{
 "about": {
  "method": "GR metrics against the GRmetrics package (SCI-120), the second run on identical inputs",
  "rules": "docs/board/memos/2026-11-07-cso-stage4-assay-campaign-addendum-2.md (tolerances) and addendum-3.md (this run)",
  "basedOnRun": {
   "file": "gr-metrics-r.json",
   "note": "the first run, kept as the record of the per-row convention"
  },
  "grmaxSource": {
   ".GRlogisticFit": [
    {
     "line": 26,
     "text": "        metadata = NULL\n    }\n    pval_GR = NULL\n    GRmax = NULL\n    GR_mean = NULL\n    AOC = NULL\n    R_square_GR = NULL"
    },
    {
     "line": 128,
     "text": "            rel_cell_avg[j] = mean(data_trapz$rel_cell_count, \n                na.rm = TRUE)\n        }\n        GRmax[i] = min(GRavg[c(l, l - 1)], na.rm = TRUE)\n        Emax[i] = min(rel_cell_avg[c(l, l - 1)], na.rm = TRUE)\n        diff_vector = diff(log10(concs), lag = 1)\n        conc_range = log10(concs[length(concs)]) - log10(concs[1])"
    },
    {
     "line": 143,
     "text": "    parameters$concentration_points = concentration_points\n    parameters$GR50 = with(parameters, GEC50 * ((1 - GRinf)/(0.5 - \n        GRinf) - 1)^(1/h_GR))\n    parameters$GRmax = GRmax\n    parameters$GR_AOC = AOC\n    parameters$r2_GR = R_square_GR\n    parameters$IC50 = with(parameters, EC50 * ((1 - Einf)/(0.5 - "
    },
    {
     "line": 189,
     "text": "            parameters$h_GR[i] = 0.01\n            parameters$GR50[i] = ifelse(parameters$flat_fit_GR[i] > \n                0.5, Inf, -Inf)\n            parameters$GRinf[i] = parameters$GRmax[i]\n        }\n    }\n    for (i in 1:dim(parameters)[1]) {"
    },
    {
     "line": 219,
     "text": "            parameters$flat_fit_rel_cell[i] = NA\n        }\n    }\n    parameters = parameters[, c(\"GR50\", \"GRmax\", \"GR_AOC\", \"GEC50\", \n        \"GRinf\", \"h_GR\", \"r2_GR\", \"pval_GR\", \"fit_GR\", \"flat_fit_GR\", \n        \"IC50\", \"Emax\", \"AUC\", \"EC50\", \"Einf\", \"h\", \"r2_rel_cell\", \n        \"pval_rel_cell\", \"fit_rel_cell\", \"flat_fit_rel_cell\", "
    }
   ],
   "GRfit": [
    {
     "line": 21,
     "text": "        \"fit_rel_cell\", \"experiment\", \"concentration_points\")]\n    rownames(colData) = colData$experiment\n    colData = S4Vectors::DataFrame(colData)\n    Metric = c(\"ctrl_cell_doublings\", \"GR50\", \"GRmax\", \"GR_AOC\", \n        \"GEC50\", \"GRinf\", \"h_GR\", \"r2_GR\", \"pval_GR\", \"flat_fit_GR\", \n        \"IC50\", \"Emax\", \"AUC\", \"EC50\", \"Einf\", \"h\", \"r2_rel_cell\", \n        \"pval_rel_cell\", \"flat_fit_rel_cell\")"
    }
   ]
  },
  "basedOn": {
   "file": "gr-metrics.json",
   "sha256": "8b9604be1fec1243062d6a8756f9944a81541393fef29b105a20a8d057869ce5",
   "oracleComputeSourceSha256": "271d354835023b2a75ed2952df21d5ec6038e49c4312c220aa9b19c5f603f646"
  },
  "package": {
   "name": "GRmetrics",
   "version": "1.32.0",
   "bioconductor": "3.20",
   "licence": "GPL-3",
   "licenceReadOn": "2026-11-07 (DESCRIPTION, in the oracle image)",
   "use": "build-time only"
  },
  "licence": "GRmetrics is GPL; it runs in the oracle image only, build-time. Its outputs join the General Counsel's held row for GPL oracle outputs.",
  "tally": {
   "grPerWell": {
    "agree": 57
   },
   "grMax": {
    "agree": 39,
    "definitional": 18
   },
   "grAoc": {
    "agree": 57
   },
   "fit": {
    "agree": 52,
    "both-without-fit": 5
   }
  },
  "recordedOn": "2026-11-07",
  "script": "pipeline/assay-analyser/oracles/gr_metrics_r2.py",
  "scriptSha256": "661dea1600e75ac5dcc05e629d413d1b6dcb95bf498e39b8923bbec7769270b2",
  "helper": {
   "script": "pipeline/assay-analyser/oracles/stage_a_oracle.py",
   "sha256": "492d85ca2fa6750db80b1c64214fd4a0b13cd4c588267244f6262c504c73e3e8"
  },
  "environment": {
