Add penguins testdata (#613)

MakieOrg · Mar 8, 2025 · bddb022 · bddb022
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diff --git a/README.md b/README.md
@@ -27,9 +27,9 @@ capabilities available to tweak figures produced by AlgebraOfGraphics.
 ## Example
 
 ``` julia
-using AlgebraOfGraphics, CairoMakie, PalmerPenguins, DataFrames
+using AlgebraOfGraphics, CairoMakie
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = AlgebraOfGraphics.penguins()
 
 set_aog_theme!()
 update_theme!(Axis = (; width = 150, height = 150))

diff --git a/README_files/figure-commonmark/cell-6-output-1.svg b/README_files/figure-commonmark/cell-6-output-1.svg
diff --git a/README_files/figure-commonmark/cell-7-output-1.svg b/README_files/figure-commonmark/cell-7-output-1.svg
diff --git a/_readme/Project.toml b/_readme/Project.toml
@@ -1,5 +1,3 @@
 [deps]
 AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-PalmerPenguins = "8b842266-38fa-440a-9b57-31493939ab85"
diff --git a/_readme/README.qmd b/_readme/README.qmd
@@ -36,9 +36,9 @@ ENV["DATADEPS_ALWAYS_ACCEPT"] = true # for PalmerPenguins download
 ```
 
 ```{julia}
-using AlgebraOfGraphics, CairoMakie, PalmerPenguins, DataFrames
+using AlgebraOfGraphics, CairoMakie
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = AlgebraOfGraphics.penguins()
 
 set_aog_theme!()
 update_theme!(Axis = (; width = 150, height = 150))

diff --git a/_readme/make.jl b/_readme/make.jl
@@ -2,6 +2,7 @@ cd(@__DIR__)
 using Pkg
 Pkg.activate(".")
 Pkg.develop(path = "..")
+Pkg.precompile()
 
 run(`quarto render README.qmd`)
 mv("README.md", "../README.md", force = true)

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -9,10 +9,8 @@ Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
-LIBSVM = "b1bec4e5-fd48-53fe-b0cb-9723c09d164b"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-PalmerPenguins = "8b842266-38fa-440a-9b57-31493939ab85"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
 ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"

diff --git a/docs/src/examples/basic-visualizations/statistical-visualizations.md b/docs/src/examples/basic-visualizations/statistical-visualizations.md
@@ -1,9 +1,9 @@
 # Statistical visualizations
 
 ````@example statistical_visualizations
-using AlgebraOfGraphics, CairoMakie, PalmerPenguins, DataFrames
+using AlgebraOfGraphics, CairoMakie, DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 data(penguins) * visual(Violin) *
     mapping(:species, :bill_depth_mm, color=:sex, dodge=:sex) |> draw

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -13,7 +13,7 @@ hero:
   actions:
     - theme: brand
       text: Getting started
-      link: /tutorials/getting-started
+      link: /tutorials/intro-i
     - theme: alt
       text: View on Github
       link: https://github.com/MakieOrg/AlgebraOfGraphics.jl
@@ -29,14 +29,12 @@ AlgebraOfGraphics (AoG) defines a language for data visualization, inspired by t
 In AlgebraOfGraphics, a few simple building blocks can be combined using `+` and `*` to quickly create complex visualizations, like this:
 
 ```@example
-using AlgebraOfGraphics, CairoMakie, PalmerPenguins, DataFrames
-
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+using AlgebraOfGraphics, CairoMakie
 set_aog_theme!() # hide
 update_theme!(Axis = (; width = 120, height = 120)) # hide
 
 spec =
-    data(penguins) *
+    data(AlgebraOfGraphics.penguins()) *
     mapping(
         :bill_length_mm => "Bill length (mm)",
         :bill_depth_mm => "Bill depth (mm)",

diff --git a/docs/src/tutorials/intro-i.md b/docs/src/tutorials/intro-i.md
@@ -28,30 +28,30 @@ Here's a short overview of similarities and differences between ggplot2 and Alge
 
 ## Preparations
 
-Now, before we can start plotting, we have to load the necessary packages and the `penguins` dataset from `PalmerPenguins`[^1] (see the [Palmer penguins website](https://allisonhorst.github.io/palmerpenguins/index.html) for more information).
-
+Now, before we can start plotting, we have to load the necessary packages.
 Ideally, you should create a new Julia environment by `cd`ing to a directory of your choice in the Julia REPL, and then running `using Pkg; Pkg.activate(".")`. The dependencies can then be installed with
 
