diff --git a/benchmarks/hodgkinhuxley.jmd b/benchmarks/hodgkinhuxley.jmd
index 137731960..f6125c1b6 100644
--- a/benchmarks/hodgkinhuxley.jmd
+++ b/benchmarks/hodgkinhuxley.jmd
@@ -13,14 +13,13 @@ using LinearAlgebra, Statistics, Distributions
using DiffEqDevTools, SciMLBase, OrdinaryDiffEq, Plots, SimpleUnPack
using ProbNumDiffEq
-# Plotting theme
-theme(:dao;
+Plots.theme(
+ :dao;
markerstrokewidth=0.5,
legend=:outertopright,
- bottom_margin=5Plots.mm,
- size = (1000, 400),
- xticks = 10.0 .^ (-16:1:16),
- yticks = 10.0 .^ (-6:1:5),
+ margin=5Plots.mm,
+ xticks=10.0 .^ (-16:1:16),
+ yticks=10.0 .^ (-6:1:5),
)
```
diff --git a/benchmarks/lotkavolterra.jmd b/benchmarks/lotkavolterra.jmd
index e4567f87c..c7190fec2 100644
--- a/benchmarks/lotkavolterra.jmd
+++ b/benchmarks/lotkavolterra.jmd
@@ -20,13 +20,12 @@ using LinearAlgebra, Statistics, Distributions
using DiffEqDevTools, ParameterizedFunctions, SciMLBase, OrdinaryDiffEq, Plots
using ProbNumDiffEq
-# Plotting theme
-theme(:dao;
+Plots.theme(
+ :dao;
markerstrokewidth=0.5,
legend=:outertopright,
- bottom_margin=5Plots.mm,
- size = (1000, 600),
- xticks = 10.0 .^ (-16:1:16),
+ margin=5Plots.mm,
+ xticks=10.0 .^ (-16:1:16),
)
```
diff --git a/benchmarks/multi-language-wrappers.jmd b/benchmarks/multi-language-wrappers.jmd
index 83049dda6..46bdcc77b 100644
--- a/benchmarks/multi-language-wrappers.jmd
+++ b/benchmarks/multi-language-wrappers.jmd
@@ -11,17 +11,14 @@ using ODEInterface, ODEInterfaceDiffEq, Sundials, SciPyDiffEq, deSolveDiffEq, MA
using LoggingExtras
using ProbNumDiffEq
-```
-```julia
-# Plotting theme
-theme(:dao;
+Plots.theme(
+ :dao;
markerstrokewidth=0.5,
legend=:outertopright,
- bottom_margin=5Plots.mm,
- size = (1000, 400),
- xticks = 10.0 .^ (-16:1:16),
- yticks = 10.0 .^ (-6:1:5),
+ margin=5Plots.mm,
+ xticks=10.0 .^ (-16:1:16),
+ yticks=10.0 .^ (-6:1:5),
)
```
diff --git a/benchmarks/pleiades.jmd b/benchmarks/pleiades.jmd
index 63b5305b6..1f426c3d4 100644
--- a/benchmarks/pleiades.jmd
+++ b/benchmarks/pleiades.jmd
@@ -13,13 +13,12 @@ using DiffEqDevTools, ParameterizedFunctions, SciMLBase, OrdinaryDiffEq, Sundial
using ModelingToolkit
using ProbNumDiffEq
-# Plotting theme
-theme(:dao;
+Plots.theme(
+ :dao;
markerstrokewidth=0.5,
legend=:outertopright,
- bottom_margin=5Plots.mm,
- size = (1000, 400),
- xticks = 10.0 .^ (-16:1:16)
+ margin=5Plots.mm,
+ xticks=10.0 .^ (-16:1:16),
)
```
@@ -129,12 +128,12 @@ plot(wp,
### Calibration
```julia
+# We can only evaluate calibration for the PN solvers
_wp = WorkPrecisionSet(wp.wps[1:end-3], wp.N-3, wp.abstols, wp.reltols, wp.prob, wp.setups[1:end-3],
wp.names[1:end-3], wp.error_estimate, wp.numruns)
plot(_wp; x=:final, y=:chi2_final,
- color=[1 2 2 2 2],
- linestyle=[:dash :solid :solid :dash :dash],
- alpha=[1 1 1 1 1],
+ color=[1 1 1 1 2 2 2 2],
+ linestyle=[:solid :solid :dash :dash :solid :solid :dash :dash],
)
function plot_chisq_interval!(df, q=0.01)
dist = Chisq(df)
diff --git a/benchmarks/rober.jmd b/benchmarks/rober.jmd
index d9958fd56..96820a5e7 100644
--- a/benchmarks/rober.jmd
+++ b/benchmarks/rober.jmd
@@ -10,18 +10,17 @@ Adapted from
[SciMLBenchmarks.jl](https://docs.sciml.ai/SciMLBenchmarksOutput/stable/DAE/ROBERDAE/).
