Merge pull request #157 from SciML/ChrisRackauckas-patch-2

don't skip the first point

Project.toml

@@ -14,6 +14,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
 PenaltyFunctions = "06bb1623-fdd5-5ca2-a01c-88eae3ea319e"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 
 [compat]
 Calculus = "0.5"
@@ -25,6 +26,7 @@ ForwardDiff = "0.10"
 LsqFit = "0.8, 0.9, 0.10, 0.11, 0.12"
 PenaltyFunctions = "0.1, 0.2"
 RecursiveArrayTools = "1.0, 2.0"
+SciMLBase = "1"
 julia = "1"
 
 [extras]

src/DiffEqParamEstim.jl

@@ -1,6 +1,8 @@
 module DiffEqParamEstim
 using DiffEqBase, LsqFit, PenaltyFunctions,
-      RecursiveArrayTools, ForwardDiff, Calculus, Distributions, LinearAlgebra, DiffEqSensitivity, Dierckx
+      RecursiveArrayTools, ForwardDiff, Calculus, Distributions,
+      LinearAlgebra, DiffEqSensitivity, Dierckx,
+      SciMLBase
 
 STANDARD_PROB_GENERATOR(prob,p) = remake(prob;u0=eltype(p).(prob.u0),p=p)
 STANDARD_PROB_GENERATOR(prob::EnsembleProblem,p) = EnsembleProblem(

src/build_loss_objective.jl

@@ -24,7 +24,7 @@ end
 (f::DiffEqObjective)(x) = f.cost_function(x)
 (f::DiffEqObjective)(x,y) = f.cost_function2(x,y)
 
-function build_loss_objective(prob::DiffEqBase.DEProblem,alg,loss,regularization=nothing,args...;
+function build_loss_objective(prob::SciMLBase.SciMLProblem,alg,loss,regularization=nothing,args...;
                               priors=nothing,mpg_autodiff = false,
                               verbose_opt = false,verbose_steps = 100,
                               prob_generator = STANDARD_PROB_GENERATOR,

src/cost_functions.jl

@@ -83,11 +83,11 @@ function (f::L2Loss)(sol::DiffEqBase.DESolution)
   sumsq = 0.0
 
   if weight == nothing
-    @inbounds for i in 2:length(sol)
+    @inbounds for i in 1:length(sol)
       for j in 1:length(sol[i])
         sumsq +=(data[j,i] - sol[j,i])^2
       end
-      if diff_weight != nothing
+      if diff_weight != nothing && i != 1
           for j in 1:length(sol[i])
             if typeof(diff_weight) <: Real
               sumsq += diff_weight*((data[j,i] - data[j,i-1] - sol[j,i] + sol[j,i-1])^2)
@@ -98,7 +98,7 @@ function (f::L2Loss)(sol::DiffEqBase.DESolution)
       end
     end
   else
-    @inbounds for i in 2:length(sol)
+    @inbounds for i in 1:length(sol)
       if typeof(weight) <: Real
         for j in 1:length(sol[i])
           sumsq = sumsq + ((data[j,i] - sol[j,i])^2)*weight
@@ -108,7 +108,7 @@ function (f::L2Loss)(sol::DiffEqBase.DESolution)
           sumsq = sumsq + ((data[j,i] - sol[j,i])^2)*weight[j,i]
         end
       end
-      if diff_weight != nothing
+      if diff_weight != nothing && i != 1
         for j in 1:length(sol[i])
           if typeof(diff_weight) <: Real
             sumsq += diff_weight*((data[j,i] - data[j,i-1] - sol[j,i] + sol[j,i-1])^2)