{ "about": { "method": "survival", "origin": "Original synthetic values, except aml, lung-by-sex and gehan (R's packaged data sets survival::aml, survival::lung, MASS::gehan; licence held for the General Counsel)", "ruling": "CSO memo of 13 October 2026 (docs/board/memos/2026-10-13-cso-survival.md); roadmap A-2 family 4", "settings": { "km": "survfit(Surv(time, status) ~ 1, conf.type = 'log-log', conf.int = level): the fit object's rows; std.err on the log S scale", "median": "quantile(fit, 0.5, conf.int = TRUE)", "risk table": "summary(fit, times = ticks, extend = TRUE)$n.risk, equal to sum(time >= t)", "log-rank": "survdiff(Surv(time, status) ~ group, rho = 0); df = sum(exp > 0) - 1; p = pchisq(chisq, df, lower.tail = FALSE)", "Gehan-Breslow-Wilcoxon": "weighted log-rank by hand in R, weights n_j, hypergeometric covariance, first group dropped", "hazard ratio": "exp((O - E)/V) for the second-named group against the reference, interval exp(. +- qnorm(1 - a/2)/sqrt(V)), V = survdiff var", "coxph": "coxph(ties = 'efron'), recorded beside the hazard ratio, never compared or shipped", "km rows": "listed in full up to 40 rows; above that every kmEvery-th row", "large case": "the table is built from generate.seed by xorshift32 (generated_text in this script); the test builds the same text and checks generate.textSha256" }, "withheldCodes": [ "UNIT_NOT_INDEPENDENT", "N_TOO_SMALL", "ONE_GROUP", "HR_TWO_GROUPS", "NO_EVENTS_TOTAL", "NO_EVENTS_GROUP" ], "tolerances": { "S(t), std.err, band bounds, midpoint medians": "1e-10 relative", "medians and bounds that are observed times, n.risk, n.event, n.censor, O, counts": "exact", "survdiff chi-squared, O - E, var, E; the Gehan-Breslow-Wilcoxon statistic": "1e-9 relative", "p from pchisq": "1e-8 relative (1e-300 absolute floor)", "hazard ratio and its bounds": "1e-9 relative", "withheld states and codes, refused rows": "exact" }, "recordedOn": "2026-10-13", "script": "pipeline/assay-analyser/oracles/survival.py", "scriptSha256": "af32d106eea458244b12b5763a3ba8c56adc832709b2753ec523698972b1c3f4", "helper": { "script": "pipeline/assay-analyser/oracles/stage_a_oracle.py", "sha256": "492d85ca2fa6750db80b1c64214fd4a0b13cd4c588267244f6262c504c73e3e8" }, "environment": { "image": "ghcr.io/biotechmat/drybench/oracle-env:11b8a5e4456df7eb@sha256:7e69891ca1d9f24838660e0a9887bdb654ce7771d2f2ac7e7275e9b1eb3b6a09", "r": "R version 4.4.3 (2025-02-28)", "packages": { "survival": "3.8-3", "MASS": "7.3-64", "jsonlite": "2.0.0" }, "python": "3.11.15", "numpy": "2.0.2", "scipy": "1.13.1", "recordedOn": "2026-10-13", "cpu": "AMD EPYC 9V74 80-Core Processor", "cpuClass": "x86-64-v3", "simd": [ "SSSE3", "SSE41", "POPCNT", "SSE42", "AVX", "F16C", "FMA3", "AVX2" ], "openblasCore": "Haswell", "threads": 1 }, "crossCheck": { "tool": "identities inside R (unit weights against survdiff, the Wilcoxon identity, the risk table)", "ran": true, "cases": 88, "agreeing": 88, "result": [ { "what": "hand-one-group A risk table", "agrees": true }, 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table", "agrees": true }, { "what": "no-censoring-wilcoxon B risk table", "agrees": true }, { "what": "no-censoring-wilcoxon unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 2.22044604925031e-15, "score": 8.88178419700125e-16, "variance": 0 } }, { "what": "no-censoring-wilcoxon Gehan-Breslow-Wilcoxon score = nA*nB - 2W", "agrees": true, "score": -18, "w": 30 }, { "what": "median-exact-half A risk table", "agrees": true }, { "what": "median-rounded-half A risk table", "agrees": true }, { "what": "median-half-last-censored A risk table", "agrees": true }, { "what": "median-not-reached A risk table", "agrees": true }, { "what": "upper-bound-not-reached A risk table", "agrees": true }, { "what": "last-subject-event A risk table", "agrees": true }, { "what": "last-subject-event B risk table", "agrees": true }, { "what": "last-subject-event unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 1.11022302462516e-16, "score": 4.44089209850063e-16, "variance": 2.22044604925031e-16 } }, { "what": "event-at-zero A risk table", "agrees": true }, { "what": "event-at-zero B risk table", "agrees": true }, { "what": "event-at-zero unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 1.99840144432528e-15, "score": 8.88178419700125e-16, "variance": 0 } }, { "what": "three-groups A risk table", "agrees": true }, { "what": "three-groups B risk table", "agrees": true }, { "what": "three-groups C risk table", "agrees": true }, { "what": "three-groups unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 7.105427357601e-15, "score": 8.88178419700125e-16, "variance": 8.88178419700125e-16 } }, { "what": "three-groups-gbw A risk table", "agrees": true }, { "what": "three-groups-gbw B risk table", "agrees": true }, { "what": "three-groups-gbw C risk table", "agrees": true }, { "what": "three-groups-gbw unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 7.105427357601e-15, "score": 8.88178419700125e-16, "variance": 8.88178419700125e-16 } }, { "what": "one-group A risk table", "agrees": true }, { "what": "crossing-curves A risk table", "agrees": true }, { "what": "crossing-curves B risk table", "agrees": true }, { "what": "crossing-curves unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 2.22044604925031e-16, "score": 8.88178419700125e-16, "variance": 4.44089209850063e-16 } }, { "what": "crossing-curves-gbw A risk table", "agrees": true }, { "what": "crossing-curves-gbw B risk table", "agrees": true }, { "what": "crossing-curves-gbw unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 2.22044604925031e-16, "score": 8.88178419700125e-16, "variance": 4.44089209850063e-16 } }, { "what": "heavy-early-censoring A risk table", "agrees": true }, { "what": "heavy-early-censoring B risk table", "agrees": true }, { "what": "heavy-early-censoring unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 0, "score": 4.44089209850063e-16, "variance": 4.44089209850063e-16 } }, { "what": "strong-separation A risk table", "agrees": true }, { "what": "strong-separation B risk table", "agrees": true }, { "what": "strong-separation unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 7.105427357601e-15, "score": 3.5527136788005e-15, "variance": 4.44089209850063e-16 } }, { "what": "reference-swapped A risk table", "agrees": true }, { "what": "reference-swapped B risk table", "agrees": true }, { "what": "reference-swapped unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 4.44089209850063e-15, "score": 8.88178419700125e-16, "variance": 2.22044604925031e-16 } }, { "what": "large-two-by-5000 A risk table", "agrees": true }, { "what": "large-two-by-5000 B risk table", "agrees": true }, { "what": "large-two-by-5000 unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 1.93267624126747e-12, "score": 1.81898940354586e-12, "variance": 4.09272615797818e-12 } }, { "what": "aml Maintained risk table", "agrees": true }, { "what": "aml Nonmaintained risk table", "agrees": true }, { "what": "aml unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 8.88178419700125e-16, "score": 8.88178419700125e-16, "variance": 8.88178419700125e-16 } }, { "what": "lung-by-sex Male risk table", "agrees": true }, { "what": "lung-by-sex Female risk table", "agrees": true }, { "what": "lung-by-sex unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 7.105427357601e-15, "score": 1.06581410364015e-14, "variance": 3.5527136788005e-14 } }, { "what": "gehan control risk table", "agrees": true }, { "what": "gehan 6-MP risk table", "agrees": true }, { "what": "gehan unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 7.105427357601e-15, "score": 3.5527136788005e-15, "variance": 8.88178419700125e-16 } }, { "what": "group-n-2 A risk table", "agrees": true }, { "what": "group-n-2 B risk table", "agrees": true }, { "what": "group-n-2 unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 8.88178419700125e-16, "score": 0, "variance": 1.11022302462516e-16 } }, { "what": "no-events A risk table", "agrees": true }, { "what": "no-events B risk table", "agrees": true }, { "what": "no-events unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 0, "score": 0, "variance": 0 } }, { "what": "refusals A risk table", "agrees": true }, { "what": "refusals B risk table", "agrees": true }, { "what": "refusals unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 0, "score": 1.66533453693773e-16, "variance": 5.55111512312578e-17 } }, { "what": "unit-undeclared A risk table", "agrees": true }, { "what": "unit-undeclared B risk table", "agrees": true }, { "what": "unit-undeclared unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 4.44089209850063e-15, "score": 8.88178419700125e-16, "variance": 2.22044604925031e-16 } }, { "what": "unit-not-independent A risk table", "agrees": true }, { "what": "unit-not-independent B risk table", "agrees": true }, { "what": "unit-not-independent unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 4.44089209850063e-15, "score": 8.88178419700125e-16, "variance": 2.22044604925031e-16 } }, { "what": "risk-ticks-on-times A risk table", "agrees": true }, { "what": "risk-ticks-on-times B risk table", "agrees": true }, { "what": "risk-ticks-on-times unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 1.99840144432528e-15, "score": 8.88178419700125e-16, "variance": 0 } }, { "what": "level-90 A risk table", "agrees": true }, { "what": "level-90 B risk table", "agrees": true }, { "what": "level-90 unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 5.55111512312578e-17, "score": 1.77635683940025e-15, "variance": 1.33226762955019e-15 } }, { "what": "level-95 A risk table", "agrees": true }, { "what": "level-95 B risk table", "agrees": true }, { "what": "level-95 unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 5.55111512312578e-17, "score": 1.77635683940025e-15, "variance": 1.33226762955019e-15 } }, { "what": "level-99 A risk table", "agrees": true }, { "what": "level-99 B risk table", "agrees": true }, { "what": "level-99 unit weights reproduce survdiff(rho = 0)", "agrees": true, "differences": { "statistic": 5.55111512312578e-17, "score": 1.77635683940025e-15, "variance": 1.33226762955019e-15 } } ], "r": { "tool": "R survival", "version": "R version 4.4.3 (2025-02-28)", "survival": "3.8.3", "script": "pipeline/assay-analyser/oracles/r/survival.R", "scriptSha256": "c9fce33cc3c79e9c51b34b42f7c6c4725f065da376838a30939dd513a18dd554", "jobs": 88 } } }, "oracle": { "engine": "R survival (survival.R)", "method": "every number from R; the withholding policy from the memo, applied here" }, "cases": [ { "name": "hand-one-group", "text": "Time\tA\n1\t1\n2\t0\n3\t1\n4\t1\n5\t1", "exclude": [], "settings": { "unit": "independent", "level": 0.95, "test": "log-rank", "reference": null, "band": false }, "expected": { "refused": [], "groups": [ { "name": "A", "n": 5, "events": 4, "censored": 1, "kmRows": 5, "kmEvery": 1, "km": [ { "time": 1, "nRisk": 5, "nEvent": 1, "nCensor": 0, "surv": 0.8, "stdErr": 0.223606797749979, "lower": 0.203809263267639, "upper": 0.969179788866743 }, { "time": 2, "nRisk": 4, "nEvent": 0, "nCensor": 1, "surv": 0.8, "stdErr": 0.223606797749979, "lower": 0.203809263267639, "upper": 0.969179788866743 }, { "time": 3, "nRisk": 3, "nEvent": 1, "nCensor": 0, "surv": 0.533333333333333, "stdErr": 0.465474668125631, "lower": 0.0683320878472029, "upper": 0.863071182738792 }, { "time": 4, "nRisk": 2, "nEvent": 1, "nCensor": 0, "surv": 0.266666666666667, "stdErr": 0.84656167328002, "lower": 0.00967700057888136, "upper": 0.686136279157012 }, { "time": 5, "nRisk": 1, "nEvent": 1, "nCensor": 0, "surv": 0, "stdErr": null, "lower": null, "upper": null } ], "band": "value", "median": { "point": 4, "interval": { "lower": 1, "upper": "not-reached" } }, "atRisk": [ 5, 4, 3, 1 ], "rTable": { "records": 5, "n.max": 5, "n.start": 5, "events": 4, "rmean": 3.4, "se(rmean)": 0.655913273399938, "median": 4, "0.95LCL": 1, "0.95UCL": null } } ], "ticks": [ 0, 2, 2.5, 5 ], "observedExpected": null, "test": { "withheld": "ONE_GROUP" }, "hazardRatio": { "withheld": "ONE_GROUP" } } }, { "name": "tie-event-censor", "text": "Time\tA\tB\n2\t1\t\n2\t0\t\n3\t1\t\n5\t1\t\n5\t0\t\n7\t1\t\n1\t\t1\n2\t\t1\n2\t\t1\n4\t\t0\n6\t\t1\n8\t\t1", "exclude": [], "settings": { "unit": "independent", "level": 