Treatment Emergence Timing

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

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

1# Reference solution for the yamaa benchmark adam-adae-onset-emergence (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 1.67# ADAE: treatment emergence decided at the second, one record per AE record.8suppressPackageStartupMessages({9  library(dplyr)10  library(readr)11  library(stringr)12})1314in_dir <- "/app/input"15out_dir <- "/app/output"16dir.create(out_dir, showWarnings = FALSE, recursive = TRUE)1718read_chr <- function(path) {19  read_csv(path, col_types = cols(.default = col_character()),20           na = c(""), trim_ws = TRUE, progress = FALSE)21}2223adsl <- read_chr(file.path(in_dir, "adsl.csv"))24ae <- read_chr(file.path(in_dir, "ae.csv"))2526# ISO 8601 datetime text to POSIXct (UTC, so a day is always 24 hours).27# A value without seconds falls on second zero; anything else is no value.28parse_dtm <- function(x) {29  x <- str_trim(x)30  full <- case_when(31    is.na(x) ~ NA_character_,32    str_detect(x, "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}$") ~ x,33    str_detect(x, "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}$") ~ paste0(x, ":00"),34    TRUE ~ NA_character_35  )36  as.POSIXct(full, format = "%Y-%m-%dT%H:%M:%S", tz = "UTC")37}3839fmt_dtm <- function(x) {40  out <- format(x, "%Y-%m-%dT%H:%M:%S", tz = "UTC")41  out[is.na(x)] <- NA_character_42  out43}4445day_secs <- 24 * 60 * 604647adsl_t <- adsl %>%48  transmute(49    STUDYID, USUBJID, EOTSTT,50    TRTSDTM = parse_dtm(TRTSDTM),51    TRTEDTM = parse_dtm(TRTEDTM)52  )5354adae <- ae %>%55  mutate(AESEQ = as.integer(AESEQ), .row = row_number()) %>%56  left_join(adsl_t, by = c("STUDYID", "USUBJID")) %>%57  mutate(58    ASTDTM = parse_dtm(AESTDTC),59    treated = !is.na(TRTSDTM),60    ongoing = !is.na(EOTSTT) & EOTSTT == "ONGOING",61    window_days = if_else(!is.na(AESER) & AESER == "N", 30, 90),62    TEENDDTM = if_else(treated & !ongoing,63                       TRTEDTM + window_days * day_secs,64                       as.POSIXct(NA, tz = "UTC")),65    TRTEMFL = case_when(66      !treated ~ NA_character_,67      is.na(ASTDTM) ~ "Y",68      ongoing & ASTDTM >= TRTSDTM ~ "Y",69      !ongoing & !is.na(TEENDDTM) & ASTDTM >= TRTSDTM & ASTDTM <= TEENDDTM ~ "Y",70      TRUE ~ NA_character_71    )72  )7374# AOCCFL: earliest treatment-emergent event with an ASTDTM, lower AESEQ on ties.75first_te <- adae %>%76  filter(TRTEMFL == "Y", !is.na(ASTDTM)) %>%77  arrange(USUBJID, ASTDTM, AESEQ) %>%78  group_by(USUBJID) %>%79  slice(1) %>%80  ungroup() %>%81  select(.row)8283adae <- adae %>%84  mutate(AOCCFL = if_else(.row %in% first_te$.row, "Y", NA_character_)) %>%85  arrange(.row) %>%86  transmute(87    STUDYID, USUBJID, AESEQ, AETERM, AESER,88    ASTDTM = fmt_dtm(ASTDTM),89    TRTSDTM = fmt_dtm(TRTSDTM),90    TRTEDTM = fmt_dtm(TRTEDTM),91    EOTSTT,92    TEENDDTM = fmt_dtm(TEENDDTM),93    TRTEMFL, AOCCFL94  )9596write_csv(adae, file.path(out_dir, "adae.csv"), na = "")

