{
  "protocol": {
    "seed": 11,
    "cycles": 150,
    "branch": 0.12,
    "gravityBias": 0.35,
    "randomness": 0.1,
    "lightBias": 0,
    "initialTiltSD": 8,
    "branchMean": 53,
    "branchSD": 12,
    "thickening": true,
    "weight": true,
    "wind": true,
    "roots": true,
    "reaction": true,
    "g": 9.81,
    "windSpeed": 1,
    "radialGrowth": 0.000006,
    "E": 4000000000,
    "rhoDry": 400,
    "rhoFresh": 800,
    "MOR": 45000000,
    "newRadius": 0.003,
    "segmentLength": 0.12,
    "assimilation": 0.003,
    "leafArea": 0.03,
    "leafLifetime": 70,
    "leafDryMass": 0.002,
    "eta": 1.4,
    "maintenance": 0.00005,
    "initialCarbon": 0.015,
    "initialRootMass": 0.01,
    "rootStiffness": 20,
    "rootCapacity": 0.5,
    "reactionStrain": 0.0005,
    "reactionGain": 0.5,
    "maxNodes": 85,
    "maxRotation": 0.3,
    "maxDeflectionRatio": 0.2,
    "initialHeightMean": 0.0942,
    "initialHeightSD": 0.0303
  },
  "rules_provenance": {
    "species": "Populus nigra",
    "branch_mean_degrees": {
      "value": 53,
      "source": "Gielen et al. 2002, Table 2, control, first growing season",
      "doi": "10.1046/j.0028-646X.2001.00301.x",
      "reported_standard_error": 1
    },
    "branch_standard_deviation": {
      "value": 12,
      "status": "exploratory; not derived from reported SE"
    },
    "initial_tilt_SD": {
      "value": 8,
      "status": "exploratory; no empirical seedling distribution acquired"
    },
    "activation_probability": {
      "value": 0.12,
      "status": "Bernoulli model form motivated by GreenLab, coefficient not empirically calibrated"
    },
    "side_probability": {
      "value": 0.5,
      "status": "isotropic environment assumption, not measured distribution"
    },
    "geometry_projection": "2D simplification of branch insertion angles measured in 3D",
    "initial_height": {
      "source": "Vujnović et al. 2023, Table 1, sand+peat 2019",
      "doi": "10.15177/seefor.23-02",
      "N": 160,
      "mean_m": 0.0942,
      "sd_m": 0.0303,
      "stage": "selected nursery seedlings, end of season",
      "sampling": "normal reconstructed; reject height <= 0.005m; cutoff is technical",
      "joint_height_diameter": "not acquired"
    }
  },
  "branch_angle_distribution": {
    "family": "clipped normal",
    "bounds_degrees": [
      5,
      85
    ],
    "mean": 53,
    "sd": 12,
    "sd_status": "exploratory"
  },
  "initial_tilt_distribution": {
    "family": "clipped normal",
    "mean_degrees_from_vertical": 0,
    "sd": 8,
    "bounds_degrees": [
      -30,
      30
    ],
    "status": "exploratory"
  },
  "activation_distribution": {
    "family": "Bernoulli per new node",
    "p": 0.12,
    "p_status": "exploratory"
  },
  "sources": [
    {
      "doi": "10.1046/j.0028-646X.2001.00301.x",
      "table": 2,
      "species": "P. nigra",
      "treatment": "control",
      "season": 1,
      "branch_type": "sylleptic",
      "mean_origin_angle": 53,
      "standard_error": 1,
      "note": "SE is not individual SD; use at birth is a modelling assumption"
    },
    {
      "doi": "10.1093/treephys/7.1-2-3-4.157",
      "use": "genotype and cohort matter, no pooled distribution extracted"
    },
    {
      "url": "https://greenlab.cirad.fr/GLUVED/html/P2_GLab/Intro/GLintro_over_003.html",
      "use": "stochastic organogenesis model form, not p estimate"
    }
  ],
  "verification": [
    {
      "seed": 11,
      "windSpeed": 0,
      "status": "completed",
      "cycle": 150,
      "balance": 5.551115123125783e-17
    },
    {
      "seed": 11,
      "windSpeed": 1,
      "status": "completed",
      "cycle": 150,
      "balance": 5.551115123125783e-17
    },
    {
      "seed": 11,
      "windSpeed": 4,
      "status": "outside_linear_domain",
      "cycle": 27,
      "balance": 1.734723475976807e-17
    },
    {
      "seed": 12,
      "windSpeed": 0,
      "status": "completed",
      "cycle": 150,
      "balance": 4.85722573273506e-17
    },
    {
      "seed": 12,
      "windSpeed": 1,
      "status": "completed",
      "cycle": 150,
      "balance": 4.85722573273506e-17
    },
    {
      "seed": 12,
      "windSpeed": 4,
      "status": "outside_linear_domain",
      "cycle": 48,
      "balance": 2.0816681711721685e-17
    },
    {
      "seed": 13,
      "windSpeed": 0,
      "status": "completed",
      "cycle": 150,
      "balance": 6.245004513516506e-17
    },
    {
      "seed": 13,
      "windSpeed": 1,
      "status": "completed",
      "cycle": 150,
      "balance": 6.245004513516506e-17
    },
    {
      "seed": 13,
      "windSpeed": 4,
      "status": "outside_linear_domain",
      "cycle": 27,
      "balance": 1.3877787807814457e-17
    }
  ],
  "browser_visual_qa": false,
  "sensitivity_hypotheses": {
    "angle_SD_degrees": [
      6,
      12,
      18
    ],
    "bud_p": [
      0.05,
      0.12,
      0.25
    ],
    "initial_tilt_SD_degrees": [
      0,
      8,
      16
    ]
  }
}