### A Pluto.jl notebook ###
# v0.17.4

using Markdown
using InteractiveUtils

# ╔═╡ d09256dd-6c0d-4e28-9e54-3f7b3ca87ecb
begin
    using CSV, UrlDownload
    using DataFrames
    import Distributions
    using EvoTrees
  	using MLJ
    using MLJClusteringInterface
  	using MLJDecisionTreeInterface
    using MLJLinearModels
    using Plots
  	import StatsBase
  	using PlutoUI
end

# ╔═╡ a068d85b-975f-4d60-a518-c1baa6f4f351
html"""
<div style="
position: absolute;
width: calc(100% - 30px);
border: 50vw solid SteelBlue;
border-top: 500px solid SteelBlue;
border-bottom: none;
box-sizing: content-box;
left: calc(-50vw + 15px);
top: -500px;
height: 300px;
pointer-events: none;
"></div>

<div style="
height: 300px;
width: 100%;
background: SteelBlue;
color: #88BBD6;
padding-top: 68px;
padding-left: 5px;
">

<span style="
font-family: Vollkorn, serif;
font-weight: 700;
font-feature-settings: 'lnum', 'pnum';
"> 

<p style="
font-family: Alegreya sans;
font-size: 1.4rem;
font-weight: 300;
opacity: 1.0;
color: #CDCDCD;
">Tutorial - Solutions to Excercises</p>
<p style="text-align: left; font-size: 2.5rem;">
Machine Learning in Julia
</p>
"""

# ╔═╡ 0f97c6bb-9ced-4cbe-9bca-7c69b794f8ce
PlutoUI.TableOfContents(title = "MLJ Tutorial - Solutions")

# ╔═╡ b67c62c2-15ab-4328-b795-033f6f2a0674
md"""
An introduction to the
[MLJ](https://alan-turing-institute.github.io/MLJ.jl/stable/)
toolbox.
"""

# ╔═╡ bc689638-fd19-4c9f-935f-ddf6a6bfbbdd
md"## Set-up"

# ╔═╡ 197fd00e-9068-46ea-af2a-25235e544a31
md"Inspect Julia version:"

# ╔═╡ f6d4f8c4-e441-45c4-8af5-148d95ea2900
VERSION

# ╔═╡ 45740c4d-b789-45dc-a6bf-47194d7e8e12
md"The following instantiates a package environment."

# ╔═╡ 42b0f1e1-16c9-4238-828a-4cc485149963
md"""
The package environment has been created using **Julia 1.6** and may not
instantiate properly for other Julia versions.
"""

# ╔═╡ 499cbc31-83ba-4583-ba1f-6363f43ec697
md"## General resources"

# ╔═╡ db5821e8-956a-4a46-95ea-2955abd45275
md"""
- [MLJ Cheatsheet](https://alan-turing-institute.github.io/MLJ.jl/dev/mlj_cheatsheet/)
- [Common MLJ Workflows](https://alan-turing-institute.github.io/MLJ.jl/dev/common_mlj_workflows/)
- [MLJ manual](https://alan-turing-institute.github.io/MLJ.jl/dev/)
- [Data Science Tutorials in Julia](https://juliaai.github.io/DataScienceTutorials.jl/)
"""

# ╔═╡ 945f2179-e861-4ae7-a949-7f3bd292fe31
md"# Exercise 2 solution"

# ╔═╡ e62654a0-cc6e-4072-8514-99938a2932db
md"From the question statememt:"

# ╔═╡ 7f9003b5-95c7-418b-a0de-1721c1bc2df2
quality0 = ["good", "poor", "poor", "excellent", missing, "good", "excellent"]

# ╔═╡ c037caf3-700e-4cc8-bca8-7eec7950fd82
begin
  quality = coerce(quality0, OrderedFactor);
  levels!(quality, ["poor", "good", "excellent"]);
  elscitype(quality)
end

# ╔═╡ e9be221c-06a1-41bc-9873-1b1430e635cc
md"# Exercise 3 solution"

# ╔═╡ 9f13b374-8918-4bae-b43e-d0ebe87da176
md"From the question statement:"

# ╔═╡ 9a417692-fea9-4606-9009-4cfb2012998f
begin
  house_csv = urldownload("https://raw.githubusercontent.com/ablaom/"*
                          "MachineLearningInJulia2020/for-MLJ-version-0.16/"*
                          "data/house.csv");
  house = DataFrames.DataFrame(house_csv)
end

