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Merge pull request #67 from yufongpeng/dev
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Release 0.7.5
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@yufongpeng
yufongpeng authored Dec 8, 2023
2 parents 9d256ae + e14b26f commit 18810ec
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8 changes: 4 additions & 4 deletions Project.toml
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name = "AnovaBase"
uuid = "946dddda-6a23-4b48-8e70-8e60d9b8d680"
authors = ["Yu-Fong Peng <sciphypar@gmail.com>"]
version = "0.7.4"
version = "0.7.5"

[deps]
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Expand All @@ -14,6 +14,6 @@ StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
[compat]
Distributions = "0.23, 0.24, 0.25"
Reexport = "0.2, 1"
StatsBase = "0.33"
StatsModels = "0.6"
julia = "1.6, 1.7, 1.8"
StatsBase = "0.33, 0.34"
StatsModels = "0.7"
julia = "1.6, 1.7, 1.8, 1.9"
4 changes: 1 addition & 3 deletions docs/make.jl
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Expand Up @@ -11,9 +11,7 @@ makedocs(
"Examples_MixedModels.md",
"Examples_FixedEffectModels.md"
],
"Interfacing AnovaBase.jl" => [
"Interface.md"
],
"Interface.md",
"Algorithm" => [
"Algorithm_AnovaGLM.md",
"Algorithm_AnovaMixedModels.md",
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4 changes: 2 additions & 2 deletions docs/src/Interface.md
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@@ -1,4 +1,4 @@
# Interface
# Interfacing AnovaBase.jl
Given model types `SomeModel` and `OtherModel`, the following functions have to be defined or used.

## [anova](./AnovaBase.md#AnovaBase.anova-Tuple{Type{<:GoodnessOfFit},%20AnovaModel})
Expand Down Expand Up @@ -62,4 +62,4 @@ This function is not essential for ANOVA; it is just for convenience to create n
`AnovaBase` provides a lot of functions to work on formula, terms and contrasts. See [Developer utility](./AnovaBase.md#Developer-utility)

## Other function
* [`dof_residual`](./AnovaBase.md#AnovaBase.dof_residual-Tuple{AnovaResult}) applies `dof_residual` to all models by default. If `dof_residual(::SomeModel)` is not valid for ANOVA, customize `dof_residual(::AnovaResult{<: AnovaModel{SomeModel}})` alternatively.
* [`dof_residual`](./AnovaBase.md#StatsAPI.dof_residual-Tuple{AnovaResult}) applies `dof_residual` to all models by default. If `dof_residual(::SomeModel)` is not valid for ANOVA, customize `dof_residual(::AnovaResult{<: AnovaModel{SomeModel}})` alternatively.
4 changes: 2 additions & 2 deletions src/AnovaBase.jl
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Expand Up @@ -3,7 +3,7 @@ module AnovaBase
using Statistics, Distributions, Reexport, Printf
@reexport using StatsModels
import StatsBase: fit!, fit, dof, dof_residual, deviance, nobs, vcov, coeftable
import StatsModels: TableRegressionModel, vectorize, collect_matrix_terms, coefnames, formula, asgn, TupleTerm
import StatsModels: TableRegressionModel, vectorize, collect_matrix_terms, coefnames, formula, asgn, TupleTerm, hasintercept
import Base: show

export
Expand Down Expand Up @@ -132,7 +132,7 @@ function FullModel(model::RegressionModel, type::Int, null::Bool, test_intercept
#err2 = ArgumentError("Invalid set of model specification for ANOVA; all coefficents are aliased with 1.")
preds = predictors(model)
pred_id = collect(eachindex(preds))
has_intercept(preds) || popfirst!(pred_id)
hasintercept(preds) || popfirst!(pred_id)
isempty(pred_id) && throw(err1) # ~ 0
if type ≡ 1
# ~ 0 + A + B..., ~ 1 + B..., ~ B as null
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19 changes: 5 additions & 14 deletions src/term.jl
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@@ -1,14 +1,5 @@
# Function related to terms
"""
has_intercept(<terms>)
Return `true` if `InterceptTerm{true}` is in the terms.
"""
has_intercept(f::FormulaTerm) = has_intercept(f.rhs)
has_intercept(f::MatrixTerm) = has_intercept(f.terms)
has_intercept(f::TupleTerm) = has_intercept(first(f))
has_intercept(::InterceptTerm{H}) where H = H
has_intercept(::AbstractTerm) = false
@deprecate has_intercept hasintercept

