Derive the Change on Standing and Orthostatic Flags

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

1import yamaa23yamaa.spec("spec.yaml").run().output

1# Reference solution for the yamaa benchmark2# adam-advs-orthostatic-criteria (R track).3#4# Written from the benchmark's full prompt and its inputs alone, as an agent5# would write it. Harbor's oracle agent runs it to check that the prompt can6# be solved and that the grader scores a correct answer 1.78library(dplyr, warn.conflicts = FALSE)9library(readr)1011vs <- read_csv(12  "/app/input/vs.csv",13  col_types = cols(14    VSSEQ = col_integer(), VSSTRESN = col_double(),15    .default = col_character()16  )17)1819# The one reading of a test in a position at a visit; no such reading,20# or a reading with no result, gives no value.21only_value <- function(mask, values) {22  picked <- values[which(mask)]23  if (length(picked) > 1) {24    stop("more than one reading for a test, position and visit")25  }26  if (length(picked) == 0) NA_real_ else picked27}2829standing <- "AFTER 3 MIN STANDING"30visits <- vs |>31  group_by(STUDYID, USUBJID, AVISIT = VISIT) |>32  summarise(33    SYSBP_SUP = only_value(VSTESTCD == "SYSBP" & VSPOS == "SUPINE", VSSTRESN),34    SYSBP_STD = only_value(35      VSTESTCD == "SYSBP" & VSPOS == "STANDING" & VSTPT == standing, VSSTRESN36    ),37    DIABP_SUP = only_value(VSTESTCD == "DIABP" & VSPOS == "SUPINE", VSSTRESN),38    DIABP_STD = only_value(39      VSTESTCD == "DIABP" & VSPOS == "STANDING" & VSTPT == standing, VSSTRESN40    ),41    HR_SUP = only_value(VSTESTCD == "HR" & VSPOS == "SUPINE", VSSTRESN),42    HR_STD = only_value(43      VSTESTCD == "HR" & VSPOS == "STANDING" & VSTPT == standing, VSSTRESN44    ),45    .groups = "drop"46  ) |>47  mutate(48    SYSBP_CHG = SYSBP_STD - SYSBP_SUP,49    DIABP_CHG = DIABP_STD - DIABP_SUP,50    HR_CHG = HR_STD - HR_SUP51  )5253change_record <- function(visits, paramcd, param, column) {54  visits |>55    filter(!is.na(.data[[column]])) |>56    transmute(57      STUDYID, USUBJID, AVISIT, PARAMCD = paramcd, PARAM = param,58      AVAL = .data[[column]], AVALC = NA_character_59    )60}6162# Either blood-pressure fall is enough for Y, even when the other63# change is missing; N needs both changes, so a visit with neither64# fall and one change missing gets no record.65hypotension <- visits |>66  mutate(67    AVALC = case_when(68      (!is.na(SYSBP_CHG) & SYSBP_CHG <= -20) |69        (!is.na(DIABP_CHG) & DIABP_CHG <= -10) ~ "Y",70      !is.na(SYSBP_CHG) & !is.na(DIABP_CHG) ~ "N",71      .default = NA_character_72    )73  ) |>74  filter(!is.na(AVALC)) |>75  transmute(76    STUDYID, USUBJID, AVISIT, PARAMCD = "OHYPO",77    PARAM = "Orthostatic Hypotension", AVAL = NA_real_, AVALC78  )7980tachycardia <- visits |>81  mutate(82    AVALC = case_when(83      !is.na(HR_CHG) & HR_CHG >= 30 ~ "Y",84      !is.na(HR_CHG) ~ "N",85      .default = NA_character_86    )87  ) |>88  filter(!is.na(AVALC)) |>89  transmute(90    STUDYID, USUBJID, AVISIT, PARAMCD = "OTACHY",91    PARAM = "Orthostatic Tachycardia", AVAL = NA_real_, AVALC92  )9394advs <- bind_rows(95  change_record(96    visits, "SYSBPOC",97    "Systolic Blood Pressure Change on Standing (mmHg)", "SYSBP_CHG"98  ),99  change_record(100    visits, "DIABPOC",101    "Diastolic Blood Pressure Change on Standing (mmHg)", "DIABP_CHG"102  ),103  change_record(104    visits, "HROC", "Heart Rate Change on Standing (beats/min)", "HR_CHG"105  ),106  hypotension,107  tachycardia108) |>109  select(STUDYID, USUBJID, AVISIT, PARAMCD, PARAM, AVAL, AVALC)110111dir.create("/app/output", showWarnings = FALSE)112write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-orthostatic-criteria (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 1.67"""Build ADVS orthostatic change and flag records from the VS dataset.89One record per subject per visit per parameter:10  SYSBPOC / DIABPOC / HROC - change records (3-minute standing minus supine)11  OHYPO / OTACHY           - flag records12"""1314import csv15import os1617INPUT_DIR = "/app/input"18OUTPUT_DIR = "/app/output"1920PARAMS = {21    "SYSBPOC": "Systolic