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Update master #1

Merged
merged 24 commits into from
Nov 13, 2023
Merged

Update master #1

merged 24 commits into from
Nov 13, 2023

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ParadaCarleton and others added 24 commits June 17, 2023 11:28
* `GeneralizedPareto` improvement

Clarifies the `GeneralizedPareto` docstring and adds a new constructor, `GeneralizedPareto(ξ)`, which defaults to unit scale and a location of 0.

* Update src/univariate/continuous/generalizedpareto.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/generalizedpareto.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/generalizedpareto.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/generalizedpareto.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Add tests

* Update src/univariate/continuous/generalizedpareto.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update test/ref/continuous_test.lst

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Add reference values of GeneralizedPareto(2.0)

---------

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
Co-authored-by: David Widmann <david.widmann@it.uu.se>
* Fix Wrong quantiles calculated for some Truncated #1726

As described in
[#1726](#1726), there occur small numbers-big number problems while evaluating quantiles on `Truncated`.

This Fix uses the knowledge on the upper bound of `Truncated` to properly limit the output.

* Update src/truncate.jl

* Update unittest

---------

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
logpdf evalutes the logarithm of the pdf of d at x, not the pdf of d at x.
* Inbounds Error Fixes for some Univariates

Addresses #1265

- Fixed univariate normal
- Fixed univariate gamma
- Fixed poisson

* Fixes some type instabilities

* Update src/univariate/continuous/normal.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/normal.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/normal.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/normal.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update src/univariate/continuous/normal.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Fixes some type instabilities and adds tests

- Fixes more type instabilities in normal
- Adds tests for normal
- Adds tests for gamma
- Adds tests for poisson

* Slight modifications in tests

- Edited tests for normal
- Edited tests for gamma
- Edited tests for poisson

* Update tests

---------

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
…bility vectors (#1738)

* Allow probability vectors other than Float64 vector for Multinomial distributions.
Tests still pass.

* Remove explicit concrete types from multinom_rand

* Added test to make sure rand works for real types other than Float64

* Removed extra test

* updated tests for type stability

* same test but not using internal function

* repeat tests under different types instead

* type stability within multinomial. may want to extend into Binomial

* Apply suggestions from code review

Type conversions implicitly at runtime covers more systems better

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* delete leftover type variable

* Simplify tests

---------

Co-authored-by: Kyle Daruwalla <daruwalla@wisc.edu>
Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
Co-authored-by: David Widmann <david.widmann@it.uu.se>
* move SparseArrays to test deps

* use Pkg format
* import Base.in

* revert `DiscreteInterval`, modify tests

* qualify Base.in
Remove note about different notation in Wikipedia (no longer true).
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix undef ref in lkj_chol sampling

* Add test for dim=1 lkjcholesky

* Update test/cholesky/lkjcholesky.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

* Update test/cholesky/lkjcholesky.jl

Co-authored-by: Seth Axen <seth@sethaxen.com>

* Update test/cholesky/lkjcholesky.jl

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

---------

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
Co-authored-by: Seth Axen <seth@sethaxen.com>
* Create MvLogitNormal

* Add MvLogitNormal to docs

* Simplify constructors

* Fix conversions

* Rearrange code

* Fix computation of  -Inf

* Add meanform and canonform

* Add back type constructor

* Add MvLogitNormal tests

* Update and test show method

* Fix testset name

* Fix for older Julia versions

* Restrict testing of `show` method to newer versions

* Add kldivergence tests

* Improve documentation

* Remove constructor with type and AbstractMvNormal params

* Update show method

* Update docstring

* Remove reference to Dirichlet

* Apply suggestions from code review

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

---------

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
* Move test utilities to an extension

* Fix signature and docstring

* Also qualify AbstractRNG

* Fix Julia < 1.9

* Fix for 1.3?

* Simplify the TestUtils stub
… existing compat) (#1793)

Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
* Add compat entries for stdlibs

* Update Project.toml

* Update Project.toml

* Update Project.toml

* Update Project.toml
@heliosdrm heliosdrm merged commit fa4d903 into heliosdrm:master Nov 13, 2023
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