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Ready for v1.4.0, Documentation building should be fixed now
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@RafaelArutjunjan
RafaelArutjunjan committed Feb 12, 2021
1 parent 709fef0 commit d887e2c
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3 changes: 2 additions & 1 deletion docs/make.jl
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Expand Up @@ -12,6 +12,7 @@ makedocs(
"Tutorial" => Any[ "Providing Data and Models" => "datamodels.md",
"Confidence Regions" => "confidence-regions.md",
"Kullback-Leibler Divergences" => "kullback-leibler.md"],
# Advanced Tutorial: Confidence Bands, Geodesics, Profile Likelihood, DataSetExact, Plotting, ODE Examples
"Contributing" => "todo.md",
],
)
Expand All @@ -22,7 +23,7 @@ makedocs(
# for more information.
deploydocs(
repo = "github.com/RafaelArutjunjan/InformationGeometry.jl.git",
# julia = "1.3",
# julia = "1.5",
# osname = "linux",
# target = "build",
)
2 changes: 1 addition & 1 deletion docs/src/index.md
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Expand Up @@ -5,7 +5,7 @@ This is the documentation of [**InformationGeometry.jl**](https://github.com/Raf

| **Build Status** |
|:----------------:|
| [![travis](https://travis-ci.com/RafaelArutjunjan/InformationGeometry.jl.svg?branch=master)](https://travis-ci.com/RafaelArutjunjan/InformationGeometry.jl) [![appveyor](https://ci.appveyor.com/api/projects/status/github/RafaelArutjunjan/InformationGeometry.jl?svg=true)](https://ci.appveyor.com/project/RafaelArutjunjan/InformationGeometry-jl) [![codecov](https://codecov.io/gh/RafaelArutjunjan/InformationGeometry.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/RafaelArutjunjan/InformationGeometry.jl) |
| [![appveyor](https://ci.appveyor.com/api/projects/status/github/RafaelArutjunjan/InformationGeometry.jl?svg=true)](https://ci.appveyor.com/project/RafaelArutjunjan/InformationGeometry-jl) [![codecov](https://codecov.io/gh/RafaelArutjunjan/InformationGeometry.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/RafaelArutjunjan/InformationGeometry.jl) |


## Main Uses
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6 changes: 3 additions & 3 deletions src/ConfidenceRegions.jl
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Expand Up @@ -15,7 +15,7 @@ loglikelihood(DM::AbstractDataModel, θ::AbstractVector{<:Number}; kwargs...) =

@inline function loglikelihood(DS::AbstractDataSet, model::ModelOrFunction, θ::AbstractVector{<:Number}; kwargs...)
Y = ydata(DS) - EmbeddingMap(DS, model, θ; kwargs...)
-0.5*(DataspaceDim(DS)*log(2pi) - logdetInvCov(DS) + transpose(Y) * InvCov(DS) * Y)
-0.5*(DataspaceDim(DS)*log(2π) - logdetInvCov(DS) + transpose(Y) * InvCov(DS) * Y)
end


Expand Down Expand Up @@ -107,7 +107,7 @@ end
# Ftest(DM::DataModel, θ::Vector, MLE::Vector, Conf=ConfVol(1))::Bool = FtestPrepared(DM,θ,sum((ydata(DM) .- map(x->DM.model(x,MLE),xdata(DM))).^2),Conf)

# equivalent to ResidualSquares(DM,MLE(DM))
RS_MLE(DM::AbstractDataModel) = logdetInvCov(DM) - Npoints(DM)*ydim(DM)*log(2pi) - 2LogLikeMLE(DM)
RS_MLE(DM::AbstractDataModel) = logdetInvCov(DM) - Npoints(DM)*ydim(DM)*log(2π) - 2LogLikeMLE(DM)
ResidualSquares(DM::AbstractDataModel, θ::AbstractVector{<:Number}) = ResidualSquares(Data(DM), Predictor(DM), θ)
function ResidualSquares(DS::AbstractDataSet, model::ModelOrFunction, θ::AbstractVector{<:Number})
Y = ydata(DS) - EmbeddingMap(DS,model,θ)
Expand Down Expand Up @@ -821,7 +821,7 @@ Returns `HyperCube` which bounds the linearized confidence region of level `Conf
"""
function LinearCuboid(DM::AbstractDataModel, Confnum::Real=1.; Padding::Number=1/30, N::Int=200)
L = sqrt(InvChisqCDF(pdim(DM),ConfVol(Confnum))) .* cholesky(inv(Symmetric(FisherMetric(DM,MLE(DM))))).L
C = [ConstructCube(Unpack([L * RotatedVector(α,dims[1],dims[2],pdim(DM)) for α in range(0,2pi,length=N)]);Padding=Padding) for dims in permutations(1:pdim(DM),2)]
C = [ConstructCube(Unpack([L * RotatedVector(α,dims[1],dims[2],pdim(DM)) for α in range(0,2π,length=N)]);Padding=Padding) for dims in permutations(1:pdim(DM),2)]
TranslateCube(Union(C), MLE(DM))
end