 ```julia
-Pkg.add(["AlgebraOfGraphics", "CairoMakie", "PalmerPenguins", "DataFrames"])
+Pkg.add(["AlgebraOfGraphics", "CairoMakie", "DataFrames"])
 ```
 
 CairoMakie is one of [Makie's backend packages](https://docs.makie.org/stable/explanations/backends/backends) which we need to actually turn our plots into images. CairoMakie is the most commonly used backend with AlgebraOfGraphics because it focuses on 2D plots and vector graphics.
 
 Whenever a Makie or AlgebraOfGraphics figure is returned from one of the code blocks in this tutorial, it is automatically displayed inline.
 For you, as you're running this code, display behavior will depend on your own IDE setup. As a fallback you can always `save("plot.png", a_plot)` and look at the resulting file.
 
+We're going to use the Palmer Penguins[^1] dataset (see the [Palmer penguins website](https://allisonhorst.github.io/palmerpenguins/index.html) for more information) which comes with AlgebraOfGraphics.
+
 [^1]: Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3): e90081. [DOI](https://doi.org/10.1371/journal.pone.0090081)
 
-Once you have installed everything, the following code to load plotting packages and data should run without errors:
+Once you have installed everything, the following code should run without errors:
 
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 first(penguins, 5)
 ```

diff --git a/docs/src/tutorials/intro-ii.md b/docs/src/tutorials/intro-ii.md
@@ -5,10 +5,9 @@ In the previous chapter, we learned how to create basic visualizations like this
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 spec = data(penguins) *
     mapping(:bill_length_mm, :bill_depth_mm, color = :species) *

diff --git a/docs/src/tutorials/intro-iii.md b/docs/src/tutorials/intro-iii.md
@@ -8,10 +8,9 @@ Let's use this version of our familiar penguin plot for modification:
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 spec = data(penguins) *
     mapping(

diff --git a/docs/src/tutorials/intro-iv.md b/docs/src/tutorials/intro-iv.md
@@ -5,10 +5,9 @@ In the previous chapters, we have seen two different features of the `mapping` f
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 layer = data(penguins) *
     mapping(

diff --git a/docs/src/tutorials/intro-v.md b/docs/src/tutorials/intro-v.md
@@ -11,10 +11,9 @@ The first alternative is still about long-format data, but it omits the tables.
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 bill_lengths = penguins.bill_length_mm
 bill_depths = penguins.bill_depth_mm

diff --git a/docs/src/tutorials/intro-vi.md b/docs/src/tutorials/intro-vi.md
@@ -10,10 +10,9 @@ Let's first bring our trusty old penguin dataset back in and draw a basic facet
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 spec = data(penguins) *
     mapping(