```julia
-using LinearAlgebra, Statistics
+using LinearAlgebra, Statistics, Distributions
using DiffEqDevTools, ParameterizedFunctions, SciMLBase, OrdinaryDiffEq, Sundials, Plots
using ModelingToolkit
using ProbNumDiffEq
-# Plotting theme
-theme(:dao;
+Plots.theme(
+ :dao;
markerstrokewidth=0.5,
legend=:outertopright,
- bottom_margin=5Plots.mm,
- size = (1000, 400),
- xticks = 10.0 .^ (-16:1:16)
+ margin=5Plots.mm,
+ xticks=10.0 .^ (-16:1:16),
)
```
@@ -41,7 +40,7 @@ mmprob = ODEProblem(sys,[],(0.0,1e5))
daeprob = DAEProblem(sys,[D(y₁)=>-0.04, D(y₂)=>0.04, D(y₃)=>0.0],[],(0.0,1e5)) # can't handle this yet
odaeprob = ODAEProblem(structural_simplify(sys),[],(0.0,1e5)) # can't handle this yet
-ref_sol = solve(daeprob,IDA(),abstol=1/10^14,reltol=1/10^14,dense=false)
+ref_sol = solve(daeprob,IDA(),abstol=1/10^14,reltol=1/10^14)
plot(ref_sol, idxs=[y₁,y₂,y₃], title="ROBER Solution", legend=false, ylims=(0, 1), xticks=:auto)
```
@@ -70,13 +69,27 @@ wp = WorkPrecisionSet(
save_everystep = SAVE_EVERYSTEP,
numruns = 10,
maxiters = Int(1e7),
- timeseries_errors = false,
- verbose = false,
)
plot(wp, palette=Plots.palette([:blue, :red], length(_setups)))
```
+### Calibration
+
+```julia
+plot(wp; x=:final, y=:chi2_final, yguide="Chi-squared (final)",
+ palette=Plots.palette([:blue, :red], length(_setups)))
+
+function plot_chisq_interval!(df, q=0.01)
+ dist = Chisq(df)
+ low, high, mid = quantile(dist, [q, 1-q])..., mean(dist)
+ hline!([low, high], linestyle=:dash, color=:black, label="",
+ fill_between=[high nothing], fillcolor=:green, fillalpha=0.15)
+ hline!([mid], linestyle=:solid, color=:black, label="")
+end
+plot_chisq_interval!(3)
+```
+
## Appendix
diff --git a/benchmarks/runall.jl b/benchmarks/runall.jl
index 6015949bb..30090f3b7 100644
--- a/benchmarks/runall.jl
+++ b/benchmarks/runall.jl
@@ -1,13 +1,17 @@
using Weave
ENV["GKSwstype"] = "nul"
+set_chunk_defaults!(
+ :fig_width=>9,
+ :fig_height=>5,
+)
FILES = [
"lotkavolterra.jmd",
"hodgkinhuxley.jmd",
- # "vanderpol.jmd",
- # "rober.jmd",
- # "pleiades.jmd",
- # "multi-language-wrappers.jmd",
+ "vanderpol.jmd",
+ "rober.jmd",
+ "pleiades.jmd",
+ "multi-language-wrappers.jmd",
]
filedir = @__DIR__
@@ -21,5 +25,6 @@ for file in FILES
)
end
-delete!(ENV, "GKSwstype");
-nothing;
+restore_chunk_defaults!()
+delete!(ENV, "GKSwstype")
+nothing
diff --git a/benchmarks/vanderpol.jmd b/benchmarks/vanderpol.jmd
index 314afc8fc..d95613b64 100644
--- a/benchmarks/vanderpol.jmd
+++ b/benchmarks/vanderpol.jmd
@@ -12,12 +12,11 @@ using LinearAlgebra, Statistics, Distributions
using DiffEqDevTools, ParameterizedFunctions, SciMLBase, OrdinaryDiffEq, Plots
using ProbNumDiffEq
-# Plotting theme
-theme(:dao;
+Plots.theme(
+ :dao;
markerstrokewidth=0.5,
legend=:outertopright,
- bottom_margin=5Plots.mm,
- size = (1000, 400),
+ margin=5Plots.mm,
xticks = 10.0 .^ (-16:1:16)
)
```
@@ -80,7 +79,7 @@ SAVE_EVERYSTEP = true;
_setups = [
"EK1($order)" => Dict(:alg => EK1(order=order, smooth=DENSE))
- for order in 3:6
+ for order in 3:7
]
labels = first.(_setups)
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_2_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_2_1.svg
index 5cc4d6ae4..90adfbdfa 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_2_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_2_1.svg
@@ -1,444 +1,444 @@
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_3_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_3_1.svg
index 4f8c41ccc..97eed2604 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_3_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_3_1.svg
@@ -1,210 +1,208 @@
-
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_4_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_4_1.svg
index 155498d13..971bc1d24 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_4_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_4_1.svg
@@ -1,204 +1,204 @@
-
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_5_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_5_1.svg
index dfc8a8b9a..9d326fbab 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_5_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_5_1.svg
