Assign Analysis Windows from the Window Table

1library(yamaa)23advs <- yamaa_domain("spec.yaml")$output4advs

1import yamaa23advs = yamaa.yamaa_domain("spec.yaml").output4advs

1# Reference solution for the yamaa benchmark adam-advs-window-table (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(purrr)9library(readr)1011raw <- read_csv(12  "/app/input/advs_raw.csv",13  col_types = cols(14    VSSEQ = col_integer(), ADT = col_date(), ADY = col_integer(),15    AVAL = col_double(), .default = col_character()16  )17)18windows <- read_csv(19  "/app/input/awindow.csv",20  col_types = cols(21    AVISITN = col_integer(), AWLO = col_integer(), AWHI = col_integer(),22    AWTARGET = col_integer(), .default = col_character()23  )24)2526# The one window in the same study whose first-to-last range, both ends27# inclusive, holds the study day. An absent bound never matches.28match_window <- function(studyid, ady) {29  if (is.na(ady)) {30    return(tibble::tibble(AVISIT = NA_character_, AVISITN = NA_integer_, AWTARGET = NA_integer_))31  }32  hit <- windows |>33    filter(34      STUDYID == studyid, !is.na(AWLO), !is.na(AWHI),35      AWLO <= ady, ady <= AWHI36    ) |>37    slice_head(n = 1)38  if (nrow(hit) == 0) {39    tibble::tibble(AVISIT = NA_character_, AVISITN = NA_integer_, AWTARGET = NA_integer_)40  } else {41    hit |> select(AVISIT, AVISITN, AWTARGET)42  }43}4445framed <- raw |>46  arrange(STUDYID, USUBJID, VSSEQ) |>47  mutate(window = map2(STUDYID, ADY, match_window)) |>48  tidyr::unnest(window) |>49  mutate(50    AWTDIFF = ADY - AWTARGET,51    AWTABS = abs(AWTDIFF)52  )5354# The record nearest its target in each study, subject, parameter, and55# visit; the lower sequence number breaks a tie.56flagged <- framed |>57  filter(!is.na(AVISIT)) |>58  arrange(AWTABS, VSSEQ) |>59  distinct(STUDYID, USUBJID, PARAMCD, AVISIT, .keep_all = TRUE) |>60  select(STUDYID, USUBJID, PARAMCD, AVISIT, VSSEQ) |>61  mutate(ANL01FL = "Y")6263advs <- framed |>64  select(-AWTABS) |>65  left_join(flagged, by = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT", "VSSEQ")) |>66  arrange(STUDYID, USUBJID, VSSEQ) |>67  select(68    STUDYID, USUBJID, PARAMCD, VSSEQ, VISIT, ADT, ADY, AVAL,69    AVISIT, AVISITN, AWTARGET, AWTDIFF, ANL01FL70  )7172dir.create("/app/output", showWarnings = FALSE)73write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-window-table (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 pl1011raw = pl.read_csv("/app/input/advs_raw.csv", infer_schema=False).with_columns(12    pl.col("VSSEQ").cast(pl.Int64, strict=False),13    pl.col("ADT").str.to_date(strict=False),14    pl.col("ADY").cast(pl.Int64, strict=False),15    pl.col("AVAL").cast(pl.Float64, strict=False),16)17windows = pl.read_csv("/app/input/awindow.csv", infer_schema=False).with_columns(18    pl.col("AVISITN").cast(pl.Int64, strict=False),19    pl.col("AWLO").cast(pl.Int64, strict=False),20    pl.col("AWHI").cast(pl.Int64, strict=False),21    pl.col("AWTARGET").cast(pl.Int64, strict=False),22)2324# The one window in the same study whose first-to-last range, both ends25# inclusive, holds the study day. An absent bound never matches.26assigned = []27for record in raw.sort(["STUDYID", "USUBJID", "VSSEQ"]).iter_rows(named=True):28    match = None29    if record["ADY"] is not None:30        candidates = windows.filter(31            (pl.col("STUDYID") == record["STUDYID"])32            & pl.col("AWLO").is_not_null()33            & pl.col("AWHI").is_not_null()34            & (pl.col("AWLO") <= record["ADY"])35            & (record["ADY"] <= pl.col("AWHI"))36        )37        if candidates.height:38            match = candidates.row(0, named=True)39    assigned.append(40        {41            **record,42            "AVISIT": match["AVISIT"] if match else None,43            "AVISITN": match["AVISITN"] if match else None,44            "AWTARGET": match["AWTARGET"] if match else None,45            "AWTDIFF": record["ADY"] - match["AWTARGET"]46            if (match and record["ADY"] is not None and match["AWTARGET"] is not None)47            else None,48        }49    )5051framed = pl.DataFrame(assigned).with_columns(52    pl.col("VSSEQ").cast(pl.Int64),53    pl.col("ADT").cast(pl.Date),54    pl.col("ADY").cast(pl.Int64),55    pl.col("AVAL").cast(pl.Float64),56    pl.col("AVISITN").cast(pl.Int64),57    pl.col("AWTARGET").cast(pl.Int64),58    pl.col("AWTDIFF").cast(pl.Int64),59    AWTABS=pl.col("AWTDIFF").abs(),60)6162# The record nearest its target in each study, subject, parameter, and63# visit; the lower sequence number breaks a tie.64flagged = (65    framed.filter(pl.col("AVISIT").is_not_null())66    .sort(["AWTABS", "VSSEQ"], nulls_last=True)67    .unique(["STUDYID", "USUBJID", "PARAMCD", "AVISIT"], keep="first", maintain_order=True)68    .select("STUDYID", "USUBJID", "PARAMCD", "AVISIT", "VSSEQ")69    .with_columns(ANL01FL=pl.lit("Y"))70)7172advs = (73    framed.drop("AWTABS")74    .join(75        flagged,76        on=["STUDYID", "USUBJID", "PARAMCD", "AVISIT", "VSSEQ"],77        how="left",78    )79    .sort(["STUDYID", "USUBJID", "VSSEQ"])80    .select(81        "STUDYID", "USUBJID", "PARAMCD", "VSSEQ", "VISIT", "ADT", "ADY",82        "AVAL", "AVISIT", "AVISITN", "AWTARGET", "AWTDIFF", "ANL01FL",83    )84)8586Path("/app/output").mkdir(parents=True, exist_ok=True)87advs.write_csv("/app/output/advs.csv")