0.95, "test": "log-rank", "reference": null, "band": false }, "expected": { "refused": [], "groups": [ { "name": "A", "n": 6, "events": 4, "censored": 2, "kmRows": 4, "kmEvery": 1, "km": [ { "time": 2, "nRisk": 6, "nEvent": 1, "nCensor": 1, "surv": 0.833333333333333, "stdErr": 0.182574185835055, "lower": 0.273122849928356, "upper": 0.974712426690894 }, { "time": 3, "nRisk": 4, "nEvent": 1, "nCensor": 0, "surv": 0.625, "stdErr": 0.341565025531987, "lower": 0.141853389931655, "upper": 0.893050604498578 }, { "time": 5, "nRisk": 3, "nEvent": 1, "nCensor": 1, "surv": 0.416666666666667, "stdErr": 0.532290647422377, "lower": 0.0559918648520529, "upper": 0.76652221955058 }, { "time": 7, "nRisk": 1, "nEvent": 1, "nCensor": 0, "surv": 0, "stdErr": null, "lower": null, "upper": null } ], "band": "value", "median": { "point": 5, "interval": { "lower": 2, "upper": "not-reached" } }, "atRisk": [ 6, 6, 3 ], "rTable": { "records": 6, "n.max": 6, "n.start": 6, "events": 4, "rmean": 4.91666666666667, "se(rmean)": 0.872350485969011, "median": 5, "0.95LCL": 2, "0.95UCL": null } }, { "name": "B", "n": 6, "events": 5, "censored": 1, "kmRows": 5, "kmEvery": 1, "km": [ { "time": 1, "nRisk": 6, "nEvent": 1, "nCensor": 0, "surv": 0.833333333333333, "stdErr": 0.182574185835055, "lower": 0.273122849928356, "upper": 0.974712426690894 }, { "time": 2, "nRisk": 5, "nEvent": 2, "nCensor": 0, "surv": 0.5, "stdErr": 0.408248290463863, "lower": 0.110948260351438, "upper": 0.803709236850057 }, { "time": 4, "nRisk": 3, "nEvent": 0, "nCensor": 1, "surv": 0.5, "stdErr": 0.408248290463863, "lower": 0.110948260351438, "upper": 0.803709236850057 }, { "time": 6, "nRisk": 2, "nEvent": 1, "nCensor": 0, "surv": 0.25, "stdErr": 0.816496580927726, "lower": 0.0123095164750105, "upper": 0.645948537398101 }, { "time": 8, "nRisk": 1, "nEvent": 1, "nCensor": 0, "surv": 0, "stdErr": null, "lower": null, "upper": null } ], "band": "value", "median": { "point": 4, "interval": { "lower": 1, "upper": "not-reached" } }, "atRisk": [ 6, 5, 2 ], "rTable": { "records": 6, "n.max": 6, "n.start": 6, "events": 5, "rmean": 4.33333333333333, "se(rmean)": 1.15269410673591, "median": 4, "0.95LCL": 1, "0.95UCL": null } } ], "ticks": [ 0, 2, 5 ], "observedExpected": { "observed": [ 4, 5 ], "expected": [ 4.14112554112554, 4.85887445887446 ] }, "test": { "kind": "log-rank", "statistic": 0.0110514059460633, "df": 1, "p": 0.916276092508477, "fewEvents": true }, "hazardRatio": { "reference": 0, "other": 1, "estimate": 1.08145682275544, "lower": 0.251154870731094, "upper": 4.65668396587262, "coxph": { "estimate": 1.11364112389264, "note": "recorded, not shipped (ruling 7)" } }, "survdiff": { "variance": [ [ 1.80216150371995, -1.80216150371995 ], [ -1.80216150371995, 1.80216150371994 ] ], "chisq": 0.0110514059460633 } } }, { "name": "tied-events-two-groups", "text": "Time\tA\tB\n3\t1\t\n3\t1\t\n3\t1\t\n5\t1\t\n7\t1\t\n7\t1\t\n9\t0\t\n3\t\t1\n3\t\t1\n4\t\t1\n4\t\t1\n6\t\t1\n6\t\t1\n6\t\t1\n10\t\t1", "exclude": [], "settings": { "unit": "independent", "level": 0.95, "test": "gehan-breslow", "reference": null, "band": false }, "expected": { "refused": [], "groups": [ { "name": "A", "n": 7, "events": 6, "censored": 1, "kmRows": 4, "kmEvery": 1, "km": [ { "time": 3, "nRisk": 7, "nEvent": 3, "nCensor": 0, "surv": 0.571428571428571, "stdErr": 0.327326835353989, "lower": 0.171866015528775, "upper": 0.83708278034918 }, { "time": 5, "nRisk": 4, "nEvent": 1, "nCensor": 0, "surv": 0.428571428571429, "stdErr": 0.436435780471985, "lower": 0.0977522021169289, "upper": 0.734373417051447 }, { "time": 7, "nRisk": 3, "nEvent": 2, "nCensor": 0, "surv": 0.142857142857143, "stdErr": 0.925820099772551, "lower": 0.00712386407623847, "upper": 0.464941355315507 }, { "time": 9, "nRisk": 1, "nEvent": 0, "nCensor": 1, "surv": 0.142857142857143, "stdErr": 0.925820099772551, 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