# ╔═╡ e926dc2e-2b3b-4683-abd3-cb77d7a79683
md"First pass:"

# ╔═╡ cb767b7d-bc7f-4759-879e-dc128f3db7b3
begin
  coerce!(house, autotype(house));
  schema(house)
end

# ╔═╡ 0ec099e3-6e30-41f6-a367-9aa3c6cf34d0
md"""
All the "sqft" fields refer to "square feet" so are
really `Continuous`. We'll regard `:yr_built` (the other `Count`
variable above) as `Continuous` as well. So:
"""

# ╔═╡ 159c8967-ab87-4b2a-bf32-94657e65284e
coerce!(house, Count => Continuous);

# ╔═╡ f93fec06-260f-4693-9afd-65a5b5facac9
md"And `:zipcode` should not be ordered:"

# ╔═╡ 17809199-b8c5-4b29-b6c8-54f5ed90a964
begin
  coerce!(house, :zipcode => Multiclass);
  schema(house)
end

# ╔═╡ 8eaa2b50-c1f7-4f8b-9292-fe822525fc77
md"""
`:bathrooms` looks like it has a lot of levels, but on further
inspection we see why, and `OrderedFactor` remains appropriate:
"""

# ╔═╡ 0f5162b2-daf6-43a1-ae5e-4b83dcbc9675
StatsBase.countmap(house.bathrooms)

# ╔═╡ 44e87adc-146a-4da9-8a29-32f11452654a
md"# Exercise 4 solution"

# ╔═╡ 9f13b374-8918-4bae-a5f1-151fcbe229a2
md"From the question statement:"

# ╔═╡ 1f822943-6f7a-4615-81bc-2d5603785a09
begin
  poisson = Distributions.Poisson
  
  age = 18 .+ 60 * rand(10);
  salary = coerce(rand(["small", "big", "huge"], 10), OrderedFactor);
  levels!(salary, ["small", "big", "huge"]);
  small = salary[1]
  
  X4 = DataFrames.DataFrame(age=age, salary=salary)
  
  n_devices(salary) = salary > small ? rand(poisson(1.3)) : rand(poisson(2.9))
  y4 = [n_devices(row.salary) for row in eachrow(X4)]
end

# ╔═╡ e3cc20c2-6492-45e0-9d87-1d1fbb0e3997
md"## 4a"

# ╔═╡ 63f952e4-5d3a-48ac-b950-fddef2a1fb10
md"There are *no* models that apply immediately:"

# ╔═╡ ae1cb765-ba67-496e-951b-64cb2a36c8e3
models(matching(X4, y4))

# ╔═╡ d30bc3a2-c019-406f-b0e6-441461cc8770
md"## 4b"

# ╔═╡ af31e97b-cfba-4caa-8cb0-de601961bc02
begin
  y4cont = coerce(y4, Continuous);
  models(matching(X4, y4cont))
end

# ╔═╡ 08f6a160-3148-40fc-a87d-950c50fb2955
md"# Exercise 6 solution"

# ╔═╡ 9f13b374-8918-4bae-8448-4bcb089096cd
md"From the question statement:"

# ╔═╡ 6df9f266-f9d9-4506-a012-a84240254fb6
begin
  csv_file = urldownload("https://raw.githubusercontent.com/ablaom/"*
                     "MachineLearningInJulia2020/"*
                     "for-MLJ-version-0.16/data/horse.csv");
  horse = DataFrames.DataFrame(csv_file); # convert to data frame
  coerce!(horse, autotype(horse));
  coerce!(horse, Count => Continuous);
  coerce!(horse,
          :surgery               => Multiclass,
          :age                   => Multiclass,
          :mucous_membranes      => Multiclass,
          :capillary_refill_time => Multiclass,
          :outcome               => Multiclass,
          :cp_data               => Multiclass);
  schema(horse)
end

# ╔═╡ 9a4ff2d2-c5b6-4488-bbdd-9799f7bb2e60
md"## 6a"

# ╔═╡ affb9923-2afa-4655-97a7-88e3af4f10ee
yHorse6, XHorse6 = unpack(horse,
              ==(:outcome),
              name -> elscitype(Tables.getcolumn(horse, name)) == Continuous);