1# Reference solution for the yamaa benchmark adam-adae-onset-emergence (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"""Derive ADAE (one record per AE record) from ADSL and AE.89Treatment emergence is judged to the second.10"""1112import csv13from datetime import datetime, timedelta14from pathlib import Path1516INPUT = Path("/app/input")17OUTPUT = Path("/app/output")1819COLUMNS = [20    "STUDYID", "USUBJID", "AESEQ", "AETERM", "AESER", "ASTDTM", "TRTSDTM",21    "TRTEDTM", "EOTSTT", "TEENDDTM", "TRTEMFL", "AOCCFL",22]2324ISO = "%Y-%m-%dT%H:%M:%S"252627def parse_dtm(value):28    """ISO 8601 date-time to the second; a value without seconds is at second zero."""29    value = (value or "").strip()30    if not value:31        return None32    for fmt in (ISO, "%Y-%m-%dT%H:%M"):33        try:34            return datetime.strptime(value, fmt)35        except ValueError:36            pass37    return None383940def fmt_dtm(value):41    return value.strftime(ISO) if value is not None else ""424344def read_csv(path):45    with open(path, newline="", encoding="utf-8") as handle:46        return list(csv.DictReader(handle))474849def main():50    adsl = {51        (row["STUDYID"], row["USUBJID"]): row52        for row in read_csv(INPUT / "adsl.csv")53    }54    ae = read_csv(INPUT / "ae.csv")5556    records = []57    for row in ae:58        subject = adsl.get((row["STUDYID"], row["USUBJID"]), {})59        trtsdtm = parse_dtm(subject.get("TRTSDTM"))60        trtedtm = parse_dtm(subject.get("TRTEDTM"))61        eotstt = (subject.get("EOTSTT") or "").strip()62        aeser = (row.get("AESER") or "").strip()63        astdtm = parse_dtm(row.get("AESTDTC"))6465        treated = trtsdtm is not None66        ongoing = eotstt == "ONGOING"6768        teenddtm = None69        if treated and not ongoing and trtedtm is not None:70            days = 30 if aeser == "N" else 9071            teenddtm = trtedtm + timedelta(days=days)7273        trtemfl = ""74        if treated:75            if astdtm is None:76                trtemfl = "Y"77            elif astdtm >= trtsdtm:78                if ongoing:79                    trtemfl = "Y"80                elif teenddtm is not None and astdtm <= teenddtm:81                    trtemfl = "Y"8283        records.append({84            "STUDYID": row["STUDYID"],85            "USUBJID": row["USUBJID"],86            "AESEQ": int(row["AESEQ"]),87            "AETERM": row["AETERM"],88            "AESER": aeser,89            "ASTDTM": astdtm,90            "TRTSDTM": trtsdtm,91            "TRTEDTM": trtedtm,92            "EOTSTT": eotstt,93            "TEENDDTM": teenddtm,94            "TRTEMFL": trtemfl,95            "AOCCFL": "",96        })9798    records.sort(key=lambda r: (r["STUDYID"], r["USUBJID"], r["AESEQ"]))99100    # First treatment-emergent event per subject by ASTDTM, lower AESEQ on ties.101    first = {}102    for rec in records:103        if rec["TRTEMFL"] != "Y" or rec["ASTDTM"] is None:104            continue105        key = (rec["STUDYID"], rec["USUBJID"])106        best = first.get(key)107        if best is None or (rec["ASTDTM"], rec["AESEQ"]) < (best["ASTDTM"], best["AESEQ"]):108            first[key] = rec109    for rec in first.values():110        rec["AOCCFL"] = "Y"111112    OUTPUT.mkdir(parents=True, exist_ok=True)113    with open(OUTPUT / "adae.csv", "w", newline="", encoding="utf-8") as handle:114        writer = csv.writer(handle, lineterminator="\n")115        writer.writerow(COLUMNS)116        for rec in records:117            writer.writerow([118                rec["STUDYID"], rec["USUBJID"], rec["AESEQ"], rec["AETERM"],119                rec["AESER"], fmt_dtm(rec["ASTDTM"]), fmt_dtm(rec["TRTSDTM"]),120                fmt_dtm(rec["TRTEDTM"]), rec["EOTSTT"], fmt_dtm(rec["TEENDDTM"]),121                rec["TRTEMFL"], rec["AOCCFL"],122            ])123124125if __name__ == "__main__":126    main()

1/* opensas reference solution for the yamaa benchmark adam-adae-onset-emergence.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 TRTSDTM TRTEDTM EOTSTT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRTSDTM : $char1024. TRTEDTM : $char1024. EOTSTT : $char1024.;9run;1011data ae;12  length STUDYID USUBJID AETERM AESER AESTDTC $1024;13  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AESER : $char1024. AESTDTC : $char1024.;15run;1617proc sql; create table joined as select a.*,b.TRTSDTM,b.TRTEDTM,b.EOTSTT from ae as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data events;19  length ASTDTM TEENDDTM $19 TRTEMFL $1;20  set joined; ASTDTM=''; TEENDDTM=''; TRTEMFL='';21  /* Datetimes collected without seconds are completed to the second so the22     onset and the first exposure compare at the moment, not the day. */23  if not missing(AESTDTC) then ASTDTM=cats(AESTDTC,ifc(lengthn(AESTDTC)=16,':00',''));24  /* The window ends 30 days after last exposure for an event recorded as25     non-serious and 90 days after for any other; while treatment is26     ongoing it has no end. Whole days keep the time of day. */27  window_days=90;28  if AESER='N' then window_days=30;29  if upcase(EOTSTT) ne 'ONGOING' and not missing(TRTEDTM) then30    TEENDDTM=cats(put(input(substr(TRTEDTM,1,10),yymmdd10.)+window_days,yymmdd10.),substr(TRTEDTM,11));31  onset=input(ASTDTM,e8601dt.); treatment=input(TRTSDTM,e8601dt.); window_end=input(TEENDDTM,e8601dt.);32  /* The window rule: onset at or after first exposure and, unless33     treatment is ongoing, at or before the window end is34     treatment-emergent. A missing onset cannot be ruled pre-treatment,35     so a treated subject's event with a missing onset is flagged Y; an36     untreated subject (no first exposure) is never treatment-emergent. */37  if not missing(treatment) then do;38    if missing(onset) then TRTEMFL='Y';39    else if onset>=treatment and (upcase(EOTSTT)='ONGOING' or (not missing(window_end) and onset<=window_end)) then TRTEMFL='Y';40  end;41run;42proc sort data=events(where=(TRTEMFL='Y' and not missing(onset))) out=eligible; by STUDYID USUBJID onset AESEQ; run;43data firstevent; set eligible; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID AESEQ; run;44proc sql; create table result as select a.*,case when not missing(b.AESEQ) then 'Y' else '' end as AOCCFL from events as a left join firstevent as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and a.AESEQ=b.AESEQ; quit;4546proc sql;47  create table final as select STUDYID, USUBJID, AESEQ, AETERM, AESER, ASTDTM, TRTSDTM, TRTEDTM, EOTSTT, TEENDDTM, TRTEMFL, AOCCFL from result;48quit;49proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;