@@ -1,390 +1,390 @@
-
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_6_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_6_1.svg
index b43299928..d51bcdfbf 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_6_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_6_1.svg
@@ -1,265 +1,265 @@
-
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_7_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_7_1.svg
index 483760400..72b5a7cfd 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_7_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_7_1.svg
@@ -1,170 +1,172 @@
-
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_8_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_8_1.svg
index d3843b920..291fa4695 100644
--- a/docs/src/benchmarks/figures/hodgkinhuxley_8_1.svg
+++ b/docs/src/benchmarks/figures/hodgkinhuxley_8_1.svg
@@ -1,164 +1,164 @@
-
diff --git a/docs/src/benchmarks/figures/hodgkinhuxley_9_1.svg b/docs/src/benchmarks/figures/hodgkinhuxley_9_1.svg
deleted file mode 100644
index f05589625..000000000
--- a/docs/src/benchmarks/figures/hodgkinhuxley_9_1.svg
+++ /dev/null
@@ -1,164 +0,0 @@
-
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_10_1.svg b/docs/src/benchmarks/figures/lotkavolterra_10_1.svg
index 67a369b3d..0d916786f 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_10_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_10_1.svg
@@ -1,330 +1,330 @@
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_11_1.svg b/docs/src/benchmarks/figures/lotkavolterra_11_1.svg
index e731998cb..600dea651 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_11_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_11_1.svg
@@ -1,431 +1,431 @@
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_12_1.svg b/docs/src/benchmarks/figures/lotkavolterra_12_1.svg
index 830042f0c..5c4a5e97d 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_12_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_12_1.svg
@@ -1,308 +1,308 @@
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_13_1.svg b/docs/src/benchmarks/figures/lotkavolterra_13_1.svg
index 69e2857c2..b5daa536d 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_13_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_13_1.svg
@@ -1,509 +1,509 @@
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_14_1.svg b/docs/src/benchmarks/figures/lotkavolterra_14_1.svg
index cf89708fc..94051f32b 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_14_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_14_1.svg
@@ -1,280 +1,280 @@
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_15_1.svg b/docs/src/benchmarks/figures/lotkavolterra_15_1.svg
index b271b3c29..cffc721d9 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_15_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_15_1.svg
@@ -1,515 +1,515 @@
-
diff --git a/docs/src/benchmarks/figures/lotkavolterra_16_1.svg b/docs/src/benchmarks/figures/lotkavolterra_16_1.svg
index ed474a259..c4ef2211b 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_16_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_16_1.svg
@@ -1,980 +1,980 @@
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diff --git a/docs/src/benchmarks/figures/lotkavolterra_17_1.svg b/docs/src/benchmarks/figures/lotkavolterra_17_1.svg
deleted file mode 100644
index 342229317..000000000
--- a/docs/src/benchmarks/figures/lotkavolterra_17_1.svg
+++ /dev/null
@@ -1,980 +0,0 @@
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diff --git a/docs/src/benchmarks/figures/lotkavolterra_18_1.svg b/docs/src/benchmarks/figures/lotkavolterra_18_1.svg
deleted file mode 100644
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+++ /dev/null
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diff --git a/docs/src/benchmarks/figures/lotkavolterra_2_1.svg b/docs/src/benchmarks/figures/lotkavolterra_2_1.svg
index aa1f679e1..a2976f6b2 100644
--- a/docs/src/benchmarks/figures/lotkavolterra_2_1.svg
+++ b/docs/src/benchmarks/figures/lotkavolterra_2_1.svg
@@ -1,148 +1,148 @@
-