Link each PK parameter to the period and treatment of its dose

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

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

1# Reference solution for the yamaa benchmark adam-adpp-period-treatment (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)910pp <- read_csv(11  "/app/input/pp.csv",12  col_types = cols(PPSTRESN = col_double(), .default = col_character())13)14ex <- read_csv(15  "/app/input/ex.csv",16  col_types = cols(EXDOSE = col_double(), .default = col_character())17)1819# The subject's dose that starts exactly at the reference date and time;20# TREATMENT 1 is period 1, TREATMENT 2 period 2.21doses <- ex |>22  transmute(23    USUBJID,24    PPRFTDTC = EXSTDTC,25    APERIOD = as.integer(sub("^TREATMENT ", "", EPOCH)),26    TRTA = EXTRT,27    DOSEA = EXDOSE,28    DOSEU = EXDOSU29  )3031adpp <- pp |>32  left_join(doses, by = c("USUBJID", "PPRFTDTC")) |>33  transmute(34    STUDYID, USUBJID,35    PARCAT1 = PPCAT, PARAMCD = PPTESTCD, PARAM = PPTEST, PPRFTDTC,36    APERIOD, TRTA, DOSEA, DOSEU,37    AVAL = PPSTRESN, AVALU = PPSTRESU38  )3940dir.create("/app/output", showWarnings = FALSE)41write_csv(adpp, "/app/output/adpp.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adpp-period-treatment (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 csv8import os9import re1011INPUT_DIR = "/app/input"12OUTPUT_DIR = "/app/output"1314OUT_FIELDS = [15    "STUDYID", "USUBJID", "PARCAT1", "PARAMCD", "PARAM", "PPRFTDTC",16    "APERIOD", "TRTA", "DOSEA", "DOSEU", "AVAL", "AVALU",17]181920def main():21    with open(os.path.join(INPUT_DIR, "ex.csv"), newline="") as f:22        ex_rows = list(csv.DictReader(f))23    with open(os.path.join(INPUT_DIR, "pp.csv"), newline="") as f:24        pp_rows = list(csv.DictReader(f))2526    # Index each subject's doses by their exact start date and time.27    doses = {}28    for ex in ex_rows:29        key = (ex["STUDYID"], ex["USUBJID"], ex["EXSTDTC"])30        doses[key] = ex3132    out_rows = []33    for pp in pp_rows:34        ex = doses.get((pp["STUDYID"], pp["USUBJID"], pp["PPRFTDTC"]))35        if ex is not None:36            match = re.search(r"\d+", ex["EPOCH"])37            aperiod = match.group(0) if match else ""38            trta = ex["EXTRT"]39            dosea = ex["EXDOSE"]40            doseu = ex["EXDOSU"]41        else:42            aperiod = trta = dosea = doseu = ""43        out_rows.append({44            "STUDYID": pp["STUDYID"],45            "USUBJID": pp["USUBJID"],46            "PARCAT1": pp["PPCAT"],47            "PARAMCD": pp["PPTESTCD"],48            "PARAM": pp["PPTEST"],49            "PPRFTDTC": pp["PPRFTDTC"],50            "APERIOD": aperiod,51            "TRTA": trta,52            "DOSEA": dosea,53            "DOSEU": doseu,54            "AVAL": pp["PPSTRESN"],55            "AVALU": pp["PPSTRESU"],56        })5758    os.makedirs(OUTPUT_DIR, exist_ok=True)59    with open(os.path.join(OUTPUT_DIR, "adpp.csv"), "w", newline="") as f:60        writer = csv.DictWriter(f, fieldnames=OUT_FIELDS)61        writer.writeheader()62        writer.writerows(out_rows)636465if __name__ == "__main__":66    main()

1/* opensas reference solution for the yamaa benchmark adam-adpp-period-treatment.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 PPTESTCD PPTEST PPCAT PPSTRESU PPSPEC PPRFTDTC $1024;7  infile "/app/input/pp.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. DOMAIN : $char1024. USUBJID : $char1024. PPSEQ PPTESTCD : $char1024.9        PPTEST : $char1024. PPCAT : $char1024. PPSTRESN PPSTRESU : $char1024. PPSPEC : $char1024.10        PPRFTDTC : $char1024.;11  ORDER=_n_;12run;1314data ex;15  length STUDYID DOMAIN USUBJID EXTRT EXDOSU EXDOSFRM EXROUTE EPOCH EXSTDTC EXENDTC $1024;16  infile "/app/input/ex.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;17  input STUDYID : $char1024. DOMAIN : $char1024. USUBJID : $char1024. EXSEQ EXTRT : $char1024.18        EXDOSE EXDOSU : $char1024. EXDOSFRM : $char1024. EXROUTE : $char1024. EPOCH : $char1024.19        EXSTDTC : $char1024. EXENDTC : $char1024.;20run;2122/* The subject's dose that starts exactly at the reference date and time;23   TREATMENT 1 is period 1, TREATMENT 2 period 2. */24proc sql;25  create table final as26  select p.STUDYID, p.USUBJID, p.PPCAT as PARCAT1, p.PPTESTCD as PARAMCD, p.PPTEST as PARAM,27         p.PPRFTDTC, input(scan(e.EPOCH, 2, ' '), best.) as APERIOD, e.EXTRT as TRTA,28         e.EXDOSE as DOSEA, e.EXDOSU as DOSEU, p.PPSTRESN as AVAL, p.PPSTRESU as AVALU29  from pp as p left join ex as e30    on p.USUBJID=e.USUBJID and p.PPRFTDTC=e.EXSTDTC31  order by p.ORDER;32quit;33proc export data=final outfile="/app/output/adpp.csv" dbms=csv replace; run;