Measure Time to the First Adverse Event

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

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

1# Reference solution for the yamaa benchmark adam-adtte-first-ae (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)910adsl <- read_csv(11  "/app/input/adsl.csv",12  col_types = cols(TRTSDT = col_date(), EOSDT = col_date(), .default = col_character())13)14adae <- read_csv(15  "/app/input/adae.csv",16  col_types = cols(AESEQ = col_integer(), ASTDT = col_date(), .default = col_character())17)1819# The subject's first adverse event by onset date, ties to the lower20# sequence; an event with no onset sorts last, so it is passed over when21# a dated event exists.22first_ae <- adae |>23  filter(!is.na(ASTDT)) |>24  arrange(STUDYID, USUBJID, ASTDT, AESEQ) |>25  distinct(STUDYID, USUBJID, .keep_all = TRUE) |>26  select(STUDYID, USUBJID, AEDT = ASTDT, AESEQ)2728adtte <- adsl |>29  left_join(first_ae, by = c("STUDYID", "USUBJID")) |>30  mutate(31    STARTDT = TRTSDT,32    # The earliest onset, or the end of study when no event carries33    # a usable onset date.34    RAWDT = coalesce(AEDT, EOSDT),35    # A date before treatment start is moved up to it, keeping its36    # event-or-censoring status and source; with no treatment start37    # the date is kept as it is.38    ADT = case_when(39      !is.na(STARTDT) & !is.na(RAWDT) & STARTDT > RAWDT ~ STARTDT,40      .default = RAWDT41    ),42    AVAL = as.integer(ADT - STARTDT) + 1L,43    CNSR = if_else(!is.na(AEDT), 0L, 1L),44    EVNTDESC = if_else(!is.na(AEDT), "AE", "END OF STUDY"),45    SRCDOM = if_else(!is.na(AEDT), "ADAE", "ADSL"),46    SRCVAR = if_else(!is.na(AEDT), "ASTDT", "EOSDT"),47    SRCSEQ = if_else(!is.na(AEDT), AESEQ, NA_integer_),48    PARAMCD = "TTAE",49    PARAM = "Time to First Adverse Event"50  ) |>51  select(52    STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR,53    EVNTDESC, SRCDOM, SRCVAR, SRCSEQ54  ) |>55  arrange(USUBJID)5657dir.create("/app/output", showWarnings = FALSE)58write_csv(adtte, "/app/output/adtte.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adtte-first-ae (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"""Create an ADTTE dataset (time to first adverse event) from ADAE and ADSL.89One record per subject (from ADSL). The first adverse event with a usable10onset date (ASTDT) is the event; subjects without a dated event are11censored at their end-of-study date (EOSDT).12"""1314import csv15from datetime import date1617INPUT_DIR = "/app/input"18OUTPUT_DIR = "/app/output"192021def parse_date(value):22    """Parse an ISO date string, returning None for blank values."""23    value = (value or "").strip()24    if not value:25        return None26    return date.fromisoformat(value)272829def fmt_date(value):30    return value.isoformat() if value is not None else ""313233def read_rows(path):34    with open(path, newline="", encoding="utf-8") as handle:35        return list(csv.DictReader(handle))363738def main():39    adsl = read_rows(f"{INPUT_DIR}/adsl.csv")40    adae = read_rows(f"{INPUT_DIR}/adae.csv")4142    events_by_subject = {}43    for row in adae:44        events_by_subject.setdefault(row["USUBJID"], []).append(row)4546    records = []47    for subj in adsl:48        startdt = parse_date(subj.get("TRTSDT"))49        eosdt = parse_date(subj.get("EOSDT"))5051        dated_events = []52        for event in events_by_subject.get(subj["USUBJID"], []):53            onset = parse_date(event.get("ASTDT"))54            if onset is not None:55                dated_events.append((onset, int(event["AESEQ"])))5657        if dated_events:58            # Earliest onset date; lowest sequence number breaks ties.59            adt, srcseq = min(dated_events)60            cnsr, evntdesc, srcdom, srcvar = 0, "AE", "ADAE", "ASTDT"61            srcseq_text = str(srcseq)62        else:63            adt = eosdt64            cnsr, evntdesc, srcdom, srcvar = 1, "END OF STUDY", "ADSL", "EOSDT"65            srcseq_text = ""6667        # A date before the treatment start is moved up to the treatment68        # start; the record keeps its event or censoring status.69        if adt is not None and startdt is not None and adt < startdt:70            adt = startdt7172        if adt is not None and startdt is not None:73            aval = str((adt - startdt).days + 1)74        else:75            aval = ""7677        records.append(78            {79                "STUDYID": subj["STUDYID"],80                "USUBJID": subj["USUBJID"],81                "PARAMCD": "TTAE",82                "PARAM": "Time to First Adverse Event",83                "STARTDT": fmt_date(startdt),84                "ADT": fmt_date(adt),85                "AVAL": aval,86                "CNSR": str(cnsr),87                "EVNTDESC": evntdesc,88                "SRCDOM": srcdom,89                "SRCVAR": srcvar,90                "SRCSEQ": srcseq_text,91            }92        )9394    fieldnames = [95        "STUDYID", "USUBJID", "PARAMCD", "PARAM", "STARTDT", "ADT",96        "AVAL", "CNSR", "EVNTDESC", "SRCDOM", "SRCVAR", "SRCSEQ",97    ]98    with open(f"{OUTPUT_DIR}/adtte.csv", "w", newline="", encoding="utf-8") as handle:99        writer = csv.DictWriter(handle, fieldnames=fieldnames)100        writer.writeheader()101        writer.writerows(records)102103104if __name__ == "__main__":105    main()

1/* opensas reference solution for the yamaa benchmark adam-adtte-first-ae.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adae;6  length STUDYID USUBJID ASTDT AEDECOD $1024;7  infile "/app/input/adae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. ASTDT : $char1024. AESEQ AEDECOD : $char1024.;9run;1011data adsl;12  length STUDYID USUBJID TRTSDT EOSDT $1024;13  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. TRTSDT : $char1024. EOSDT : $char1024.;15run;1617proc sort data=adae(where=(ASTDT ne '')) out=events; by STUDYID USUBJID ASTDT AESEQ; run;18data firstevent; set events; by STUDYID USUBJID; if first.USUBJID; run;19proc sql; create table joined as select a.*,b.ASTDT,b.AESEQ from adsl as a left join firstevent as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;20data result;21  length PARAMCD $8 PARAM $40 STARTDT ADT $10 EVNTDESC $20 SRCDOM $4 SRCVAR $16;22  set joined; PARAMCD='TTAE'; PARAM='Time to First Adverse Event'; STARTDT=TRTSDT;23  if not missing(ASTDT) then do; ADT=ASTDT; CNSR=0; EVNTDESC='AE'; SRCDOM='ADAE'; SRCVAR='ASTDT'; SRCSEQ=AESEQ; end;24  else do; ADT=EOSDT; CNSR=1; EVNTDESC='END OF STUDY'; SRCDOM='ADSL'; SRCVAR='EOSDT'; end;25  if not missing(STARTDT) and not missing(ADT) then do;26    if ADT<STARTDT then ADT=STARTDT;27    AVAL=input(ADT,yymmdd10.)-input(STARTDT,yymmdd10.)+1;28  end;29run;3031proc sql;32  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR, EVNTDESC, SRCDOM, SRCVAR, SRCSEQ from result;33quit;34proc export data=final outfile="/app/output/adtte.csv" dbms=csv replace; run;