diff --git a/docs/src/tutorials/intro-vii.md b/docs/src/tutorials/intro-vii.md
@@ -15,10 +15,9 @@ For that to work, we just have to take care that the facets of these layers don'
 ```@example tut
 using AlgebraOfGraphics
 using CairoMakie
-using PalmerPenguins
 using DataFrames
 
-penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+penguins = DataFrame(AlgebraOfGraphics.penguins())
 
 cols = [:flipper_length_mm, :island, :bill_depth_mm, :species]
 

diff --git a/src/AlgebraOfGraphics.jl b/src/AlgebraOfGraphics.jl
@@ -75,6 +75,7 @@ include("guides/legend.jl")
 include("guides/colorbar.jl")
 include("draw.jl")
 include("paginate.jl")
+include("testdata.jl")
 
 include("precompiles.jl")
 

diff --git a/src/testdata.jl b/src/testdata.jl
@@ -0,0 +1,12 @@
+# nonmissing rows from Palmer Penguins data, licensed CC0, see https://allisonhorst.github.io/palmerpenguins/
+function penguins()
+    (;
+        species = mapreduce(Base.splat(fill), vcat, [("Adelie", 146), ("Gentoo", 119), ("Chinstrap", 68)]),
+        island = mapreduce(Base.splat(fill), vcat, [("Torgersen", 15), ("Biscoe", 10), ("Dream", 19), ("Biscoe", 18), ("Torgersen", 16), ("Dream", 16), ("Biscoe", 16), ("Torgersen", 16), ("Dream", 20), ("Biscoe", 119), ("Dream", 68)]),
+        bill_length_mm = [39.1,39.5,40.3,36.7,39.3,38.9,39.2,41.1,38.6,34.6,36.6,38.7,42.5,34.4,46.0,37.8,37.7,35.9,38.2,38.8,35.3,40.6,40.5,37.9,40.5,39.5,37.2,39.5,40.9,36.4,39.2,38.8,42.2,37.6,39.8,36.5,40.8,36.0,44.1,37.0,39.6,41.1,36.0,42.3,39.6,40.1,35.0,42.0,34.5,41.4,39.0,40.6,36.5,37.6,35.7,41.3,37.6,41.1,36.4,41.6,35.5,41.1,35.9,41.8,33.5,39.7,39.6,45.8,35.5,42.8,40.9,37.2,36.2,42.1,34.6,42.9,36.7,35.1,37.3,41.3,36.3,36.9,38.3,38.9,35.7,41.1,34.0,39.6,36.2,40.8,38.1,40.3,33.1,43.2,35.0,41.0,37.7,37.8,37.9,39.7,38.6,38.2,38.1,43.2,38.1,45.6,39.7,42.2,39.6,42.7,38.6,37.3,35.7,41.1,36.2,37.7,40.2,41.4,35.2,40.6,38.8,41.5,39.0,44.1,38.5,43.1,36.8,37.5,38.1,41.1,35.6,40.2,37.0,39.7,40.2,40.6,32.1,40.7,37.3,39.0,39.2,36.6,36.0,37.8,36.0,41.5,46.1,50.0,48.7,50.0,47.6,46.5,45.4,46.7,43.3,46.8,40.9,49.0,45.5,48.4,45.8,49.3,42.0,49.2,46.2,48.7,50.2,45.1,46.5,46.3,42.9,46.1,47.8,48.2,50.0,47.3,42.8,45.1,59.6,49.1,48.4,42.6,44.4,44.0,48.7,42.7,49.6,45.3,49.6,50.5,43.6,45.5,50.5,44.9,45.2,46.6,48.5,45.1,50.1,46.5,45.0,43.8,45.5,43.2,50.4,45.3,46.2,45.7,54.3,45.8,49.8,49.5,43.5,50.7,47.7,46.4,48.2,46.5,46.4,48.6,47.5,51.1,45.2,45.2,49.1,52.5,47.4,50.0,44.9,50.8,43.4,51.3,47.5,52.1,47.5,52.2,45.5,49.5,44.5,50.8,49.4,46.9,48.4,51.1,48.5,55.9,47.2,49.1,46.8,41.7,53.4,43.3,48.1,50.5,49.8,43.5,51.5,46.2,55.1,48.8,47.2,46.8,50.4,45.2,49.9,46.5,50.0,51.3,45.4,52.7,45.2,46.1,51.3,46.0,51.3,46.6,51.7,47.0,52.0,45.9,50.5,50.3,58.0,46.4,49.2,42.4,48.5,43.2,50.6,46.7,52.0,50.5,49.5,46.4,52.8,40.9,54.2,42.5,51.0,49.7,47.5,47.6,52.0,46.9,53.5,49.0,46.2,50.9,45.5,50.9,50.8,50.1,49.0,51.5,49.8,48.1,51.4,45.7,50.7,42.5,52.2,45.2,49.3,50.2,45.6,51.9,46.8,45.7,55.8,43.5,49.6,50.8,50.2],   
