Once-Measured Carryforward

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

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

1# Reference solution for the yamaa benchmark adam-advs-carryforward (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)1011plan <- read_csv(12  "/app/input/plan.csv",13  col_types = cols(ASEQ = col_integer(), ADT = col_date(), .default = col_character())14)15vs <- read_csv(16  "/app/input/vs.csv",17  col_types = cols(18    VSSEQ = col_integer(), VSDTC = col_date(), VSSTRESN = col_double(),19    .default = col_character()20  )21)22adsl <- read_csv(23  "/app/input/adsl.csv",24  col_types = cols(TRTSDT = col_date(), .default = col_character())25)2627# The record collected for a planned measurement: same subject, test code28# as the parameter, and collection date as the planned date.29collected <- plan |>30  left_join(31    vs |> select(STUDYID, USUBJID, VSSEQ, VSTESTCD, VSDTC, AVALCOL = VSSTRESN),32    by = c("STUDYID", "USUBJID", "PARAMCD" = "VSTESTCD", "ADT" = "VSDTC")33  )3435# The collected value, otherwise the most recent earlier value for the36# same subject and parameter, in planned order.37carried <- collected |>38  arrange(STUDYID, USUBJID, PARAMCD, ADT, ASEQ) |>39  group_by(STUDYID, USUBJID, PARAMCD) |>40  fill(AVALCOL, .direction = "down") |>41  mutate(AVAL = AVALCOL) |>42  ungroup()4344# The latest height on or before treatment start, repeated on every45# record of the subject.46heights <- vs |>47  filter(VSTESTCD %in% "HEIGHT", !is.na(VSSTRESN)) |>48  left_join(adsl |> select(STUDYID, USUBJID, TRTSDT), by = c("STUDYID", "USUBJID")) |>49  filter(!is.na(VSDTC), VSDTC <= TRTSDT) |>50  arrange(STUDYID, USUBJID, VSDTC, VSSEQ) |>51  group_by(STUDYID, USUBJID) |>52  summarise(HEIGHTBL = last(VSSTRESN), .groups = "drop")5354advs <- carried |>55  left_join(adsl |> select(STUDYID, USUBJID, TRTSDT), by = c("STUDYID", "USUBJID")) |>56  left_join(heights, by = c("STUDYID", "USUBJID")) |>57  arrange(USUBJID, ASEQ) |>58  select(STUDYID, USUBJID, ASEQ, VSSEQ, PARAMCD, ADT, AVAL, TRTSDT, HEIGHTBL)5960dir.create("/app/output", showWarnings = FALSE)61write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-carryforward (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 1.67"""Build ADVS with one record per planned measurement.89Reads ADSL, PLAN and VS from /app/input and writes /app/output/advs.csv.10A collected VS record belongs to a planned measurement when study,11subject, test code (= planned parameter code) and collection date12(= ADT) all match. Uncollected planned measurements carry forward the13most recent earlier collected value for the same subject and parameter14(LOCF). HEIGHTBL is the latest height collected on or before the15subject's treatment start date.16"""1718import csv19import os2021INPUT_DIR = "/app/input"22OUTPUT_DIR = "/app/output"232425def read_csv(name):26    with open(os.path.join(INPUT_DIR, name), newline="") as f:27        return list(csv.DictReader(f))282930def main():31    adsl = read_csv("adsl.csv")32    plan = read_csv("plan.csv")33    vs = read_csv("vs.csv")3435    trtsdt = {row["USUBJID"]: row["TRTSDT"] for row in adsl}3637    # Collected records keyed by (study, subject, test code).38    collected = {}39    for row in vs:40        key = (row["STUDYID"], row["USUBJID"], row["VSTESTCD"])41        collected.setdefault(key, []).append(row)42    for rows in collected.values():43        rows.sort(key=lambda r: (r["VSDTC"], int(r["VSSEQ"])))4445    def heightbl(usubjid):46        start = trtsdt.get(usubjid, "")47        best = None48        for row in vs:49            if (50                row["USUBJID"] == usubjid51                and row["VSTESTCD"] == "HEIGHT"52                and row["VSDTC"] <= start53            ):54                if best is None or (row["VSDTC"], int(row["VSSEQ"])) > (55                    best["VSDTC"],56                    int(best["VSSEQ"]),57                ):58                    best = row59        return best["VSSTRESN"] if best is not None else ""6061    out_rows = []62    for p in plan:63        key = (p["STUDYID"], p["USUBJID"], p["PARAMCD"])64        records = collected.get(key, [])65        match = None66        earlier = None67        for row in records:68            if row["VSDTC"] == p["ADT"]:69                match = row70            elif row["VSDTC"] < p["ADT"]:71                earlier = row72        if match is not None:73            vsseq = match["VSSEQ"]74            aval = match["VSSTRESN"]75        else:76            vsseq = ""77            aval = earlier["VSSTRESN"] if earlier is not None else ""78        out_rows.append(79            {80                "STUDYID": p["STUDYID"],81                "USUBJID": p["USUBJID"],82                "ASEQ": p["ASEQ"],83                "VSSEQ": vsseq,84                "PARAMCD": p["PARAMCD"],85                "ADT": p["ADT"],86                "AVAL": aval,87                "TRTSDT": trtsdt.get(p["USUBJID"], ""),88                "HEIGHTBL": heightbl(p["USUBJID"]),89            }90        )9192    os.makedirs(OUTPUT_DIR, exist_ok=True)93    fieldnames = [94        "STUDYID",95        "USUBJID",96        "ASEQ",97        "VSSEQ",98        "PARAMCD",99        "ADT",100        "AVAL",101        "TRTSDT",102        "HEIGHTBL",103    ]104    with open(os.path.join(OUTPUT_DIR, "advs.csv"), "w", newline="") as f:105        writer = csv.DictWriter(f, fieldnames=fieldnames)106        writer.writeheader()107        writer.writerows(out_rows)108109110if __name__ == "__main__":111    main()

