Post-Index Event Flags

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-post-index (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)910ae <- read_csv(11  "/app/input/ae.csv",12  col_types = cols(AESEQ = col_integer(), .default = col_character())13)1415# Each subject's index event: the earliest start date, with the16# higher sequence number ordered after on the same date.17first_index <- ae |>18  filter(AEDECOD %in% "COVID-19", !is.na(AESTDTC), AESTDTC != "") |>19  arrange(USUBJID, AESTDTC, AESEQ) |>20  distinct(USUBJID, .keep_all = TRUE) |>21  select(USUBJID, FIRST_DT = AESTDTC, FIRST_SEQ = AESEQ)2223adae <- ae |>24  left_join(first_index, by = "USUBJID") |>25  mutate(26    ASTDT = if_else(is.na(AESTDTC) | AESTDTC == "", NA_character_, AESTDTC),27    AFTIDXFL = if_else(28      !is.na(ASTDT) & !is.na(FIRST_DT) &29        (ASTDT > FIRST_DT | (ASTDT == FIRST_DT & AESEQ > FIRST_SEQ)),30      "Y",31      NA_character_32    )33  ) |>34  select(STUDYID, USUBJID, AESEQ, AEDECOD, ASTDT, AFTIDXFL)3536dir.create("/app/output", showWarnings = FALSE)37write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-post-index (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)1415# Each subject's index event: the earliest start date, with the16# higher sequence number ordered after on the same date. ISO dates sort17# as text.18first_index = (19    ae.filter(20        (pl.col("AEDECOD") == "COVID-19") & pl.col("AESTDTC").is_not_null()21    )22    .sort(["USUBJID", "AESTDTC", "AESEQ"], nulls_last=True)23    .unique("USUBJID", keep="first", maintain_order=True)24    .select("USUBJID", FIRST_DT="AESTDTC", FIRST_SEQ="AESEQ")25)2627adae = (28    ae.join(first_index, on="USUBJID", how="left", maintain_order="left")29    .with_columns(ASTDT=pl.col("AESTDTC"))30    .with_columns(31        AFTIDXFL=pl.when(32            pl.col("ASTDT").is_not_null()33            & pl.col("FIRST_DT").is_not_null()34            & (35                (pl.col("ASTDT") > pl.col("FIRST_DT"))36                | (37                    (pl.col("ASTDT") == pl.col("FIRST_DT"))38                    & (pl.col("AESEQ") > pl.col("FIRST_SEQ"))39                )40            )41        ).then(pl.lit("Y"))42    )43    .select("STUDYID", "USUBJID", "AESEQ", "AEDECOD", "ASTDT", "AFTIDXFL")44)4546Path("/app/output").mkdir(exist_ok=True)47adae.write_csv("/app/output/adae.csv")

1/* opensas reference solution for the yamaa benchmark adam-adae-post-index.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ae;6  length STUDYID USUBJID AEDECOD AESTDTC $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AEDECOD : $char1024. AESTDTC : $char1024.;9run;1011proc sort data=ae(where=(AEDECOD='COVID-19' and AESTDTC ne '')) out=indices; by STUDYID USUBJID AESTDTC AESEQ; run;12data firstindex; set indices; by STUDYID USUBJID; if first.USUBJID; run;13proc sql;14  create table result as select a.*,a.AESTDTC as ASTDT,15  case when not missing(a.AESTDTC) and not missing(b.AESTDTC) and (a.AESTDTC>b.AESTDTC or (a.AESTDTC=b.AESTDTC and a.AESEQ>b.AESEQ)) then 'Y' else '' end as AFTIDXFL16  from ae as a left join firstindex as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID;17quit;1819proc sql;20  create table final as select STUDYID, USUBJID, AESEQ, AEDECOD, ASTDT, AFTIDXFL from result;21quit;22proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;