+        bill_depth_mm = [18.7,17.4,18.0,19.3,20.6,17.8,19.6,17.6,21.2,21.1,17.8,19.0,20.7,18.4,21.5,18.3,18.7,19.2,18.1,17.2,18.9,18.6,17.9,18.6,18.9,16.7,18.1,17.8,18.9,17.0,21.1,20.0,18.5,19.3,19.1,18.0,18.4,18.5,19.7,16.9,18.8,19.0,17.9,21.2,17.7,18.9,17.9,19.5,18.1,18.6,17.5,18.8,16.6,19.1,16.9,21.1,17.0,18.2,17.1,18.0,16.2,19.1,16.6,19.4,19.0,18.4,17.2,18.9,17.5,18.5,16.8,19.4,16.1,19.1,17.2,17.6,18.8,19.4,17.8,20.3,19.5,18.6,19.2,18.8,18.0,18.1,17.1,18.1,17.3,18.9,18.6,18.5,16.1,18.5,17.9,20.0,16.0,20.0,18.6,18.9,17.2,20.0,17.0,19.0,16.5,20.3,17.7,19.5,20.7,18.3,17.0,20.5,17.0,18.6,17.2,19.8,17.0,18.5,15.9,19.0,17.6,18.3,17.1,18.0,17.9,19.2,18.5,18.5,17.6,17.5,17.5,20.1,16.5,17.9,17.1,17.2,15.5,17.0,16.8,18.7,18.6,18.4,17.8,18.1,17.1,18.5,13.2,16.3,14.1,15.2,14.5,13.5,14.6,15.3,13.4,15.4,13.7,16.1,13.7,14.6,14.6,15.7,13.5,15.2,14.5,15.1,14.3,14.5,14.5,15.8,13.1,15.1,15.0,14.3,15.3,15.3,14.2,14.5,17.0,14.8,16.3,13.7,17.3,13.6,15.7,13.7,16.0,13.7,15.0,15.9,13.9,13.9,15.9,13.3,15.8,14.2,14.1,14.4,15.0,14.4,15.4,13.9,15.0,14.5,15.3,13.8,14.9,13.9,15.7,14.2,16.8,16.2,14.2,15.0,15.0,15.6,15.6,14.8,15.0,16.0,14.2,16.3,13.8,16.4,14.5,15.6,14.6,15.9,13.8,17.3,14.4,14.2,14.0,17.0,15.0,17.1,14.5,16.1,14.7,15.7,15.8,14.6,14.4,16.5,15.0,17.0,15.5,15.0,16.1,14.7,15.8,14.0,15.1,15.2,15.9,15.2,16.3,14.1,16.0,16.2,13.7,14.3,15.7,14.8,16.1,17.9,19.5,19.2,18.7,19.8,17.8,18.2,18.2,18.9,19.9,17.8,20.3,17.3,18.1,17.1,19.6,20.0,17.8,18.6,18.2,17.3,17.5,16.6,19.4,17.9,19.0,18.4,19.0,17.8,20.0,16.6,20.8,16.7,18.8,18.6,16.8,18.3,20.7,16.6,19.9,19.5,17.5,19.1,17.0,17.9,18.5,17.9,19.6,18.7,17.3,16.4,19.0,17.3,19.7,17.3,18.8,16.6,19.9,18.8,19.4,19.5,16.5,17.0,19.8,18.1,18.2,19.0,18.7],
+        flipper_length_mm = [181,186,195,193,190,181,195,182,191,198,185,195,197,184,194,174,180,189,185,180,187,183,187,172,180,178,178,188,184,195,196,190,180,181,184,182,195,186,196,185,190,182,190,191,186,188,190,200,187,191,186,193,181,194,185,195,185,192,184,192,195,188,190,198,190,190,196,197,190,195,191,184,187,195,189,196,187,193,191,194,190,189,189,190,202,205,185,186,187,208,190,196,178,192,192,203,183,190,193,184,199,190,181,197,198,191,193,197,191,196,188,199,189,189,187,198,176,202,186,199,191,195,191,210,190,197,193,199,187,190,191,200,185,193,193,187,188,190,192,185,190,184,195,193,187,201,211,230,210,218,215,210,211,219,209,215,214,216,214,213,210,217,210,221,209,222,218,215,213,215,215,215,215,210,220,222,209,207,230,220,220,213,219,208,208,208,225,210,216,222,217,210,225,213,215,