Assign a Composite Responder Status

1library(yamaa)23adrs <- yamaa_domain("spec.yaml")$output4adrs

1import yamaa23adrs = yamaa.yamaa_domain("spec.yaml").output4adrs

1# Reference solution for the yamaa benchmark adam-adrs-composite-response (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(.default = col_character())13)14raw <- read_csv(15  "/app/input/adrs_raw.csv",16  col_types = cols(PCHG = col_double(), .default = col_character())17)1819# The checks apply in a fixed order: a safety or discontinuation rule20# first, then a missing component, then the 75% reduction threshold.21adrs <- raw |>22  left_join(select(adsl, USUBJID, SAEFL, DCSREAS), by = "USUBJID") |>23  mutate(24    PARAMCD = "RESP75",25    PARAM = "EASI-75 Response",26    safety = SAEFL %in% "Y" | (!is.na(DCSREAS) & DCSREAS != ""),27    AVALC = case_when(28      safety ~ "NON-RESPONDER",29      is.na(PCHG) ~ "NOT EVALUABLE",30      PCHG <= -75 ~ "RESPONDER",31      .default = "NON-RESPONDER"32    ),33    ARSN = case_when(34      safety ~ "SAFETY OR DISCONTINUATION RULE",35      is.na(PCHG) ~ "COMPONENT MISSING",36      PCHG <= -75 ~ "THRESHOLD MET",37      .default = "THRESHOLD NOT MET"38    ),39    AVAL = case_when(40      AVALC == "RESPONDER" ~ 1L,41      AVALC == "NON-RESPONDER" ~ 0L42    )43  ) |>44  select(45    STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, PCHG, SAEFL, DCSREAS,46    AVALC, ARSN, AVAL47  ) |>48  arrange(USUBJID, AVISIT)4950dir.create("/app/output", showWarnings = FALSE)51write_csv(adrs, "/app/output/adrs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adrs-composite-response (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)12raw = pl.read_csv("/app/input/adrs_raw.csv", infer_schema=False).with_columns(13    pl.col("PCHG").cast(pl.Float64)14)1516base = raw.join(adsl.select("USUBJID", "SAEFL", "DCSREAS"), on="USUBJID", how="left")1718# The checks apply in a fixed order: a safety or discontinuation rule19# first, then a missing component, then the 75% reduction threshold.20safety = (pl.col("SAEFL") == "Y") | (21    pl.col("DCSREAS").is_not_null() & (pl.col("DCSREAS") != "")22)23avalc = (24    pl.when(safety)25    .then(pl.lit("NON-RESPONDER"))26    .when(pl.col("PCHG").is_null())27    .then(pl.lit("NOT EVALUABLE"))28    .when(pl.col("PCHG") <= -75)29    .then(pl.lit("RESPONDER"))30    .otherwise(pl.lit("NON-RESPONDER"))31)32arsn = (33    pl.when(safety)34    .then(pl.lit("SAFETY OR DISCONTINUATION RULE"))35    .when(pl.col("PCHG").is_null())36    .then(pl.lit("COMPONENT MISSING"))37    .when(pl.col("PCHG") <= -75)38    .then(pl.lit("THRESHOLD MET"))39    .otherwise(pl.lit("THRESHOLD NOT MET"))40)4142adrs = (43    base.with_columns(44        PARAMCD=pl.lit("RESP75"),45        PARAM=pl.lit("EASI-75 Response"),46        AVALC=avalc,47        ARSN=arsn,48    )49    .with_columns(50        AVAL=pl.when(pl.col("AVALC") == "RESPONDER")51        .then(1)52        .when(pl.col("AVALC") == "NON-RESPONDER")53        .then(0)54        .otherwise(None)55        .cast(pl.Int64)56    )57    .select(58        "STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVISIT", "PCHG",59        "SAEFL", "DCSREAS", "AVALC", "ARSN", "AVAL",60    )61    .sort(["USUBJID", "AVISIT"])62)6364Path("/app/output").mkdir(exist_ok=True)65adrs.write_csv("/app/output/adrs.csv")

1/* opensas reference solution for the yamaa benchmark adam-adrs-composite-response.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adrs_raw;6  length STUDYID USUBJID PARAMCD AVISIT $1024;7  infile "/app/input/adrs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. AVISIT : $char1024. PCHG;9run;1011data adsl;12  length STUDYID USUBJID SAEFL DCSREAS $1024;13  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. SAEFL : $char1024. DCSREAS : $char1024.;15run;1617proc sql; create table joined as select a.*,b.SAEFL,b.DCSREAS from adrs_raw as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data result;19  length PARAM $40 AVALC $20 ARSN $40;20  set joined; PARAMCD='RESP75'; PARAM='EASI-75 Response';21  if SAEFL='Y' or not missing(DCSREAS) then do; AVALC='NON-RESPONDER'; ARSN='SAFETY OR DISCONTINUATION RULE'; AVAL=0; end;22  else if missing(PCHG) then do; AVALC='NOT EVALUABLE'; ARSN='COMPONENT MISSING'; end;23  else if PCHG<=-75 then do; AVALC='RESPONDER'; ARSN='THRESHOLD MET'; AVAL=1; end;24  else do; AVALC='NON-RESPONDER'; ARSN='THRESHOLD NOT MET'; AVAL=0; end;25run;2627proc sql;28  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, PCHG, SAEFL, DCSREAS, AVALC, ARSN, AVAL from result;29quit;30proc export data=final outfile="/app/output/adrs.csv" dbms=csv replace; run;