all the ICCs

.github/workflows/style.yml

@@ -1,35 +1,40 @@
 name: Style-Enforcer
 on:
-  push:
-    branches:
-      - 'main'
-    tags: '*'
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
-    # note: keep in sync with `format/run.jl`
     paths-ignore:
       - 'README.md'
       - '.gitignore'
+permissions: {}
 jobs:
   format-check:
-    name: Style Enforcement (Julia ${{ matrix.julia-version }} - ${{ github.event_name }})
-    # Run on push's or non-draft PRs
-    if: (github.event_name == 'push') || (github.event.pull_request.draft == false)
+    name: Style Enforcement
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
     strategy:
       matrix:
-        julia-version: [1.6]
+        julia-version: [min]
     steps:
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+      - uses: julia-actions/setup-julia@fa02766e078afaaf09b14210362cee14137e6a32 # v3.0.2
         with:
           version: ${{ matrix.julia-version }}
-      - uses: actions/checkout@v7
-      - name: Instantiate `format` environment and format
+      - name: Install JuliaFormatter
+        shell: julia --project=@format --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.add(PackageSpec(; name="JuliaFormatter", version="1"))
+      - name: Check formatting
+        shell: julia --project=@format --color=yes {0}
         run: |
-          julia --project=format -e 'using Pkg; Pkg.instantiate()'
-          julia --project=format 'format/run.jl'
-      - uses: reviewdog/action-suggester@v1
-        if: github.event_name == 'pull_request'
+          using JuliaFormatter
+          format(".", YASStyle(); verbose=true) || exit(1)
+      # Add formatting suggestions to non-draft PRs even if "Check formatting" fails
+      - uses: reviewdog/action-suggester@2558ba17e65a9039e73764a73009fc05fef28a46 # v1.24.3
+        if: ${{ !cancelled() && github.event.pull_request.draft == false }}
         with:
           tool_name: JuliaFormatter
-          fail_on_error: true

.gitignore

@@ -27,3 +27,4 @@ Manifest-v*.toml
 # Editor files
 .vscode/*
 *~
+coverage/lcov.info

Project.toml

@@ -1,14 +1,16 @@
 name = "MixedModelsExtras"
 uuid = "781a26e1-49f4-409a-8f4c-c3159d78c17e"
-version = "2.4.0"
+version = "3.0.0"
 authors = ["Phillip Alday <me@phillipalday.com> and contributors"]
 
 [deps]
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
@@ -25,6 +27,7 @@ MixedModelsDatasets = "0.2"
 ProgressMeter = "1"
 Random = "1"
 RDatasets = "0.7.7, 0.8"
+SpecialFunctions = "2"
 StableRNGs = "1"
 Statistics = "1"
 StatsBase = "0.33, 0.34"
@@ -37,12 +40,11 @@ julia = "1.10"
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 MixedModelsDatasets = "7e9fb7ac-9f67-43bf-b2c8-96ba0796cbb6"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "Aqua", "DataFrames", "Distributions", "MixedModelsDatasets", "RDatasets", "Suppressor", "StableRNGs"]
+test = ["Test", "Aqua", "DataFrames", "MixedModelsDatasets", "RDatasets", "Suppressor", "StableRNGs"]

docs/Project.toml

@@ -1,6 +1,8 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 MixedModelsExtras = "781a26e1-49f4-409a-8f4c-c3159d78c17e"
+StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
+StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
 [compat]
 Documenter = "1.3"

docs/make.jl

@@ -1,12 +1,29 @@
 using Documenter
 using MixedModelsExtras
+using StatsAPI
+using StatsModels
+
+# `vif` and `gvif` are re-exported from StatsAPI and `termnames` from StatsModels, so
+# the API page renders docstrings that live outside this package. Pkg installs those
+# packages without a `.git` directory, so Documenter cannot work out where their source
+# lives and fails with a `MissingRemoteError`. Naming the remote together with a commit
+# lets it build the source links without consulting git.
+function upstream(mod, org, name)
+    return pkgdir(mod) => (Remotes.GitHub(org, name), "v$(pkgversion(mod))")
+end
 
 makedocs(;
          repo=Remotes.GitHub("JuliaMixedModels", "MixedModelsExtras.jl"),
+         remotes=Dict(upstream(StatsAPI, "JuliaStats", "StatsAPI.jl"),
+                      upstream(StatsModels, "JuliaStats", "StatsModels.jl")),
+         # the default branch is named explicitly because Documenter otherwise probes
+         # the remote and falls back to "master" when it cannot reach it
+         format=Documenter.HTML(; edit_link="main"),
          sitename="MixedModelsExtras",
          doctest=true,
          checkdocs=:exports,
          warnonly=[:cross_references],
-         pages=["index.md", "api.md"])
+         pages=["index.md", "icc.md", "api.md"])
 
-deploydocs(; repo="github.com/JuliaMixedModels/MixedModelsExtras.jl.git", push_preview=true)
+deploydocs(; repo="github.com/JuliaMixedModels/MixedModelsExtras.jl.git",
+           devbranch="main", push_preview=true)

docs/src/api.md

@@ -20,12 +20,27 @@ adjr2(::LinearMixedModel)
 ```
 
 
-## Intra-Class Correlation Coefficient
+## Intraclass Correlation Coefficient
+
+See [Intraclass Correlation Coefficients](@ref) for the taxonomy of coefficients, guidance
+on choosing between them, and references.
 
 ```@docs
 icc
 ```
 
+```@docs
+InterraterICC
+```
+
+```@docs
+InterraterICCTable
+```
+
+```@docs
+IccBootstrap
+```
+
 ## Bootstrapped Likelihood Ratio Test
 
 ```@docs