   "image": "ghcr.io/biotechmat/drybench/oracle-env:98857a6c3c44fad1@sha256:f0d38586cae0ade811e7925f7c2e3604a138acc4419522073c4553ee71798470",
   "r": "R version 4.4.3 (2025-02-28)",
   "packages": {
    "jsonlite": "2.0.0",
    "GRmetrics": "1.32.0"
   },
   "python": "3.11.15",
   "numpy": "2.0.2",
   "scipy": "1.13.1",
   "recordedOn": "2026-11-07",
   "cpu": "AMD EPYC 9V45 96-Core Processor",
   "cpuClass": "x86-64-v3",
   "simd": [
    "SSSE3",
    "SSE41",
    "POPCNT",
    "SSE42",
    "AVX",
    "F16C",
    "FMA3",
    "AVX2"
   ],
   "openblasCore": "Haswell",
   "threads": 1
  },
  "crossCheck": {
   "tool": "GRmetrics 1.32.0 (Bioconductor 3.20) GRfit, GRgetValues and GRgetMetrics",
   "version": "R version 4.4.3 (2025-02-28)",
   "script": "pipeline/assay-analyser/oracles/r/gr_metrics_r2.R",
   "scriptSha256": "4a7e6bdd7acc35f514c850a7925386286c1111f45ae36385d309e754c33f7e9d",
   "ran": true,
   "licence": "GPL-3 (DESCRIPTION, read 7 November 2026); build-time only",
   "agreement": "recorded per experiment with a verdict (agree, definitional, engine-lower-rss, disagree); see about.tally"
  }
 },
 "cases": [
  {
   "name": "cytostatic",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.440892098500626e-16
   },
   "package": {
    "GR50": 1.00043703342667e-06,
    "GRmax": 0.010405310224871,
    "GR_AOC": 0.499910485747305,
    "GEC50": 1.00086970526479e-06,
    "GRinf": -0.000216302268302882,
    "h_GR": 1.00028135596051,
    "r2_GR": 0.999867416113111,
    "pval_GR": 9.54829821879619e-32,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": 0.010405310224871012,
     "n": 2
    },
    "grAoc": 0.4999104857473047,
    "fitted": {
     "grInf": -0.00021692554529698836,
     "logGec50": -5.9996219304532294,
     "h": 1.0002770218582218,
     "rss": 0.0003691989537602645
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "shown",
     "logValue": -5.999810256556289
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.0003691989537602645,
    "packageParamsRss": 0.00036919895834177817,
    "refitFromPackageRss": 0.0003691989537602666,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "cytotoxic",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.996003610813204e-16
   },
   "package": {
    "GR50": 5.0015914542402e-07,
    "GRmax": -0.484891410473595,
    "GR_AOC": 0.74986151785668,
    "GEC50": 1.00049073304298e-06,
    "GRinf": -0.500159084344272,
    "h_GR": 0.999980815805807,
    "r2_GR": 0.999951321014861,
    "pval_GR": 3.15305919169611e-35,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": -0.48489141047359513,
     "n": 2
    },
    "grAoc": 0.7498615178566803,
    "fitted": {
     "grInf": -0.5001608400522394,
     "logGec50": -5.999785259865059,
     "h": 0.9999773313022867,
     "rss": 0.0003048179274952717
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "shown",
     "logValue": -6.300891927555333
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.0003048179274952717,
    "packageParamsRss": 0.00030481793746259733,
    "refitFromPackageRss": 0.0003048179274952729,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "cytotoxic-steep",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.6629367034256575e-15
   },
   "package": {
    "GR50": 7.07135078839292e-07,
    "GRmax": -0.499600252194168,
    "GR_AOC": 0.749857618675106,
    "GEC50": 1.00114703270396e-06,
    "GRinf": -0.500396487907913,
    "h_GR": 1.99477592778185,
    "r2_GR": 0.999961775265028,
    "pval_GR": 4.55780629241387e-36,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": -0.49960025219416754,
     "n": 2
    },
    "grAoc": 0.7498576186751065,
    "fitted": {
     "grInf": -0.5003964812227119,
     "logGec50": -5.999502358713906,
     "h": 1.9947739072038522,
     "rss": 0.0003119497025115451
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "shown",
