diff --git a/10_BayesianDiffEq.ipynb b/10_BayesianDiffEq.ipynb
index 198e59b31..109d8ce7f 100644
--- a/10_BayesianDiffEq.ipynb
+++ b/10_BayesianDiffEq.ipynb
@@ -13,7 +13,24 @@
"cell_type": "code",
"execution_count": 1,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "┌ Info: Precompiling DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0]\n",
+ "└ @ Base loading.jl:1260\n",
+ "┌ Info: Precompiling DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa]\n",
+ "└ @ Base loading.jl:1260\n",
+ "┌ Info: Precompiling DiffEqSensitivity [41bf760c-e81c-5289-8e54-58b1f1f8abe2]\n",
+ "└ @ Base loading.jl:1260\n",
+ "┌ Info: Precompiling Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]\n",
+ "└ @ Base loading.jl:1260\n",
+ "┌ Info: Precompiling StatsPlots [f3b207a7-027a-5e70-b257-86293d7955fd]\n",
+ "└ @ Base loading.jl:1260\n"
+ ]
+ }
+ ],
"source": [
"using Turing, Distributions, DataFrames, DifferentialEquations, DiffEqSensitivity\n",
"\n",
@@ -49,111 +66,111 @@
"\n",
"\n"
+ "\n"
]
},
"execution_count": 2,
@@ -436,75 +453,18 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
"┌ Info: Found initial step size\n",
- "│ ϵ = 0.0125\n",
+ "│ ϵ = 0.025\n",
"└ @ Turing.Inference /Users/vaibhav/.julia/packages/Turing/GMBTf/src/inference/hmc.jl:629\n",
"┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
"│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
- "└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n",
- "┌ Warning: The current proposal will be rejected due to numerical error(s).\n",
- "│ isfinite.((θ, r, ℓπ, ℓκ)) = (true, false, false, false)\n",
"└ @ AdvancedHMC /Users/vaibhav/.julia/packages/AdvancedHMC/WJCQA/src/hamiltonian.jl:47\n"
]
},
@@ -525,23 +485,23 @@
"Summary Statistics\n",
" parameters mean std naive_se mcse ess r_hat\n",
" ────────── ────── ────── ──────── ────── ───────── ──────\n",
- " theta[1] 2.4051 0.0657 0.0007 0.0011 4124.2708 1.0001\n",
- " theta[2] 1.3384 0.0720 0.0008 0.0011 4704.0990 1.0004\n",
- " theta[3] 2.7012 0.1862 0.0020 0.0024 5266.9500 0.9999\n",
- " theta[4] 1.9285 0.0492 0.0005 0.0008 3959.7446 0.9999\n",
- " σ[1] 1.2781 0.0649 0.0007 0.0008 5694.3945 1.0001\n",
+ " theta[1] 2.1999 0.0061 0.0001 0.0001 2932.9824 1.0000\n",
+ " theta[2] 1.0000 0.0025 0.0000 0.0000 2976.0464 1.0001\n",
+ " theta[3] 2.0001 0.0028 0.0000 0.0000 4960.5915 1.0002\n",
+ " theta[4] 0.4000 0.0007 0.0000 0.0000 2917.9182 0.9999\n",
+ " σ[1] 0.0151 0.0011 0.0000 0.0000 4999.8943 1.0003\n",
"\n",
"Quantiles\n",
" parameters 2.5% 25.0% 50.0% 75.0% 97.5%\n",
" ────────── ────── ────── ────── ────── ──────\n",
- " theta[1] 2.2589 2.3635 2.4142 2.4588 2.4956\n",
- " theta[2] 1.2078 1.2893 1.3352 1.3837 1.4937\n",
- " theta[3] 2.3634 2.5713 2.6925 2.8212 3.0914\n",
- " theta[4] 1.8186 1.8960 1.9360 1.9685 1.9965\n",
- " σ[1] 1.1600 1.2329 1.2743 1.3204 1.4144\n"
+ " theta[1] 2.1878 2.1957 2.1999 2.2040 2.2119\n",
+ " theta[2] 0.9951 0.9983 1.0000 1.0017 1.0048\n",
+ " theta[3] 1.9948 1.9982 2.0001 2.0019 2.0057\n",
+ " theta[4] 0.3987 0.3996 0.4000 0.4004 0.4013\n",
+ " σ[1] 0.0131 0.0143 0.0150 0.0158 0.0174\n"
]
},
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
@@ -562,7 +522,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
@@ -571,5434 +531,5410 @@
"\n",
"\n"
]
},
- "execution_count": 5,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
@@ -7681,13 +7617,6 @@
"model = fitlv(averagedata)\n",
"chain = sample(model, NUTS(.65),500)"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {