Merge branch 'main' of github.com:RePsychLing/SMLP2024 into pa/rm_r

.gitattributes

@@ -1 +1,5 @@
 *.arrow filter=lfs diff=lfs merge=lfs -text
+*.Rds filter=lfs diff=lfs merge=lfs -text
+*.RDs filter=lfs diff=lfs merge=lfs -text
+*.RDS filter=lfs diff=lfs merge=lfs -text
+*.rds filter=lfs diff=lfs merge=lfs -text

Makefile

@@ -8,6 +8,7 @@ cleanup:
 clean: cleanup
 	rm -rf .quarto/_freeze
 	rm -rf _freeze/
+	rm -rf _build/
 
 publish:
 	quarto publish gh-pages

Project.toml

@@ -28,6 +28,7 @@ MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 MixedModelsDatasets = "7e9fb7ac-9f67-43bf-b2c8-96ba0796cbb6"
 MixedModelsExtras = "781a26e1-49f4-409a-8f4c-c3159d78c17e"
 MixedModelsMakie = "b12ae82c-6730-437f-aff9-d2c38332a376"
+MixedModelsSerialization = "b32ace64-3998-4ca6-afd0-a0db4a0482b2"
 MixedModelsSim = "d5ae56c5-23ca-4a1f-b505-9fc4796fc1fe"
 PooledArrays = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
@@ -46,7 +47,7 @@ ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 [compat]
 AlgebraOfGraphics = "0.8"
 Arrow = "2"
-BoxCox = "0.3"
+BoxCox = "0.3.3"
 CSV = "0.10"
 CairoMakie = "0.12"
 Chain = "0.5,0.6"
@@ -59,6 +60,7 @@ MacroTools = "0.5"
 MixedModels = "4.22"
 MixedModelsExtras = "1, 2"
 MixedModelsMakie = "0.4"
+MixedModelsSerialization = "0.1"
 MixedModelsSim = "0.2.7"
 RCall = "0.13, 0.14"
 Random = "1"

_quarto.yml

@@ -37,6 +37,7 @@ project:
   - singularity.qmd
   - sleepstudy.qmd
   - sleepstudy_speed.qmd
+  - transformation.qmd
   - useful_packages.qmd
 
 # editor_options:
@@ -93,10 +94,11 @@ website:
         - largescaledesigned.qmd
         - mrk17.qmd
         - partial_within.qmd
-      - section: "Contrast coding"
+      - section: "Contrast coding and transformations"
         contents:
         - contrasts_fggk21.qmd
         - contrasts_kwdyz11.qmd
+        - transformation.qmd
       - glmm.qmd
       - section: "Bootstrap and profiling"
         contents:

_typos.toml

@@ -13,6 +13,8 @@ missings = "missings"
 Lik = "Lik"
 missings = "missings"
 represention = "representation"
+GAMMs = "GAMMs"
+
 
 [type.qmd]
 extend-glob = ["*.qmd"]

contrasts_fggk21.qmd

@@ -179,9 +179,9 @@ m_ovi_SeqDiff_2 = let
 end
 ```
 
-The difference between older and younger childrend is larger for `Star_r` than for `Run` (0.2473).  `S20_r` did not differ significantly from `Star_r` (-0.0377) and `SLJ` (-0.0113) The largest difference in developmental gain was between `BPT` and `SLJ` (0.3355).
+The difference between older and younger children is larger for `Star_r` than for `Run` (0.2473).  `S20_r` did not differ significantly from `Star_r` (-0.0377) and `SLJ` (-0.0113) The largest difference in developmental gain was between `BPT` and `SLJ` (0.3355).
 
-P**lease note that standard errors of this LMM are anti-conservative because the LMM is missing a lot of information in the RES (e..g., contrast-related VCs snd CPs for `Child`, `School`, and `Cohort`.**
+**Please note that standard errors of this LMM are anti-conservative because the LMM is missing a lot of information in the RES (e..g., contrast-related VCs snd CPs for `Child`, `School`, and `Cohort`.**
 
 Next we add the main effect of `Sex` and its interaction with the four test contrasts.
 
@@ -268,9 +268,9 @@ contr3 = Dict(
   :Test => HypothesisCoding(
     [
       -1 -1 -1 -1 +4
-      -1 +1 0 0 0
-       0 -1 +1 0 0
-       0 0 -1 +1 0
+      -1 +1  0  0  0
+       0 -1 +1  0  0
+       0  0 -1 +1  0
     ];
     levels=["Run", "Star_r", "S20_r", "SLJ", "BPT"],
     labels=["BPT-other", "Star-End", "S20-Star", "SLJ-S20"],
@@ -294,10 +294,10 @@ contr1b = Dict(
   :Sex => EffectsCoding(; levels=["Girls", "Boys"]),
   :Test => HypothesisCoding(
     [
-      -1 +1 0 0 0
-      0 -1 +1 0 0
-      0 0 -1 +1 0
-      0 0 0 -1 +1
+      -1 +1  0  0  0
+       0 -1 +1  0  0
+       0  0 -1 +1  0
+       0  0  0 -1 +1
     ];
     levels=["Run", "Star_r", "S20_r", "SLJ", "BPT"],
     labels=["Star-Run", "S20-Star", "SLJ-S20", "BPT-SLJ"],
@@ -375,10 +375,10 @@ contr4 = Dict(
   :Sex => EffectsCoding(; levels=["Girls", "Boys"]),
   :Test => HypothesisCoding(
     [
-      -1 0 0 0 +1
+      -1  0  0  0 +1
       -3 +2 +2 +2 -3
-      0 +2 -1 -1 0
-      0 0 +1 -1 0
+       0 +2 -1 -1  0
+       0  0 +1 -1  0
     ];
     levels=["Run", "Star_r", "S20_r", "SLJ", "BPT"],
     labels=["c5.1", "c234.15", "c2.34", "c3.4"],
@@ -407,10 +407,10 @@ contr4b = merge(
     :Sex => EffectsCoding(; levels=["Girls", "Boys"]),
     :Test => HypothesisCoding(
       [
-        0.49 -0.04 0.20 0.03 -0.85
-        0.70 -0.56 -0.21 -0.13 0.37
-        0.31 0.68 -0.56 -0.35 0.00
-        0.04 0.08 0.61 -0.78 0.13
+        0.49 -0.04  0.20  0.03 -0.85
+        0.70 -0.56 -0.21 -0.13  0.37
+        0.31  0.68 -0.56 -0.35  0.00
+        0.04  0.08  0.61 -0.78  0.13
       ];
       levels=["Run", "Star_r", "S20_r", "SLJ", "BPT"],
       labels=["c5.1", "c234.15", "c12.34", "c3.4"],