     "logValue": -6.150497992884516
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.0003119497025115451,
    "packageParamsRss": 0.0003119497032277936,
    "refitFromPackageRss": 0.0003119497025115476,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "partial",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 2.4424906541753444e-15
   },
   "package": {
    "GR50": null,
    "GRmax": 0.604761375063031,
    "GR_AOC": 0.199969247216054,
    "GEC50": 1.00257517474257e-06,
    "GRinf": 0.599715101877604,
    "h_GR": 1.00162307849084,
    "r2_GR": 0.998931486566989,
    "pval_GR": 1.69918196858688e-24,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": 0.6047613750630306,
     "n": 2
    },
    "grAoc": 0.19996924721605397,
    "fitted": {
     "grInf": 0.5997148045747305,
     "logGec50": -5.99888229973461,
     "h": 1.0016186838985783,
     "rss": 0.00047758555193065346
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "not-reached"
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.00047758555193065346,
    "packageParamsRss": 0.0004775855526695973,
    "refitFromPackageRss": 0.00047758555193065514,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "flat",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "definitional",
    "grAoc": "agree",
    "fit": "both-without-fit"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.440892098500626e-16
   },
   "package": {
    "GR50": null,
    "GRmax": 0.894158098934664,
    "GR_AOC": 0.100128038538931,
    "GEC50": 0.0,
    "GRinf": 0.894158098934664,
    "h_GR": 0.01,
    "r2_GR": -0.048814989622378,
    "pval_GR": 1.0,
    "fit": "flat"
   },
   "oracle": {
    "grMax": {
     "value": 0.9056811466583647,
     "n": 2
    },
    "grAoc": 0.10012803853893121,
    "fitted": null,
    "gec50": null,
    "grInf": null,
    "gr50": null,
    "withheld": "no-response"
   },
   "withholding": {
    "engine": "no-response",
    "package": "flat (F test p >= 0.05)"
   }
  },
  {
   "name": "few-doublings",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.996003610813204e-16
   },
   "package": {
    "GR50": 1.00121646352527e-06,
    "GRmax": 0.0111641548096482,
    "GR_AOC": 0.499751743822865,
    "GEC50": 1.00226837476251e-06,
    "GRinf": -0.00052571594581575,
    "h_GR": 1.00075981971765,
    "r2_GR": 0.999172935498844,
    "pval_GR": 2.18934924253052e-25,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": 0.011164154809648164,
     "n": 2
    },
    "grAoc": 0.4997517438228648,
    "fitted": {
     "grInf": -0.0005260914886803054,
     "logGec50": -5.999015464328115,
     "h": 1.0007589986645973,
     "rss": 0.0023085737501305622
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "shown",
     "logValue": -5.999471834971598
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.0023085737501305622,
    "packageParamsRss": 0.002308573750552072,
    "refitFromPackageRss": 0.0023085737501305657,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "separate-time-zero",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.440892098500626e-16
   },
   "package": {
    "GR50": 1.00043703342667e-06,
    "GRmax": 0.010405310224871,
    "GR_AOC": 0.499910485747305,
    "GEC50": 1.00086970526479e-06,
    "GRinf": -0.000216302268302882,
    "h_GR": 1.00028135596051,
    "r2_GR": 0.999867416113111,
    "pval_GR": 9.54829821879619e-32,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": 0.010405310224871012,
     "n": 2
    },
    "grAoc": 0.4999104857473047,
    "fitted": {
     "grInf": -0.00021692554529698836,
     "logGec50": -5.9996219304532294,
     "h": 1.0002770218582218,
     "rss": 0.0003691989537602645
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "shown",
     "logValue": -5.999810256556289
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.0003691989537602645,
