Reorganize website into thematic sections

.gitignore

@@ -51,3 +51,8 @@ site_libs/
 
 
 **/*.quarto_ipynb
+.claude/settings.local.json
+data/emotikon.rds
+data/fggk21_Child.arrow
+data/fggk21_Score.arrow
+data/fggk21.arrow

Project.toml

@@ -1,7 +1,7 @@
 name = "SMLP2026"
 uuid = "2d4e6da2-0493-4b51-b329-ae5cd97e516e"
-authors = ["Phillip Alday <me@phillipalday.com>", "Douglas Bates <dmbates@gmail.com>", "Reinhold Kliegl <reinhold.kliegl@gmail.com>"]
 version = "1.0.0"
+authors = ["Phillip Alday <me@phillipalday.com>", "Douglas Bates <dmbates@gmail.com>", "Reinhold Kliegl <reinhold.kliegl@gmail.com>"]
 
 [deps]
 AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
@@ -34,6 +34,7 @@ MixedModelsSim = "d5ae56c5-23ca-4a1f-b505-9fc4796fc1fe"
 PooledArrays = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+RData = "df47a6cb-8c03-5eed-afd8-b6050d6c41da"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RegressionFormulae = "545c379f-4ec2-4339-9aea-38f2fb6a8ba2"
 SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
@@ -66,6 +67,7 @@ MixedModelsMakie = "0.4"
 MixedModelsSerialization = "0.2"
 MixedModelsSim = "0.2.7"
 RCall = "0.14"
+RData = "1.1.0"
 Random = "1"
 RegressionFormulae = "0.1.3"
 StableRNGs = "1.0.3"

_metadata.yml

@@ -1,4 +1,7 @@
-author: "Phillip Alday, Douglas Bates, and Reinhold Kliegl"
+author: 
+  - "Phillip Alday"
+  - "Douglas Bates" 
+  - "Reinhold Kliegl"
 format:
   html:
     toc: true

_quarto.yml

@@ -18,31 +18,31 @@ project:
   execute-dir: project
   output-dir: _build/
   render:
-  - about.qmd
-  - AoGPlots.qmd
-  - arrow.qmd
-  - bootstrap.qmd
-  - check_emotikon_transform.qmd
-  - contrasts_fggk21.qmd
-  - contrasts_kwdyz11.qmd
-  - fggk21.qmd
-  - glmm.qmd
   - index.qmd
-  - kb07.qmd
-  - kkl15.qmd
-  - kwdyz11.qmd
-  - largescaledesigned.qmd
-  - mrk17.qmd
-  - partial_within.qmd
-  - pkg.qmd
-  - profiling.qmd
-  - selection.qmd
-  - shrinkageplot.qmd
-  - singularity.qmd
-  - sleepstudy.qmd
-  - sleepstudy_speed.qmd
-  - transformation.qmd
-  - useful_packages.qmd
+  - getting-started/about.qmd
+  - getting-started/useful_packages.qmd
+  - getting-started/pkg.qmd
+  - getting-started/arrow.qmd
+  - lmm-intro/sleepstudy.qmd
+  - lmm-intro/singularity.qmd
+  - model-specification/partial_within.qmd
+  - model-specification/mrk17.qmd
+  - model-specification/largescaledesigned.qmd
+  - contrasts/transformation.qmd
+  - contrasts/contrasts_fggk21.qmd
+  - contrasts/contrasts_kwdyz11.qmd
+  - contrasts/sleepstudy_speed.qmd
+  - inference/bootstrap.qmd
+  - inference/profiling.qmd
+  - inference/kb07.qmd
+  - inference/power_simulation.qmd
+  - glmm/glmm.qmd
+  - visualization/shrinkageplot.qmd
+  - visualization/AoGPlots.qmd
+  - examples/emotikon/fggk21.qmd
+  - examples/emotikon/check_emotikon_transform.qmd
+  - examples/visual-attention/kwdyz11.qmd
+  - examples/visual-attention/kkl15.qmd
 