Blood Pressure Change on Standing (mmHg)",22    "DIABPOC": "Diastolic Blood Pressure Change on Standing (mmHg)",23    "HROC": "Heart Rate Change on Standing (beats/min)",24    "OHYPO": "Orthostatic Hypotension",25    "OTACHY": "Orthostatic Tachycardia",26}2728# Source test code behind each change parameter.29CHANGE_TESTS = {30    "SYSBPOC": "SYSBP",31    "DIABPOC": "DIABP",32    "HROC": "HR",33}343536def parse_number(text):37    """Return the numeric value of a cell, or None when missing."""38    if text is None:39        return None40    text = text.strip()41    if not text:42        return None43    return float(text)444546def format_number(value):47    """Write integral values without a decimal point."""48    if value == int(value):49        return str(int(value))50    return repr(value)515253def main():54    with open(os.path.join(INPUT_DIR, "vs.csv"), newline="") as handle:55        rows = list(csv.DictReader(handle))5657    # readings[(study, subject, visit, test)] = (supine, standing_3min)58    readings = {}59    visit_order = {}60    subject_order = []61    for row in rows:62        key = (row["STUDYID"], row["USUBJID"])63        if key not in visit_order:64            visit_order[key] = []65            subject_order.append(key)66        if row["VISIT"] not in visit_order[key]:67            visit_order[key].append(row["VISIT"])68        value = parse_number(row["VSSTRESN"])69        if value is None:70            slot_value = None71        else:72            slot_value = value73        entry = readings.setdefault(74            (row["STUDYID"], row["USUBJID"], row["VISIT"], row["VSTESTCD"]),75            {"supine": None, "standing": None},76        )77        if row["VSPOS"] == "SUPINE":78            entry["supine"] = slot_value79        elif row["VSPOS"] == "STANDING" and "3 MIN" in row["VSTPT"]:80            # Only the reading after three minutes standing is used;81            # the one-minute standing reading never counts.82            entry["standing"] = slot_value8384    def change(study, subject, visit, test):85        entry = readings.get((study, subject, visit, test))86        if entry is None or entry["supine"] is None or entry["standing"] is None:87            return None88        return entry["standing"] - entry["supine"]8990    records = []91    for study, subject in subject_order:92        for visit in visit_order[(study, subject)]:93            changes = {94                param: change(study, subject, visit, test)95                for param, test in CHANGE_TESTS.items()96            }97            for param in ("SYSBPOC", "DIABPOC", "HROC"):98                if changes[param] is not None:99                    records.append(100                        [study, subject, visit, param, PARAMS[param],101                         format_number(changes[param]), ""]102                    )103            # Orthostatic hypotension flag.104            sys_chg = changes["SYSBPOC"]105            dia_chg = changes["DIABPOC"]106            sys_fall = sys_chg is not None and sys_chg <= -20107            dia_fall = dia_chg is not None and dia_chg <= -10108            if sys_fall or dia_fall:109                avalc = "Y"110            elif sys_chg is not None and dia_chg is not None:111                avalc = "N"112            else:113                avalc = None  # neither meets threshold, one change missing114            if avalc is not None:115                records.append(116                    [study, subject, visit, "OHYPO", PARAMS["OHYPO"], "", avalc]117                )118            # Orthostatic tachycardia flag.119            hr_chg = changes["HROC"]120            if hr_chg is not None:121                avalc = "Y" if hr_chg >= 30 else "N"122                records.append(123                    [study, subject, visit, "OTACHY", PARAMS["OTACHY"], "", avalc]124                )125126    os.makedirs(OUTPUT_DIR, exist_ok=True)127    with open(os.path.join(OUTPUT_DIR, "advs.csv"), "w", newline="") as handle:128        writer = csv.writer(handle)129        writer.writerow(130            ["STUDYID", "USUBJID", "AVISIT", "PARAMCD", "PARAM", "AVAL", "AVALC"]131        )132        writer.writerows(records)133134135if __name__ == "__main__":136    main()