"""
any_not_aliased_with_1(<terms>)
Expand Down Expand Up @@ -201,31 +192,31 @@ Set{Int64} with 3 elements:
select_super_interaction(f::MatrixTerm, id::Int) = select_super_interaction(f.terms, id)
function select_super_interaction(f::TupleTerm, id::Int)
s = id ≡ 1 ? Set(eachindex(f)) : Set([idn for idn in eachindex(f) if isinteract(f, id, idn)])
has_intercept(f) || filter!(!=(1), s)
hasintercept(f) || filter!(!=(1), s)
s
end

@doc doc_select_interaction
select_sub_interaction(f::MatrixTerm, id::Int) = select_sub_interaction(f.terms, id)
function select_sub_interaction(f::TupleTerm, id::Int)
s = id ≡ 1 ? Set(Int[]) : Set([idn for idn in eachindex(f) if isinteract(f, idn, id)])
has_intercept(f) || filter!(!=(1), s)
hasintercept(f) || filter!(!=(1), s)
s
end

@doc doc_select_interaction
select_not_super_interaction(f::MatrixTerm, id::Int) = select_not_super_interaction(f.terms, id)
function select_not_super_interaction(f::TupleTerm, id::Int)
s = id ≡ 1 ? Set(Int[]) : Set([idn for idn in eachindex(f) if !isinteract(f, id, idn)])
has_intercept(f) || filter!(!=(1), s)
hasintercept(f) || filter!(!=(1), s)
s
end

@doc doc_select_interaction
select_not_sub_interaction(f::MatrixTerm, id::Int) = select_not_sub_interaction(f.terms, id)
function select_not_sub_interaction(f::TupleTerm, id::Int)
s = id ≡ 1 ? Set(eachindex(f)) : Set([idn for idn in eachindex(f) if !isinteract(f, idn, id)])
has_intercept(f) || filter!(!=(1), s)
hasintercept(f) || filter!(!=(1), s)
s
end

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4 changes: 2 additions & 2 deletions test/runtests.jl
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Expand Up @@ -75,7 +75,7 @@ anovatable(::AnovaResult{<: FullModel{StatsModels.TableRegressionModel{Int64, Ma
1, 1, Int),
mm)
conterm = ContinuousTerm(:y, 0.0, 0.0, 0.0, 0.0)
fterm = FunctionTerm(log, x->log(x), (:t, ), :(log(t)), [])
fterm = FunctionTerm(log, [Term(:t)], :(log(t)))
caterm() = CategoricalTerm(:x, StatsModels.ContrastsMatrix(StatsModels.FullDummyCoding(), [1, 2, 3]))
caterm(i) = CategoricalTerm(Symbol("x$i"), StatsModels.ContrastsMatrix(StatsModels.DummyCoding(), [1, 2, 3]))
global model5 = StatsModels.TableRegressionModel(
Expand Down Expand Up @@ -188,7 +188,7 @@ anovatable(::AnovaResult{<: FullModel{StatsModels.TableRegressionModel{Int64, Ma
end
global f = FormulaTerm(conterm, MatrixTerm((InterceptTerm{true}(), caterm(), fterm, InteractionTerm((caterm(), fterm)))))
@testset "term.jl" begin
@test AnovaBase.has_intercept(f.rhs)
@test AnovaBase.hasintercept(f.rhs)
@test AnovaBase.any_not_aliased_with_1(f.rhs)
@test !AnovaBase.any_not_aliased_with_1(MatrixTerm((InterceptTerm{true}(), caterm(), caterm(1), caterm(2), InteractionTerm((caterm(), caterm(1), caterm(2))))))
@test AnovaBase.any_not_aliased_with_1(MatrixTerm((InterceptTerm{true}(), caterm(), conterm, fterm, InteractionTerm((caterm(), conterm, fterm)))))
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Registration pull request created: JuliaRegistries/General/96760

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

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 v0.7.5 -m "<description of version>" 18810ec838d99aab61f47e50e5d9e86ea169eab5
git push origin v0.7.5

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