    "packageParamsRss": 0.00036919895834177817,
    "refitFromPackageRss": 0.0003691989537602666,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "unbracketed",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 2.886579864025407e-15
   },
   "package": {
    "GR50": 2.49785160546304e-05,
    "GRmax": 0.00129063387413331,
    "GR_AOC": 0.182637406133257,
    "GEC50": 4.96225670982707e-05,
    "GRinf": -0.493890598487869,
    "h_GR": 1.00085868353733,
    "r2_GR": 0.999743203465445,
    "pval_GR": 1.89109466480069e-29,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": 0.0012906338741333068,
     "n": 2
    },
    "grAoc": 0.18263740613325713,
    "fitted": {
     "grInf": -0.4939146296293275,
     "logGec50": -4.304304621713467,
     "h": 1.0008428595419991,
     "rss": 0.0005031743909031589
    },
    "gec50": "not-bracketed",
    "grInf": "plateau",
    "gr50": {
     "status": "shown",
     "logValue": -4.6024324206338845
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.0005031743909031589,
    "packageParamsRss": 0.0005031744106749347,
    "refitFromPackageRss": 0.0005031743909031617,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "step-like",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "definitional",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 18,
    "disagree": 0,
    "worst": 4.6629367034256575e-15
   },
   "package": {
    "GR50": 1.56610135146673e-06,
    "GRmax": -0.500252315935893,
    "GR_AOC": 0.656021454789321,
    "GEC50": 1.80601344501218e-06,
    "GRinf": -0.51970741718659,
    "h_GR": 5.0,
    "r2_GR": 0.997722983028774,
    "pval_GR": 7.22653549776422e-22,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": -0.4997503120945492,
     "n": 2
    },
    "grAoc": 0.6560214547893206,
    "fitted": {
     "grInf": -0.5197074040092262,
     "logGec50": -5.74327907146056,
     "h": 4.999999999999999,
     "rss": 0.02276620532967519
    },
    "gec50": null,
    "grInf": null,
    "gr50": null,
    "withheld": "search-limit"
   },
   "fit": {
    "engineRss": 0.02276620532967519,
    "packageParamsRss": 0.02276620532968861,
    "refitFromPackageRss": 0.022766205329675163,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  }
 ],
 "example": [
  {
   "name": "BT20/drugA/0/48",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "definitional",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 27,
    "disagree": 0,
    "worst": 4.218847493575595e-15
   },
   "package": {
    "GR50": 0.0754422161735407,
    "GRmax": 0.0146909374102715,
    "GR_AOC": 0.537212335977701,
    "GEC50": 0.0750490129306536,
    "GRinf": 0.00238653010689791,
    "h_GR": 0.915584752346248,
    "r2_GR": 0.96703130530174,
    "pval_GR": 2.99413867029566e-19,
    "fit": "sigmoid"
   },
   "oracle": {
    "grMax": {
     "value": 0.045710154080916755,
     "n": 3
    },
    "grAoc": 0.5372123359777006,
    "fitted": {
     "grInf": 0.0023858036455206505,
     "logGec50": -1.124654616550602,
     "h": 0.9155797155379828,
     "rss": 0.12234583256999697
    },
    "gec50": "shown",
    "grInf": "shown",
    "gr50": {
     "status": "shown",
     "logValue": -1.1223858435266671
    },
    "withheld": null
   },
   "fit": {
    "engineRss": 0.12234583256999697,
    "packageParamsRss": 0.12234583257968469,
    "refitFromPackageRss": 0.12234583256999702,
    "parameters": {
     "gec50": true,
     "h": true,
     "grInf": true
    }
   }
  },
  {
   "name": "BT20/drugA/0/72",
   "verdicts": {
    "grPerWell": "agree",
    "grMax": "agree",
    "grAoc": "agree",
    "fit": "agree"
   },
   "perWell": {
    "compared": 27,
    "disagree": 0,
    "worst": 4.884981308350689e-15
   },
   "package": {
    "GR50": 0.103956228802033,
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