 # editor_options:
 #   chunk_output_type: console
@@ -84,33 +84,48 @@ website:
     search: true
     collapse-level: 1
     contents:
-      - section: "Getting started with Julia"
+      - section: "Getting Started"
         contents:
-        - useful_packages.qmd
-        - pkg.qmd
-        - arrow.qmd
-      - section: "Worked examples"
+        - index.qmd
+        - getting-started/about.qmd
+        - getting-started/useful_packages.qmd
+        - getting-started/pkg.qmd
+        - getting-started/arrow.qmd
+      - section: "Introduction to Linear Mixed Models"
         contents:
-        - sleepstudy.qmd
-        - sleepstudy_speed.qmd
-        - kwdyz11.qmd
-        - kkl15.qmd
-        - largescaledesigned.qmd
-        - mrk17.qmd
-        - partial_within.qmd
-      - section: "Contrast coding and transformations"
+        - lmm-intro/sleepstudy.qmd
+        - lmm-intro/singularity.qmd
+      - section: "Model Specification and Random Effects"
         contents:
-        - contrasts_fggk21.qmd
-        - contrasts_kwdyz11.qmd
-        - transformation.qmd
-      - glmm.qmd
-      - section: "Bootstrap and profiling"
+        - model-specification/partial_within.qmd
+        - model-specification/mrk17.qmd
+        - model-specification/largescaledesigned.qmd
+      - section: "Contrast Coding and Transformations"
         contents:
-        - bootstrap.qmd
-        - profiling.qmd
-        - kb07.qmd
-      - section: "Visualizations and diagnostics"
+        - contrasts/transformation.qmd
+        - contrasts/contrasts_fggk21.qmd
+        - contrasts/contrasts_kwdyz11.qmd
+        - contrasts/sleepstudy_speed.qmd
+      - section: "Inference: Uncertainty Quantification"
         contents:
-        - singularity.qmd
-        - shrinkageplot.qmd
-        - AoGPlots.qmd
+        - inference/bootstrap.qmd
+        - inference/profiling.qmd
+        - inference/kb07.qmd
+        - inference/power_simulation.qmd
+      - section: "Generalized Linear Mixed Models"
+        contents:
+        - glmm/glmm.qmd
+      - section: "Visualization and Diagnostics"
+        contents:
+        - visualization/shrinkageplot.qmd
+        - visualization/AoGPlots.qmd
+      - section: "Extended Worked Examples"
+        contents:
+        - section: "The Emotikon Project"
+          contents:
+          - examples/emotikon/fggk21.qmd
+          - examples/emotikon/check_emotikon_transform.qmd
+        - section: "Visual Attention Experiments"
+          contents:
+          - examples/visual-attention/kwdyz11.qmd
+          - examples/visual-attention/kkl15.qmd

contrasts_fggk21.qmd → contrasts/contrasts_fggk21.qmd

@@ -50,11 +50,10 @@ using ProgressMeter
 using StableRNGs
 using Statistics
 using StatsBase
-
 using MixedModels: likelihoodratiotest
 using SMLP2026: dataset
 
-progress = isinteractive()
+const progress = isinteractive()
 ```
 
 ```{julia}

sleepstudy_speed.qmd → contrasts/sleepstudy_speed.qmd

@@ -1,5 +1,5 @@
 ---
-title: "The sleepstudy: Speed - for a change ..."
+title: "The Belenky Sleep Study: Speed Metrics and Between-Group Comparisons"
 engine: julia
 julia:
   exeflags: ["--project", "--threads=auto"]

check_emotikon_transform.qmd → examples/emotikon/check_emotikon_transform.qmd

@@ -1,5 +1,5 @@
 ---
-title: Transformed and original metrics in Emotikon
+title: "Emotikon: Comparing Original and Transformed Metrics"
 engine: julia
 julia:
   exeflags: ["--project", "--threads=auto"]
@@ -25,7 +25,7 @@ using DataFrameMacros
 using MixedModels
 using MixedModelsMakie
 using RCall
-using SMLP2026: dataset
+using SMLP2026: dataset, FITSDIR
 using Serialization
 using StatsBase
 ```
@@ -44,13 +44,6 @@ describe(dat)
 
 ### Data and figure with z-scores based on original metric
 
-```{julia}
-# dat_om = rcopy(R"readRDS('./data/fggk21_om.rds')");  #Don't know what the _om is
-# @transform!(dat_om, :a1 = :age - 8.5);
-# select!(groupby(dat_om, :Test), :, :score => zscore => :zScore);
-# describe(dat_om)
-```
-
 ## LMMs
 
 ### Contrasts
@@ -80,7 +73,7 @@ f1 = @formula zScore ~
 
 ```{julia}
 m1x = LinearMixedModel(f1, dat; contrasts)
-restoreoptsum!(m1x, "./fits/fggk21_m1_optsum.json")
+restoreoptsum!(m1x, joinpath(FITSDIR, "fggk21_m1_optsum.json"))
 ```
 
 ```{julia}
@@ -91,22 +84,22 @@ VarCorr(m1x)
 
   - Command for fitting LMM m1_om = fit(MixedModel, f1, dat_om, contrasts=contr)
   - Minimizing 10502 Time: 0 Time: 2:09:40 ( 0.74  s/it)
-  - Store with: julia> saveoptsum("./fits/fggk21_m1_om_optsum.json", m1_om)
-  - Only for short-term and when desperate: julia> serialize("./fits/m1_om.jls", m1_om);
+  - Store with: julia> saveoptsum(joinpath(FITSDIR, "fggk21_m1_om_optsum.json"), m1_om)
+  - Only for short-term and when desperate: julia> serialize(joinpath(FITSDIR, "m1_om.jls"), m1_om);
 