1/* opensas reference solution for the yamaa benchmark adam-advs-carryforward.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID TRTSDT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRTSDT : $char1024.;9run;1011data plan;12  length STUDYID USUBJID PARAMCD ADT $1024;13  infile "/app/input/plan.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. ASEQ PARAMCD : $char1024. ADT : $char1024.;15run;1617data vs;18  length STUDYID USUBJID VSTESTCD VSDTC $1024;19  infile "/app/input/vs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VSTESTCD : $char1024. VSDTC : $char1024. VSSTRESN;21run;2223proc sql;24  create table heights as select a.STUDYID,a.USUBJID,a.VSSTRESN as HEIGHTBL,a.VSDTC,a.VSSEQ from vs as a inner join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID25    where a.VSTESTCD='HEIGHT' and not missing(a.VSSTRESN) and a.VSDTC ne '' and a.VSDTC<=b.TRTSDT;26quit;27proc sort data=heights; by STUDYID USUBJID descending VSDTC descending VSSEQ; run;28data height; set heights; by STUDYID USUBJID; if first.USUBJID; run;29proc sql;30  create table collected as select a.*,b.VSSEQ,b.VSSTRESN as AVALCOL,c.TRTSDT,d.HEIGHTBL from plan as a31    left join vs as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and a.PARAMCD=b.VSTESTCD and a.ADT=b.VSDTC32    left join adsl as c on a.STUDYID=c.STUDYID and a.USUBJID=c.USUBJID left join height as d on a.STUDYID=d.STUDYID and a.USUBJID=d.USUBJID;33quit;34proc sort data=collected; by STUDYID USUBJID PARAMCD ADT ASEQ; run;35data result;36  retain carried; set collected; by STUDYID USUBJID PARAMCD;37  if first.PARAMCD then carried=.;38  if not missing(AVALCOL) then carried=AVALCOL;39  AVAL=carried;40run;4142proc sql;43  create table final as select STUDYID, USUBJID, ASEQ, VSSEQ, PARAMCD, ADT, AVAL, TRTSDT, HEIGHTBL from result;44quit;45proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;