1/* opensas reference solution for the yamaa benchmark adam-advs-window-table.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data advs_raw;6  length STUDYID USUBJID PARAMCD VISIT ADT $1024;7  infile "/app/input/advs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. VSSEQ VISIT : $char1024. VISITNUM ADT : $char1024. ADY AVAL;9run;1011data awindow;12  length STUDYID AVISIT $1024;13  infile "/app/input/awindow.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. AVISIT : $char1024. AVISITN AWLO AWHI AWTARGET;15run;1617proc sql;18  create table candidates as select a.*,b.AVISIT,b.AVISITN,b.AWTARGET,a.ADY-b.AWTARGET as AWTDIFF from advs_raw as a left join awindow as b19    on a.STUDYID=b.STUDYID and not missing(a.ADY) and not missing(b.AWLO) and not missing(b.AWHI) and a.ADY>=b.AWLO and a.ADY<=b.AWHI;20quit;21data ordered; set candidates; distance=abs(AWTDIFF); nodistance=missing(distance); run;22proc sort data=ordered; by STUDYID USUBJID PARAMCD AVISITN nodistance distance VSSEQ; run;23data result; length ANL01FL $1; set ordered; by STUDYID USUBJID PARAMCD AVISITN; if first.AVISITN and not missing(AVISITN) then ANL01FL='Y'; run;2425proc sql;26  create table final as select STUDYID, USUBJID, PARAMCD, VSSEQ, VISIT, ADT, ADY, AVAL, AVISIT, AVISITN, AWTARGET, AWTDIFF, ANL01FL from result;27quit;28proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;