210,220,210,225,217,220,208,220,208,224,208,221,214,231,219,230,229,220,223,216,221,221,217,216,230,209,220,215,223,212,221,212,224,212,228,218,218,212,230,218,228,212,224,214,226,216,222,203,225,219,228,215,228,215,210,219,208,209,216,229,213,230,217,230,222,214,215,222,212,213,192,196,193,188,197,198,178,197,195,198,193,194,185,201,190,201,197,181,190,195,181,191,187,193,195,197,200,200,191,205,187,201,187,203,195,199,195,210,192,205,210,187,196,196,196,201,190,212,187,198,199,201,193,203,187,197,191,203,202,194,206,189,195,207,202,193,210,198],
+        body_mass_g = [3750,3800,3250,3450,3650,3625,4675,3200,3800,4400,3700,3450,4500,3325,4200,3400,3600,3800,3950,3800,3800,3550,3200,3150,3950,3250,3900,3300,3900,3325,4150,3950,3550,3300,4650,3150,3900,3100,4400,3000,4600,3425,3450,4150,3500,4300,3450,4050,2900,3700,3550,3800,2850,3750,3150,4400,3600,4050,2850,3950,3350,4100,3050,4450,3600,3900,3550,4150,3700,4250,3700,3900,3550,4000,3200,4700,3800,4200,3350,3550,3800,3500,3950,3600,3550,4300,3400,4450,3300,4300,3700,4350,2900,4100,3725,4725,3075,4250,2925,3550,3750,3900,3175,4775,3825,4600,3200,4275,3900,4075,2900,3775,3350,3325,3150,3500,3450,3875,3050,4000,3275,4300,3050,4000,3325,3500,3500,4475,3425,3900,3175,3975,3400,4250,3400,3475,3050,3725,3000,3650,4250,3475,3450,3750,3700,4000,4500,5700,4450,5700,5400,4550,4800,5200,4400,5150,4650,5550,4650,5850,4200,5850,4150,6300,4800,5350,5700,5000,4400,5050,5000,5100,5650,4600,5550,5250,4700,5050,6050,5150,5400,4950,5250,4350,5350,3950,5700,4300,4750,5550,4900,4200,5400,5100,5300,4850,5300,4400,5000,4900,5050,4300,5000,4450,5550,4200,5300,4400,5650,4700,5700,5800,4700,5550,4750,5000,5100,5200,4700,5800,4600,6000,4750,5950,4625,5450,4725,5350,4750,5600,4600,5300,4875,5550,4950,5400,4750,5650,4850,5200,4925,4875,4625,5250,4850,5600,4975,5500,5500,4700,5500,4575,5500,5000,5950,4650,5500,4375,5850,6000,4925,4850,5750,5200,5400,3500,3900,3650,3525,3725,3950,3250,3750,4150,3700,3800,3775,3700,4050,3575,4050,3300,3700,3450,4400,3600,3400,2900,3800,3300,4150,3400,3800,3700,4550,3200,4300,3350,4100,3600,3900,3850,4800,2700,4500,3950,3650,3550,3500,3675,4450,3400,4300,3250,3675,3325,3950,3600,4050,3350,3450,3250,4050,3800,3525,3950,3650,3650,4000,3400,3775,4100,3775],
+        sex = ["female", "male"][[2,1,1,1,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,2,1,2,1,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,2,1,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,2,1,2,2,1,1,2,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,2,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,2,1,2,1,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,1,2,1,2,2,1,2,1,1,2,1,2,2,1,1,2,1,2,1,2,1,2,2,1,2,1,1,2,1,2,2,1]],
+    )
+end