Deprecate has_intercept, doc update

Author: yufongpeng

docs/make.jl

@@ -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",

docs/src/Interface.md

@@ -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})
@@ -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.

src/AnovaBase.jl

@@ -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
@@ -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

src/term.jl

@@ -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>)
@@ -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