1/* opensas reference solution for the yamaa benchmark adam-advs-orthostatic-criteria.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data vs;6  length STUDYID USUBJID VISIT VSTESTCD VSPOS VSTPT $1024;7  infile "/app/input/vs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VISIT : $char1024. VSTESTCD : $char1024. VSPOS : $char1024. VSTPT : $char1024. VSSTRESN;9run;1011/* A test with more than one supine reading, or more than one reading12   after three minutes standing, at one visit stops the run rather13   than choosing one: count the readings of each kind first, before14   the aggregations below can pick one. */15proc sql;16  create table dup_readings as17    select STUDYID, USUBJID, VISIT, VSTESTCD, count(*) as N18      from (select STUDYID, USUBJID, VISIT, VSTESTCD, VSPOS,19              case when VSPOS='SUPINE' then '' else VSTPT end as TPTKEY20              from vs21              where VSTESTCD in ('SYSBP','DIABP','HR')22                and (VSPOS='SUPINE' or (VSPOS='STANDING' and VSTPT='AFTER 3 MIN STANDING'))) as r23      group by STUDYID, USUBJID, VISIT, VSTESTCD, VSPOS, TPTKEY24      having count(*) > 1;25quit;2627data _null_;28  set dup_readings;29  abort;30run;3132/* One row per subject and visit: the supine reading and the reading33   after three minutes standing of each test. The reading after one34   minute standing is never used. */35proc sql;36  create table visits as select STUDYID, USUBJID, VISIT as AVISIT,37    max(case when VSTESTCD='SYSBP' and VSPOS='SUPINE' then VSSTRESN end) as SYSBP_SUP,38    max(case when VSTESTCD='SYSBP' and VSPOS='STANDING' and VSTPT='AFTER 3 MIN STANDING' then VSSTRESN end) as SYSBP_STD,39    max(case when VSTESTCD='DIABP' and VSPOS='SUPINE' then VSSTRESN end) as DIABP_SUP,40    max(case when VSTESTCD='DIABP' and VSPOS='STANDING' and VSTPT='AFTER 3 MIN STANDING' then VSSTRESN end) as DIABP_STD,41    max(case when VSTESTCD='HR' and VSPOS='SUPINE' then VSSTRESN end) as HR_SUP,42    max(case when VSTESTCD='HR' and VSPOS='STANDING' and VSTPT='AFTER 3 MIN STANDING' then VSSTRESN end) as HR_STD43    from vs group by STUDYID, USUBJID, VISIT;44quit;4546/* Changes are standing minus supine. Either blood-pressure fall is47   enough for Y, even when the other change is missing; N needs both48   changes. A missing value never meets a threshold in these tests49   because each comparison first checks the value is present. */50data flagged;51  length OHYPO OTACHY $1;52  set visits;53  SYSBP_CHG=SYSBP_STD-SYSBP_SUP;54  DIABP_CHG=DIABP_STD-DIABP_SUP;55  HR_CHG=HR_STD-HR_SUP;56  if (not missing(SYSBP_CHG) and SYSBP_CHG<=-20) or (not missing(DIABP_CHG) and DIABP_CHG<=-10) then OHYPO='Y';57  else if not missing(SYSBP_CHG) and not missing(DIABP_CHG) then OHYPO='N';58  if not missing(HR_CHG) and HR_CHG>=30 then OTACHY='Y';59  else if not missing(HR_CHG) then OTACHY='N';60run;6162proc sql;63  create table result as64    select STUDYID, USUBJID, AVISIT, 'DIABPOC' as PARAMCD, 'Diastolic Blood Pressure Change on Standing (mmHg)' as PARAM, DIABP_CHG as AVAL, '' as AVALC from flagged where not missing(DIABP_CHG)65    union all66    select STUDYID, USUBJID, AVISIT, 'SYSBPOC' as PARAMCD, 'Systolic Blood Pressure Change on Standing (mmHg)' as PARAM, SYSBP_CHG as AVAL, '' as AVALC from flagged where not missing(SYSBP_CHG)67    union all68    select STUDYID, USUBJID, AVISIT, 'HROC' as PARAMCD, 'Heart Rate Change on Standing (beats/min)' as PARAM, HR_CHG as AVAL, '' as AVALC from flagged where not missing(HR_CHG)69    union all70    select STUDYID, USUBJID, AVISIT, 'OHYPO' as PARAMCD, 'Orthostatic Hypotension' as PARAM, . as AVAL, OHYPO as AVALC from flagged where not missing(OHYPO)71    union all72    select STUDYID, USUBJID, AVISIT, 'OTACHY' as PARAMCD, 'Orthostatic Tachycardia' as PARAM, . as AVAL, OTACHY as AVALC from flagged where not missing(OTACHY);73quit;7475proc export data=result(keep=STUDYID USUBJID AVISIT PARAMCD PARAM AVAL AVALC) outfile="/app/output/advs.csv" dbms=csv replace; run;