{
 "about": {
  "method": "outlier-candidates",
  "origin": "Self-constructed data with seeded noise and planted departures; not experimental data",
  "ruling": "CSO memo of 11 October 2026, item 7 (docs/board/memos/2026-10-11-cso-assay-depth-stage.md)",
  "alpha": 0.05,
  "minimumResidualDf": 6,
  "grubbsMinimumN": 6,
  "zeroResidual": 1e-20,
  "fourPL": "y = bottom + (top - bottom) / (1 + 10^((logIC50 - x) * hill)), x = log10 concentration; fitted by curve_fit (lm, tolerances 1e-15); the engine is tested on these estimates",
  "tolerances": {
   "leverage, residuals, internal and external t": "1e-6 relative (1e-9 absolute for a residual)",
   "p and adjusted p, G, critical values": "1e-6 relative",
   "candidates, indices and withheld reasons": "exact"
  },
  "recordedOn": "2026-10-13",
  "script": "pipeline/assay-analyser/oracles/outliers_scipy.py",
  "scriptSha256": "db14b97e5cf9e09bbc81a8268f561256deca44c3202e045b50a7a78a394d7deb",
  "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": {
    "jsonlite": "2.0.0",
    "car": "3.1-5",
    "outliers": "0.15"
   },
   "python": "3.11.15",
   "numpy": "2.0.2",
   "scipy": "1.13.1",
   "recordedOn": "2026-10-13",
   "cpu": "INTEL(R) XEON(R) PLATINUM 8573C",
   "cpuClass": "x86-64-v3",
   "simd": [
    "SSSE3",
    "SSE41",
    "POPCNT",
    "SSE42",
    "AVX",
    "F16C",
    "FMA3",
    "AVX2"
   ],
   "openblasCore": "Haswell",
   "threads": 1
  },
  "crossCheck": {
   "tool": "R stats::rstudent, hatvalues; car::outlierTest; outliers::grubbs.test",
   "version": "R version 4.4.3 (2025-02-28)",
   "car": "3.1-5",
   "outliers": "0.15",
   "script": "pipeline/assay-analyser/oracles/r/outlier_checks.R",
   "scriptSha256": "59a2ec78b788450f5cf561e15b6a19e6477f745adee5624ba92d2046bf901c5d",
   "ran": true,
   "settings": "lm(y ~ x); outlierTest(cutoff = Inf, n.max = Inf) for every Bonferroni p; grubbs.test(type = 10, two.sided = TRUE) for G, and its p only where 2 res <= 1 (the package folds a doubled p above 1 to 2 - p; the CSO's ruling 1(e) of 13 October 2026, as amended); car::outlierTest(lm(x ~ 1)) as the gate on the Grubbs p in every group",
   "notCompared": "the 4PL cases (R has no hat matrix for nls; the SciPy numeric Jacobian is the oracle there)",
   "tolerances": {
    "all": "1e-6 relative"
   },
   "cases": 5,
   "agreeing": 5,
   "result": [
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     "hatRelative": 5.647656255701885e-16,
     "bonferroniRelative": 1.4390242344661603e-14,
     "agrees": true
    },
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     "case": "linear-clean",
     "rstudentRelative": 1.5743002032714418e-14,
     "hatRelative": 2.1807952269422717e-15,
     "bonferroniRelative": 9.780417671229223e-15,
     "agrees": true
    },
    {
     "case": "control-planted",
     "GRelative": 5.645219187384613e-16,
     "carBonferroni": 0.00193139786501834,
     "carRelative": 2.907825132871702e-14,
     "packageP": 0.00193139786501817,
     "packageRelative": 5.894240134199396e-14,
     "agrees": true
    },
    {
     "case": "control-clean",
     "GRelative": 4.820877115542828e-16,
     "carBonferroni": 0.273148601606079,
     "carRelative": 5.0806732036023254e-15,
     "packageP": 0.273148601606078,
     "packageRelative": 1.422588497008651e-15,
     "agrees": true
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    {
     "case": "control-even",
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     "carBonferroni": 1.07179676972447,
     "carRelative": 0.0,
     "packageP": 0.928203230275511,
     "packagePNote": "outliers two-sided fold (2 res > 1); engine reports the bound",
     "agrees": true
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   ]
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 },
 "oracle": {
  "engine": "NumPy (hat matrix by inversion), SciPy curve_fit, scipy.stats.t",
  "jacobian": "central finite differences, step 1e-6 x max(1, |parameter|)"
 },
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   "name": "4pl-clean",
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