO';59  ORD = ORD + 100000;60  keep STUDYID USUBJID PARAMCD PARAM AVISIT AVAL AVALU ORD;61run;6263data result; set collected ratios; run;64proc sort data=result; by ORD; run;6566proc sql;67  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, AVALU from result;68quit;69proc export data=final outfile="/app/output/adpp.csv" dbms=csv replace; run;