I got the following code from : https://juliadynamics.github.io/JuliaDynamics/

using DynamicalSystems, PyPlot

ds = Systems.roessler()
tr = trajectory(ds, 1000.0; dt = 0.05)

τ = estimate_delay(tr[:, 1], "mi_min") # first minimum of mutual information

figure(figsize = (10, 6)); subplot(1,2,1)
for method in ["afnn", "fnn", "f1nn"]
    Ds = estimate_dimension(tr[:, 1], τ, 1:6, method)
    plot(1:6, Ds ./ maximum(Ds), label = method, marker = "o")
end
legend(); xlabel("\$\\gamma\$ (temporal neighbors)")

subplot(1,2,2, projection = "3d")
rec = embed(tr[:, 1], 4, τ)
plot3D(rec[1:2000, 1],rec[1:2000, 2],rec[1:2000, 3])

The estimate_dimension function does not work. What is the correct way to do in version 2.3.2?

I tried this:

ds = Systems.roessler()
tr = trajectory(ds, 1000.0; dt = 0.05)

τ = estimate_delay(tr[:, 1], "mi_min") # first minimum of mutual information
grassberger_dim(tr[:, 1], estimate_boxsizes(tr[:, 1]), τ)

But I got ERROR: MethodError: no method matching estimate_boxsizes(::Vector{Float64}) . Isn't estimate_boxsizes supposed to take just the dataset?

@jaredhowland Since I do not know how to build the website locally (please share a link/knowledge how to), is it possible to get the automatic building working? GitHub states that the problem is a symlink:

https://help.github.com/articles/page-build-failed-file-is-a-symlink/

@jaredhowland I can see from here: https://github.com/JuliaDynamics/JuliaDynamics/blob/master/src/_codesnippets/make.jl that in the original QuantumOptics the code examples where done automatically. This is not necessary here, we don't have to run Julia.

But could you please tell me where in the source code do I have to paste the code part, and how can I link in videos instead of just images? In the index.html I see:

        <div class="row">
            <div class="col-lg-12">
                <div class="tab-content">
                    {% include codesnippet.html id="example1" name="test" imgname="test.svg" title="Particle in Harmonic Trap"%}
                    {% include codesnippet.html id="example2" name="test" imgname="test.svg" title="Squeezed Fock State" %}
                    {% include codesnippet.html id="example3" name="test" imgname="test.svg" title="Spin-3/2-System" %}
                    {% include codesnippet.html id="example4" name="test" imgname="test.svg" title="Three-Level System" %}
                    {% include codesnippet.html id="example5" name="test" imgname="test.svg" title="Jaynes-Cummings System" %}
                </div>
            </div>
</div>

but from this I can't really deduce how to proceed...

I am not sure which parts of the README are true and which are not, since I am not sure how the website works...

For example, I think the first part of the readme is not true anymore, this website is not built out of many other repositories. All relevant information for the website is contained here in this repo.

@jaredhowland could you please delete information in the README that is outdated? My goal is to be able to handle this repo without your help, but unfortunately some babysteps need to be taken first...

Another example: In the software requirements, I don't think Documenter is actually used in this website either, correct?

In the 2.0 CahousTools notebook:

psos_regular = poincaresos(lor, (2, 0.0), 2000.0, Ttr = 1000.0)
summary(psos_regular)

gives an error:

AssertionError: tprev ≤ t ≤ tnext

Stacktrace:
[1] (::SimpleDiffEq.SimpleATsit5Integrator{false,StaticArrays.SArray{Tuple{3},Float64,1,3},Float64,Array{Float64,1},DiffEqBase.ODEFunction{false,typeof(DynamicalSystemsBase.Systems.loop),LinearAlgebra.UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(SimpleDiffEq.defaultnorm)})(::Float64) at C:\Users\Denis.julia\packages\SimpleDiffEq\1icT4\src\tsit5\atsit5.jl:528
[2] #15 at C:\Users\Denis.julia\packages\ChaosTools\6FSL8\src\orbitdiagrams\poincare.jl:117 [inlined]
[3] DerivativeFree at C:\Users\Denis.julia\packages\Roots\xWzoi\src\find_zero.jl:266 [inlined]
[4] decide_convergence(::Roots.A42, ::Roots.DerivativeFree{getfield(ChaosTools, Symbol("##15#16")){SimpleDiffEq.SimpleATsit5Integrator{false,StaticArrays.SArray{Tuple{3},Float64,1,3},Float64,Array{Float64,1},DiffEqBase.ODEFunction{false,typeof(DynamicalSystemsBase.Systems.loop),LinearAlgebra.UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(SimpleDiffEq.defaultnorm)},PlaneCrossing{Tuple{Int64,Float64}}}}, ::Roots.UnivariateZeroState{Float64,Float64}, ::Roots.UnivariateZeroOptions{Float64,Float64,Float64,Float64}) at C:\Users\Denis.julia\packages\Roots\xWzoi\src\find_zero.jl:589
[5] find_zero(::Roots.A42, ::Roots.DerivativeFree{getfield(ChaosTools, Symbol("##15#16")){SimpleDiffEq.SimpleATsit5Integrator{false,StaticArrays.SArray{Tuple{3},Float64,1,3},Float64,Array{Float64,1},DiffEqBase.ODEFunction{false,typeof(DynamicalSystemsBase.Systems.loop),LinearAlgebra.UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(SimpleDiffEq.defaultnorm)},PlaneCrossing{Tuple{Int64,Float64}}}}, ::Roots.UnivariateZeroOptions{Float64,Float64,Float64,Float64}, ::Roots.UnivariateZeroState{Float64,Float64}, ::Roots.NullTracks) at C:\Users\Denis.julia\packages\Roots\xWzoi\src\find_zero.jl:573
[6] #find_zero#4(::Roots.NullTracks, ::Bool, ::Base.Iterators.Pairs{Symbol,Float64,Tuple{Symbol,Symbol},NamedTuple{(:xrtol, :atol),Tuple{Float64,Float64}}}, ::Function, ::Function, ::Tuple{Float64,Float64}, ::Roots.A42, ::Nothing) at C:\Users\Denis.julia\packages\Roots\xWzoi\src\find_zero.jl:532
[7] #find_zero at .\none:0 [inlined] (repeats 2 times)
[8] poincaresos(::SimpleDiffEq.SimpleATsit5Integrator{false,StaticArrays.SArray{Tuple{3},Float64,1,3},Float64,Array{Float64,1},DiffEqBase.ODEFunction{false,typeof(DynamicalSystemsBase.Systems.loop),LinearAlgebra.UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(SimpleDiffEq.defaultnorm)}, ::PlaneCrossing{Tuple{Int64,Float64}}, ::Float64, ::Float64, ::StaticArrays.SArray{Tuple{3},Int64,1,3}, ::NamedTuple{(:xrtol, :atol),Tuple{Float64,Float64}}) at C:\Users\Denis.julia\packages\ChaosTools\6FSL8\src\orbitdiagrams\poincare.jl:143
[9] #poincaresos#14(::Int64, ::Float64, ::Bool, ::UnitRange{Int64}, ::StaticArrays.SArray{Tuple{3},Float64,1,3}, ::NamedTuple{(:xrtol, :atol),Tuple{Float64,Float64}}, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::ContinuousDynamicalSystem{false,StaticArrays.SArray{Tuple{3},Float64,1,3},3,typeof(DynamicalSystemsBase.Systems.loop),Array{Float64,1},typeof(DynamicalSystemsBase.Systems.loop_jac),StaticArrays.SArray{Tuple{3,3},Float64,2,9},false}, ::Tuple{Int64,Float64}, ::Float64) at C:\Users\Denis.julia\packages\ChaosTools\6FSL8\src\orbitdiagrams\poincare.jl:81
[10] (::getfield(ChaosTools, Symbol("#kw##poincaresos")))(::NamedTuple{(:Ttr,),Tuple{Float64}}, ::typeof(poincaresos), ::ContinuousDynamicalSystem{false,StaticArrays.SArray{Tuple{3},Float64,1,3},3,typeof(DynamicalSystemsBase.Systems.loop),Array{Float64,1},typeof(DynamicalSystemsBase.Systems.loop_jac),StaticArrays.SArray{Tuple{3,3},Float64,2,9},false}, ::Tuple{Int64,Float64}, ::Float64) at .\none:0
[11] top-level scope at In[17]:1

clicked from notebook 0, it's kind of comical

Hi all,
it's only a tiny observation I stumbled uppon. The link to "Getting Started" returns a 404 because the url scheme changed.
Julia's setup instructions shoud refer to new Getting Started aka https://docs.julialang.org/en/v1/manual/getting-started/ .
Thanks for you incredible work!

best,
GMGassner