fix in plots of third notebook

5d8c423e · Bentriou Mahmoud · ed3f850c · 5d8c423e
Commit 5d8c423e authored Feb 18, 2021 by Bentriou Mahmoud
--- a/examples/notebooks/3_ABC-SMC_with_ContinuousTimeModel.ipynb
+++ b/examples/notebooks/3_ABC-SMC_with_ContinuousTimeModel.ipynb
@@ -23,6 +23,7 @@
    "parametric_SIR = ParametricModel(SIR, (:ki, Uniform(0.001, 0.0015)))\n",
    "\n",
    "vec_observations = [simulate(SIR)]\n",
+    "\n",
    "function dist_obs(vec_sim::Vector{Trajectory}, vec_observations::Vector{Trajectory})\n",
    "    return dist_lp(vec_sim[1], vec_observations[1]; p=2)\n",
    "end\n",
@@ -40,8 +41,15 @@
   "outputs": [],
   "source": [
    "using Plots\n",
-    "histogram(res_abc.mat_p_end, weights = res_abc.weights_end)"
+    "histogram(vec(res_abc.mat_p_end), weights = res_abc.weights)"
   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
  }
 ],
 "metadata": {

 %% Cell type:markdown id: tags:

 # ABC-SMC with ContinuousTimeModel

 The package allows the run of ABC-SMC algorithm with models defined by the package.

 %% Cell type:code id: tags:

 ``` julia
 using MarkovProcesses
 using Distributions

 load_model("SIR")
 set_time_bound!(SIR, 100.0)
 parametric_SIR = ParametricModel(SIR, (:ki, Uniform(0.001, 0.0015)))

 vec_observations = [simulate(SIR)]
+
 function dist_obs(vec_sim::Vector{Trajectory}, vec_observations::Vector{Trajectory})
    return dist_lp(vec_sim[1], vec_observations[1]; p=2)
 end

 epsilon = 0.5 * dist_obs([simulate(SIR)], vec_observations)
 @show epsilon

 res_abc = abc_smc(parametric_SIR, vec_observations, dist_obs, nbr_particles = 100, tolerance = epsilon)
 ```

 %% Cell type:code id: tags:

 ``` julia
 using Plots
-histogram(res_abc.mat_p_end, weights = res_abc.weights_end)
+histogram(vec(res_abc.mat_p_end), weights = res_abc.weights)
+```
+
+%% Cell type:code id: tags:
+
+``` julia
 ```