use dataset improvements, remove RChunks

Project.toml

@@ -33,7 +33,6 @@ 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"

contrasts_kwdyz11.qmd

@@ -10,18 +10,17 @@ fig-format: png
 
 ```{julia}
 #| code-fold: true
+using AlgebraOfGraphics
 using CairoMakie
 using Chain
 using DataFrames
 using MixedModels
-using RData: load as rload
 using SMLP2024: dataset
 using StatsBase
 using StatsModels
 
 CairoMakie.activate!(; type="png")
 
-import ProgressMeter
 progress = false
 ```
 
@@ -439,7 +438,7 @@ Three factors:
 2 x 3 = 6 measures / subject
 
 ```{julia}
-dat2 = load("data/Exp_2x2x3.rds");
+dat2 = dataset(:exp_2x2x3)
 ```
 
 We select an LMM supported by the data. 
@@ -479,35 +478,20 @@ A: A2 & B: B3               0.523243      0.950202   0.55    0.5819
 ───────────────────────────────────────────────────────────────────
 ```
 
-The  following figure also appears only in interactive chunk execution. The chunk generates also an error when rendered.
-
-```{r}
-#| eval: true
-
-library(tidyverse)
-dat2 = readRDS("data/Exp_2x2x3.rds");
-
-cbPalette <- c("#000000", "#E69F00", "#56B4E9", "#009E73",
-               "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
-
-tbl1 <- 
-  dat2 |> 
-  group_by(Subj, A, B) |> 
-  reframe(N=n(),dv=mean(dv)) |> 
-  group_by(A, B) |> 
-  reframe(N=n(), dv_M=mean(dv), dv_SD=sd(dv), dv_SE=dv_SD/sqrt(N))
-tbl1
-
-fig1 <- 
-  tbl1 |> 
-  ggplot(aes(y=dv_M, x=B, group=A, color=A)) + 
-  geom_point() + 
-  geom_line() +
-  scale_color_manual(values=cbPalette[2:3]) +
-  theme_bw()
-
-print(fig1)
-NULL
+```{julia}
+using Chain
+tbl1 = @chain DataFrame(dat2) begin
+  groupby(_, [:Subj, :A, :B])
+  combine(_, nrow => :n, :dv => mean => :dv)
+  groupby(_, [:A, :B])
+  combine(_, 
+          :dv => mean => :dv_M,
+          :dv => std => :dv_SD,
+          :dv => sem => :dv_SE)
+end 
+
+fig1 = data(tbl1) * mapping(:B, :dv_M; color=:A) * (visual(Lines) + visual(Scatter))
+draw(fig1)
 ```