Treatment Emergence Timing

1library(yamaa)23adae <- yamaa_domain("spec.yaml")$output4adae

1import yamaa23adae = yamaa.yamaa_domain("spec.yaml").output4adae

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 1.67library(dplyr, warn.conflicts = FALSE)8library(readr)9library(stringr)1011ae <- read_csv(12  "/app/input/ae.csv",13  col_types = cols(AESEQ = col_integer(), .default = col_character())14)15adsl <- read_csv(16  "/app/input/adsl.csv",17  col_types = cols(.default = col_character())18)1920# Datetimes collected without seconds are completed to the second so the21# onset and the first exposure compare at the moment, not the day.22complete_seconds <- function(x) {23  if_else(24    !is.na(x) & str_detect(x, "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}$"),25    paste0(x, ":00"),26    x27  )28}2930ae <- ae |>31  mutate(ASTDTM = complete_seconds(AESTDTC)) |>32  select(STUDYID, USUBJID, AESEQ, AETERM, ASTDTM)3334adsl <- adsl |>35  mutate(TRTSDTM = complete_seconds(TRTSDTM), TEENDDTM = complete_seconds(TEENDDTM)) |>36  select(USUBJID, TRTSDTM, TEENDDTM)3738# The window rule: onset inside [first exposure, window end] is39# treatment-emergent. A missing onset cannot be ruled pre-treatment,40# so a treated subject's event with a missing onset is flagged Y; an41# untreated subject (no first exposure) is never treatment-emergent.42adae <- ae |>43  left_join(adsl, by = "USUBJID") |>44  mutate(45    TRTEMFL = case_when(46      is.na(TRTSDTM) ~ NA_character_,47      is.na(ASTDTM) ~ "Y",48      ASTDTM >= TRTSDTM & ASTDTM <= TEENDDTM ~ "Y",49      .default = NA_character_50    )51  )5253# The subject's earliest treatment-emergent event with a known onset,54# ordered by onset moment with the lower AESEQ settling ties at the55# same second.56first <- adae |>57  filter(TRTEMFL %in% "Y", !is.na(ASTDTM)) |>58  arrange(USUBJID, ASTDTM, AESEQ) |>59  distinct(USUBJID, .keep_all = TRUE) |>60  select(USUBJID, FIRST_SEQ = AESEQ)6162adae <- adae |>63  left_join(first, by = "USUBJID") |>64  mutate(65    AOCCFL = if_else(!is.na(FIRST_SEQ) & AESEQ == FIRST_SEQ, "Y", NA_character_)66  ) |>67  select(68    STUDYID, USUBJID, AESEQ, AETERM, ASTDTM, TRTSDTM, TEENDDTM,69    TRTEMFL, AOCCFL70  )7172dir.create("/app/output", showWarnings = FALSE)73write_csv(adae, "/app/output/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 1.67from pathlib import Path89import polars as pl1011ae = pl.read_csv("/app/input/ae.csv", infer_schema=False).with_columns(12    pl.col("AESEQ").cast(pl.Int64)13)14adsl = pl.read_csv("/app/input/adsl.csv", infer_schema=False)151617def complete_seconds(frame: pl.DataFrame, name: str, out: str) -> pl.DataFrame:18    # Datetimes collected without seconds are completed to the second so19    # the onset and the first exposure compare at the moment, not the day.20    return frame.with_columns(21        pl.when(pl.col(name).str.contains(r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}$"))22        .then(pl.col(name) + ":00")23        .otherwise(pl.col(name))24        .alias(out)25    )262728ae = complete_seconds(ae, "AESTDTC", "ASTDTM").select(29    "STUDYID", "USUBJID", "AESEQ", "AETERM", "ASTDTM"30)31adsl = (32    complete_seconds(adsl, "TRTSDTM", "TRTSDTM")33    .pipe(complete_seconds, "TEENDDTM", "TEENDDTM")34    .select("USUBJID", "TRTSDTM", "TEENDDTM")35)3637# The window rule: onset inside [first exposure, window end] is38# treatment-emergent. A missing onset cannot be ruled pre-treatment,39# so a treated subject's event with a missing onset is flagged Y; an40# untreated subject (no first exposure) is never treatment-emergent.41adae = ae.join(adsl, on="USUBJID", how="left", maintain_order="left").with_columns(42    TRTEMFL=pl.when(pl.col("TRTSDTM").is_null())43    .then(None)44    .when(pl.col("ASTDTM").is_null())45    .then(pl.lit("Y"))46    .when(47        (pl.col("ASTDTM") >= pl.col("TRTSDTM"))48        & (pl.col("ASTDTM") <= pl.col("TEENDDTM"))49    )50    .then(pl.lit("Y"))51    .otherwise(None)52)5354# The subject's earliest treatment-emergent event with a known onset,55# ordered by onset moment with the lower AESEQ settling ties at the56# same second. ISO datetimes sort as text once seconds are completed.57first = (58    adae.filter(59        (pl.col("TRTEMFL") == "Y") & pl.col("ASTDTM").is_not_null()60    )61    .sort(["USUBJID", "ASTDTM", "AESEQ"], nulls_last=True)62    .unique("USUBJID", keep="first", maintain_order=True)63    .select("USUBJID", FIRST_SEQ="AESEQ")64)6566adae = (67    adae.join(first, on="USUBJID", how="left")68    .with_columns(69        AOCCFL=pl.when(70            pl.col("FIRST_SEQ").is_not_null() & (pl.col("AESEQ") == pl.col("FIRST_SEQ"))71        ).then(pl.lit("Y"))72    )73    .select(74        "STUDYID",75        "USUBJID",76        "AESEQ",77        "AETERM",78        "ASTDTM",79        "TRTSDTM",80        "TEENDDTM",81        "TRTEMFL",82        "AOCCFL",83    )84)8586Path("/app/output").mkdir(exist_ok=True)87adae.write_csv("/app/output/adae.csv")

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 TRTENDTM TEENDDTM $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRTSDTM : $char1024. TRTENDTM : $char1024. TEENDDTM : $char1024.;9run;1011data ae;12  length STUDYID USUBJID AETERM AESTDTC $1024;13  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AESTDTC : $char1024.;15run;1617proc sql; create table joined as select a.*,b.TRTSDTM,b.TEENDDTM 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 $19 TRTEMFL $1;20  set joined; ASTDTM=''; 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  onset=input(ASTDTM,e8601dt.); treatment=input(TRTSDTM,e8601dt.); window_end=input(TEENDDTM,e8601dt.);25  /* The window rule: onset inside [first exposure, window end] is26     treatment-emergent. A missing onset cannot be ruled pre-treatment,27     so a treated subject's event with a missing onset is flagged Y; an28     untreated subject (no first exposure) is never treatment-emergent. */29  if not missing(treatment) then do;30    if missing(onset) then TRTEMFL='Y';31    else if onset>=treatment and onset<=window_end then TRTEMFL='Y';32  end;33run;34proc sort data=events(where=(TRTEMFL='Y' and not missing(onset))) out=eligible; by STUDYID USUBJID onset AESEQ; run;35data firstevent; set eligible; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID AESEQ; run;36proc 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;3738proc sql;39  create table final as select STUDYID, USUBJID, AESEQ, AETERM, ASTDTM, TRTSDTM, TEENDDTM, TRTEMFL, AOCCFL from result;40quit;41proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;