 #### ... restoreoptsum!()
 
 ```{julia}
 #| eval: false
 m1_om = LinearMixedModel(f1, dat; contrasts);
-restoreoptsum!(m1_om, "./fits/fggk21_m1_om_optsum.json");
+restoreoptsum!(m1_om, joinpath(FITSDIR, "fggk21_m1_om_optsum.json"));
 ```
 
 #### ... deserialize()
 
 ```{julia}
 #| eval: false
-m1x_om = deserialize("./fits/m1_om.jls")
+m1x_om = deserialize(joinpath(FITSDIR, "m1_om.jls"))
 ```
 
 ```{julia}

fggk21.qmd → examples/emotikon/fggk21.qmd

@@ -1,5 +1,5 @@
 ---
-title: Basics with Emotikon Project
+title: "The Emotikon Project: Model Complexification and PCA"
 engine: julia
 julia:
   exeflags: ["--project", "--threads=auto"]
@@ -34,9 +34,9 @@ using MixedModelsMakie: simplelinreg
 using Random
 using Statistics
 using StatsBase
-using SMLP2026: dataset, fit_or_restore
+using SMLP2026: dataset, fit_or_restore, DATADIR
 
-const progress=false
+const progress = isinteractive()
 ```
 
 # Readme
@@ -849,7 +849,7 @@ bic(m1)  # objective(m1) + dof(m1)*log(nobs(m1))
 ```
 + julia> coeftable(m1)     # StatsBase.coeftable: fixed-effects statiscs;
 						     default level=0.95
-+ julia> Arrow.write("./data/m_cpx_fe.arrow", DataFrame(coeftable(m1)));
++ julia> Arrow.write(joinpath(DATADIR, "m_cpx_fe.arrow"), DataFrame(coeftable(m1)));
 + julia> coef(m1)          # StatsBase.coef - parts of the table
 + julia> fixef(m1)         # MixedModels.fixef: not the same as coef()
                              for rank-deficient case
@@ -865,7 +865,7 @@ coeftable(m1) # StatsBase.coeftable: fixed-effects statiscs; default level=0.95
 ```
 
 ```{julia}
-#Arrow.write("./data/m_cpx_fe.arrow", DataFrame(coeftable(m1)));
+#Arrow.write(joinpath(DATADIR, "m_cpx_fe.arrow"), DataFrame(coeftable(m1)));
 ```
 
 ```{julia}
@@ -1009,6 +1009,12 @@ shrinkageplot!(Figure(; size=(800, 800)), m1, :Cohort)
 shrinkageplot!(Figure(; size=(800, 800)), m2, :Cohort)
 ```
 
+## See Also
+
+- [Mixed Models Tutorial: Contrast Coding](../../contrasts/contrasts_fggk21.qmd) — applies a full range of contrast schemes (effect, Helmert, hypothesis, PCA-based) to the same Emotikon dataset.
+- [Emotikon: Comparing Original and Transformed Metrics](check_emotikon_transform.qmd) — investigates whether the age × Sex × Test interaction changes when tasks are analyzed in their original time metric rather than speed.
+- [Creating Multi-Panel Plots](../../visualization/AoGPlots.qmd) — reproduces the publication figure from @Fuehner2021 using AlgebraOfGraphics.
+
 ::: {#refs}
 :::
 

kkl15.qmd → examples/visual-attention/kkl15.qmd

@@ -1,5 +1,5 @@
 ---
-title: 'RePsychLing Kliegl, Kuschela, & Laubrock (2015)- Reduction of Model Complexity'
+title: "Visual Attention: Replication and Model Reduction (Kliegl et al., 2015)"
 engine: julia
 julia:
   exeflags: ["--project", "--threads=auto"]

kwdyz11.qmd → examples/visual-attention/kwdyz11.qmd

@@ -1,5 +1,5 @@
 ---
-title: "RePsychLing Kliegl et al. (2011)"
+title: "Visual Attention Effects: Kliegl et al. (2011)"
 engine: julia
 julia:
   exeflags: ["--project", "--threads=auto"]
@@ -398,6 +398,11 @@ First, the correlation between GM and the spatial effect is well defined.
 Second, as discussed throughout this script, the CP between spatial and attraction effect is close to the 1.0 border and clearly not well defined.
 Therefore, this CP will be replicated with a larger sample in script `kkl15.jl` [@Kliegl2015].
 
+# See Also
+
+- [Visual Attention: Replication and Model Reduction (Kliegl et al., 2015)](kkl15.qmd) — direct replication and follow-up of this experiment, with an additional focus on reducing model complexity.
+- [Contrast Coding of Visual Attention Effects](../../contrasts/contrasts_kwdyz11.qmd) — applies _a priori_ contrast coding to this same dataset to test theoretically motivated hypotheses.
+
 # References
 
 ::: {#refs}