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4 changes: 2 additions & 2 deletions src/Geodesics.jl
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Expand Up @@ -134,7 +134,7 @@ end

# ADAPT FOR PLANES
function ConstLengthGeodesics(DM::AbstractDataModel,Metric::Function,MLE::Vector,Conf::Real=ConfVol(1), N::Int=100; tol::Real=6e-11)
angles = [2*pi*n/N for n in 1:N]
angles = [2π*n/N for n in 1:N]
Initials = [ [MLE...,cos(alpha),sin(alpha)] for alpha in angles]
solving = 0
function Constructor(Initial)
Expand Down Expand Up @@ -174,7 +174,7 @@ end

function ConstParamGeodesics(Metric::Function,MLE::Vector,Endtime::Number=10.,N::Int=100;
Boundaries::Union{Function,Nothing}=nothing, tol::Real=1e-13, parallel::Bool=false)
Initials = [ [cos(alpha),sin(alpha)] for alpha in range(0,2pi,length=N)]; solving = 0
Initials = [ [cos(alpha),sin(alpha)] for alpha in range(0,2π;length=N)]; solving = 0
Map = parallel ? pmap : map
function Constructor(Initial)
solving += 1
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2 changes: 1 addition & 1 deletion src/Plotting.jl
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Expand Up @@ -623,7 +623,7 @@ PlotMatrix(inv(FisherMetric(DM,MLE)),MLE)
"""
function PlotMatrix(Mat::AbstractMatrix, MLE::AbstractVector{<:Number}=zeros(size(Mat,1)); dims::Tuple{Int,Int}=(1,2), N::Int=400, plot::Bool=true, kwargs...)
!(length(MLE) == size(Mat,1) == size(Mat,2)) && throw("PlotMatrix: Dimensional mismatch.")
C = sqrt(quantile(Chisq(length(MLE)),ConfVol(1))) .* cholesky(Symmetric(Mat)).L; angles = range(0,2pi,length=N)
C = sqrt(quantile(Chisq(length(MLE)),ConfVol(1))) .* cholesky(Symmetric(Mat)).L; angles = range(0,2π;length=N)
F(α::Number) = MLE + C * RotatedVector(α,dims[1],dims[2],length(MLE))
Data = Unpack(F.(angles))
if plot display(Plots.plot!(ToCols(Data)...;label="Matrix", kwargs...)) end
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2 changes: 1 addition & 1 deletion src/Subspaces.jl
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Expand Up @@ -58,7 +58,7 @@ Shift(PlaneBegin::Plane, PlaneEnd::Plane) = TranslatePlane(PlaneEnd, PlaneEnd.st

IsOnPlane(PL::Plane, x::AbstractVector, ProjectionOp::AbstractMatrix=ProjectionOperator(PL))::Bool = DistanceToPlane(PL, x, ProjectionOp) < 4e-15
TranslatePlane(PL::Plane, v::AbstractVector) = Plane(PL.stütz + v, PL.Vx, PL.Vy)
RotatePlane(PL::Plane, rads::Real=pi/2) = Plane(PL.stütz,cos(rads)*PL.Vx + sin(rads)*PL.Vy, cos(rads)*PL.Vy - sin(rads)*PL.Vx)
RotatePlane(PL::Plane, rads::Real=π/2) = Plane(PL.stütz,cos(rads)*PL.Vx + sin(rads)*PL.Vy, cos(rads)*PL.Vy - sin(rads)*PL.Vx)
function RotationMatrix(PL::Plane, rads::Real)
V = PL.Vx*transpose(PL.Vx) + PL.Vy*transpose(PL.Vy)
W = PL.Vx*transpose(PL.Vy) - PL.Vy*transpose(PL.Vx)
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@JuliaRegistrator register()

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Registration pull request created: JuliaRegistries/General/29938

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v1.4.0 -m "<description of version>" d887e2c85769bd02c3335e68e11ae2b508ad40e2
git push origin v1.4.0

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