Merge pull request #4 from max-de-rooij/ensemble-modelling

Update model

README.md

@@ -1,7 +1,5 @@
 # MealModel
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://max-de-rooij.github.io/MealModel.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://max-de-rooij.github.io/MealModel.jl/dev/)
 [![Build Status](https://github.com/max-de-rooij/MealModel.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/max-de-rooij/MealModel.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![codecov](https://codecov.io/gh/max-de-rooij/MealModel.jl/branch/main/graph/badge.svg?token=GDWQBJQBXD)](https://codecov.io/gh/max-de-rooij/MealModel.jl)
 

notebooks/MealModel.ipynb

@@ -0,0 +1,47 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using MealModel"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "MixedMealModel(SciMLBase.ODEProblem{Vector{Float64}, Tuple{Float64, Float64}, true, Vector{Float64}, SciMLBase.ODEFunction{true, SciMLBase.FullSpecialize, MealModel.var\"#3#4\"{Float64, Float64, Float64, Float64, Float64, Float64, Float64}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, Nothing}, Base.Pairs{Symbol, SciMLSensitivity.ForwardDiffSensitivity{0, nothing}, Tuple{Symbol}, NamedTuple{(:sensealg,), Tuple{SciMLSensitivity.ForwardDiffSensitivity{0, nothing}}}}, SciMLBase.StandardODEProblem}(SciMLBase.ODEFunction{true, SciMLBase.FullSpecialize, MealModel.var\"#3#4\"{Float64, Float64, Float64, Float64, Float64, Float64, Float64}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, Nothing}(MealModel.var\"#3#4\"{Float64, Float64, Float64, Float64, Float64, Float64, Float64}(0.1, 9.0, 3.0, 31.0, 1.0, 0.00113, 0.005551), LinearAlgebra.UniformScaling{Bool}(true), nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, nothing, SciMLBase.DEFAULT_OBSERVED, nothing, nothing), [0.0, 5.0, 0.0, 18.0, 0.0, 18.0, 18.0, 18.0, 0.33, 0.0, 0.0, 0.0, 1.3], (0.0, 480.0), [0.0105, 0.28, 0.00607, 0.000235, 0.0424, 2.2975, 1.15, 7.27, 0.0383, 0.284  …  0.0385, 0.0713, 208.88, 0.0088, 0.0163, 1.0e-5, 0.0119, 75000.0, 60000.0, 84.2], Base.Pairs(:sensealg => SciMLSensitivity.ForwardDiffSensitivity{0, nothing}()), SciMLBase.StandardODEProblem()), [1, 5, 6, 17, 20, 21, 23, 25])"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "model = MixedMealModel()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.9.3",
+   "language": "julia",
+   "name": "julia-1.9"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.9.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

src/MealModel.jl

@@ -5,7 +5,6 @@ using Trapz
 
 include("model/Model.jl")
 include("simulation/Simulation.jl")
-include("assimilation/Assimilation.jl")
 
 # model constructor
 export MixedMealModel

src/assimilation/Loss.jl

@@ -33,6 +33,9 @@ function make_loss(model::MixedMealModel, error::Function; save_timestep = 0.5)
   _loss
 end
 
+make_loss(model::MixedMealModel, data...; save_timestep = 0.5) = make_loss(model, make_error(
+  model, data...; save_timestep = save_timestep); save_timestep = save_timestep)
+
 function make_error(model::MixedMealModel, glucose_data, glucose_timepoints, insulin_data, insulin_timepoints, tg_data, tg_timepoints, nefa_data, nefa_timepoints; save_timestep = 0.5)
 
   # times