Measure Time to the First Adverse Event

1library(yamaa)23adtte <- yamaa_domain("spec.yaml")$output4adtte

1import yamaa23adtte = yamaa.yamaa_domain("spec.yaml").output4adtte

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 1.67from pathlib import Path89import polars as pl1011adsl = pl.read_csv("/app/input/adsl.csv", infer_schema=False, null_values="").with_columns(12    pl.col("TRTSDT").str.to_date(strict=False),13    pl.col("EOSDT").str.to_date(strict=False),14)15adae = pl.read_csv("/app/input/adae.csv", infer_schema=False, null_values="").with_columns(16    pl.col("AESEQ").cast(pl.Int64, strict=False),17    pl.col("ASTDT").str.to_date(strict=False),18)1920# The subject's first adverse event by onset date, ties to the lower21# sequence; an event with no onset sorts last, so it is passed over when22# a dated event exists.23first_ae = (24    adae.filter(pl.col("ASTDT").is_not_null())25    .sort(["STUDYID", "USUBJID", "ASTDT", "AESEQ"])26    .unique(["STUDYID", "USUBJID"], keep="first", maintain_order=True)27    .select("STUDYID", "USUBJID", AEDT="ASTDT", AESEQ="AESEQ")28)2930adtte = (31    adsl.join(first_ae, on=["STUDYID", "USUBJID"], how="left", maintain_order="left")32    .with_columns(33        STARTDT=pl.col("TRTSDT"),34        # The earliest onset, or the end of study when no event carries35        # a usable onset date.36        RAWDT=pl.coalesce("AEDT", "EOSDT"),37    )38    .with_columns(39        # A date before treatment start is moved up to it, keeping its40        # event-or-censoring status and source; with no treatment start41        # the date is kept as it is.42        ADT=pl.when(pl.col("STARTDT") > pl.col("RAWDT"))43        .then(pl.col("STARTDT"))44        .otherwise(pl.col("RAWDT")),45    )46    .with_columns(47        AVAL=(pl.col("ADT") - pl.col("STARTDT")).dt.total_days() + 1,48        CNSR=pl.when(pl.col("AEDT").is_not_null()).then(0).otherwise(1),49        EVNTDESC=pl.when(pl.col("AEDT").is_not_null())50        .then(pl.lit("AE"))51        .otherwise(pl.lit("END OF STUDY")),52        SRCDOM=pl.when(pl.col("AEDT").is_not_null())53        .then(pl.lit("ADAE"))54        .otherwise(pl.lit("ADSL")),55        SRCVAR=pl.when(pl.col("AEDT").is_not_null())56        .then(pl.lit("ASTDT"))57        .otherwise(pl.lit("EOSDT")),58        SRCSEQ=pl.when(pl.col("AEDT").is_not_null())59        .then(pl.col("AESEQ"))60        .otherwise(None),61        PARAMCD=pl.lit("TTAE"),62        PARAM=pl.lit("Time to First Adverse Event"),63    )64    .select(65        "STUDYID",66        "USUBJID",67        "PARAMCD",68        "PARAM",69        "STARTDT",70        "ADT",71        "AVAL",72        "CNSR",73        "EVNTDESC",74        "SRCDOM",75        "SRCVAR",76        "SRCSEQ",77    )78    .sort("USUBJID")79)8081Path("/app/output").mkdir(parents=True, exist_ok=True)82adtte.write_csv("/app/output/adtte.csv", null_value="")

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;