Merge branch 'main' of github.com:RePsychLing/MixedModelsSim.jl into db/plutonotebook

Author: palday

.github/workflows/Documenter.yml

@@ -0,0 +1,23 @@
+name: Documenter
+on:
+  push:
+    branches: [main]
+    tags: [v*]
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+jobs:
+  Documenter:
+    name: Documentation
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: 1.6-nightly
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-docdeploy@latest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/Tier1.yml

@@ -2,16 +2,18 @@ name: Tier1
 on:
   push:
     branches:
-      - master
+      - main
     paths-ignore:
       - 'LICENSE.md'
       - 'README.md'
+      - 'docs/*'
   pull_request:
     branches:
-      - master
+      - main
     paths-ignore:
       - 'LICENSE.md'
       - 'README.md'
+      - 'docs/*'
   release:
     types:
       - created
@@ -34,10 +36,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - uses: julia-actions/[email protected]
         if: startsWith(matrix.os, 'Ubuntu')
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      - uses: julia-actions/julia-docdeploy@releases/v1
-        if: startsWith(matrix.os, 'Ubuntu')
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/Tier2.yml

@@ -2,16 +2,18 @@ name: Tier2
 on:
   push:
     branches:
-      - master
+      - main
     paths-ignore:
       - 'LICENSE.md'
       - 'README.md'
+      - 'docs/*'
   pull_request:
     branches:
-      - master
+      - main
     paths-ignore:
       - 'LICENSE.md'
       - 'README.md'
+      - 'docs/*'
   release:
     types:
       - created
@@ -21,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: [nightly]
+        julia-version: [1.5, nightly]
         julia-arch: [x64, x86]
         os: [ubuntu-18.04, macos-10.15, windows-2019]
         exclude:

Project.toml

@@ -1,7 +1,7 @@
 name = "MixedModelsSim"
 uuid = "d5ae56c5-23ca-4a1f-b505-9fc4796fc1fe"
 authors = ["Phillip Alday", "Douglas Bates", "Lisa DeBruine", "Reinhold Kliegl"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

README.md

@@ -6,15 +6,15 @@
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://RePsychLing.github.io/MixedModelsSim.jl/dev)
 ![T1-url][T1-img]
 ![T2-url][T2-img]
-[![Codecov](https://codecov.io/gh/RePsychLing/MixedModelsSim.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/RePsychLing/MixedModelsSim.jl)
+[![Codecov](https://codecov.io/gh/RePsychLing/MixedModelsSim.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/RePsychLing/MixedModelsSim.jl)
 
 This package provides some utility functions for generating experimental designs, especially those with crossed factors.
 
 ## Installation
 
 `MixedModelsSim` is registered in the Julia package registry and can be installed via the pkg REPL:
 ```julia
-(@v1.4) pkg> add MixedModelsSim
+(@v1.5) pkg> add MixedModelsSim
 ```
 
 ## Purpose

docs/Project.toml

@@ -10,5 +10,5 @@ MixedModelsSim = "d5ae56c5-23ca-4a1f-b505-9fc4796fc1fe"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [compat]
-Documenter = "0.23, 0.24, 0.25"
+Documenter = "0.26"
 julia = "1.5"

docs/make.jl

@@ -1,15 +1,15 @@
-using Documenter, MixedModelsSim
+using Documenter
+using MixedModelsSim
 
-makedocs(;
-    modules = [MixedModelsSim],
-    format = Documenter.HTML(assets = String[]),
-    pages = ["Home" => "index.md"
-             "Full Example" => "simulation.md"],
-    repo = "https://github.com/RePsychLing/MixedModelsSim.jl/blob/{commit}{path}#L{line}",
+makedocs(
+    root = joinpath(dirname(pathof(MixedModelsSim)), "..", "docs"),
     sitename = "MixedModelsSim.jl",
+    doctest = true,
     authors = "Phillip Alday, Douglas Bates, Lisa DeBruine, Reinhold Kliegl",
-    source = joinpath("..", "docs", "src"),
-    build = joinpath("..", "docs", "build"),
+    pages = [
+        "index.md",
+        "simulation.md",
+    ],
 )
 
 deploydocs(; repo = "github.com/RePsychLing/MixedModelsSim.jl", push_preview = true)

src/utilities.jl

@@ -158,7 +158,7 @@ end
 """
     create_re(sigmas...; corrmat=Matrix{Float64}(I, length(sigmas), length(sigmas))
 
-Create the covariance matrix for a random effect from the standard deviations and correlation matrix.
+Create the covariance factor for a random effect from the standard deviations and correlation matrix.
 
 The `sigmas` should be specified in the same order as the random slopes in the
 output of `VarCorr(m)`.
@@ -167,18 +167,13 @@ The correlation matrix defaults to the identiy matrix, i.e. no correlation betwe
 random effects.
 
 !!! note
-    The return value is the lower Cholesky of the covariance matrix, which is what
+    The return value is the lower Cholesky factor of the covariance matrix, which is what
     [`update!`](@ref) requires.
 """
 function create_re(sigmas...; corrmat=nothing)
-    dim = length(sigmas)
-    ss = diagm([sigmas...])
+    ss = Diagonal([sigmas...])
 
-    if isnothing(corrmat)
-        LowerTriangular(ss)
-    else
-        cholesky(ss * corrmat * ss).L
-    end
+    isnothing(corrmat) ? LowerTriangular(ss) : ss * cholesky(Symmetric(corrmat, :L)).L
 end