# ╔═╡ 9995fba2-e61b-4877-b372-8c9866e51852
md"## 6b - i"

# ╔═╡ 29825df3-1e51-4b8d-8f3d-b82f1e7b6f7a
begin
  train6, test6 = partition(eachindex(yHorse6), 0.7)
  model6Linear = (@load LogisticClassifier pkg = MLJLinearModels)();
  model6Linear.lambda = 100
  mach6Linear = machine(model6Linear, XHorse6, yHorse6)
  fit!(mach6Linear, rows = train6)
  fitted_params(mach6Linear)
end

# ╔═╡ 7f98042d-d94a-401b-9c42-dbb0c1fc3d6b
begin
	coefs_given_feature = Dict(fitted_params(mach6Linear).coefs)
  	coefs_given_feature[:pulse]
end

# ╔═╡ ff68e7ef-ed45-48fc-8847-d199101a1711
md"""
## 6b - ii
"""

# ╔═╡ c01a3d86-3f7e-494b-ab04-579e5608ae53
begin
  yhat6 = predict(mach6Linear, rows = test6)		 # or predict(mach6, X[test6,:])
  err = cross_entropy(yhat6, yHorse6[test6]) |> mean
end

# ╔═╡ 1af34706-479e-42a8-86cf-35420d9e6995
md"## 6b - iii"

# ╔═╡ be4e773b-284c-406f-a29a-8d0445351914
md"""
The predicted probabilities of the actual observations in the test
are given by
"""

# ╔═╡ f8bc8787-ea6a-4935-be65-28d0fcca50a8
p = broadcast(pdf, yhat6, yHorse6[test6]);

# ╔═╡ 7e046dfe-49ce-47e4-9a2e-c468345d87d1
md"The number of times this probability exceeds 50% is:"

# ╔═╡ 2f3f1724-0d11-4159-b5fa-cb79ebf595ef
n50 = filter(x -> x > 0.5, p) |> length

# ╔═╡ 4c06c69e-8a21-43d7-91c5-524da38aa391
md"Or, as a proportion:"

# ╔═╡ 89b9ee21-1940-4e5e-ad90-b4405b216771
n50/length(test6)

# ╔═╡ 83fba101-4cf1-48aa-895b-997a92b731e0
md"## 6b - iv"

# ╔═╡ 0fb6fa7a-f0c0-4926-a525-e9b04a4bd246
misclassification_rate(mode.(yhat6), yHorse6[test6])

# ╔═╡ e56be556-d75a-40c9-80f0-ba7781e173cf
md"## 6c - i"

# ╔═╡ 28a64fbd-ceeb-44b3-9cbc-9a2c39793333
begin
  model6Tree = (@load RandomForestClassifier pkg = DecisionTree)()
  mach6Tree = machine(model6Tree, XHorse6, yHorse6)
  evaluate!(mach6Tree, resampling = CV(nfolds = 6), measure = cross_entropy)
  
  r6 = range(model6Tree, :n_trees, lower = 10, upper = 70, scale = :log10)
end

# ╔═╡ 5d00e3fe-feb5-4394-b887-2b16710e5502
md"""
Since random forests are inherently randomized, we generate multiple
curves:
"""

# ╔═╡ c25a8ee7-61b3-4b07-9452-5298a8a4a401
begin
  plt6 = plot()
  for i in 1:4
      one_curve = learning_curve(mach6Tree,
                             range = r6,
                             resampling = Holdout(),
                             measure = cross_entropy)
      plot!(one_curve.parameter_values, one_curve.measurements)
  end
  xlabel!(plt6, "n_trees")
  ylabel!(plt6, "cross entropy")
  savefig("exercise_6ci.png")
  plt6
end

# ╔═╡ 0e8a02cd-4571-45d8-b017-96f1602f2cad
md"## 6c - ii"

# ╔═╡ eb277481-dc8b-48b4-9afa-2d0873c6690c
 model6Tree.n_trees = 90

# ╔═╡ 5a351c52-5915-4e2b-8be2-2a4017c45345
evaluate!(mach6Tree, 
			resampling = CV(nfolds = 9),
            measure = cross_entropy,
            rows = train6).measurement[1]

# ╔═╡ faef6958-7f5d-42e4-a7ad-80d84f5b0070
md"## 6c - iii"

# ╔═╡ 240987eb-4252-42e3-8378-5aa686f0b407
err_forest = evaluate!(mach6Tree, resampling = Holdout(),
                       measure = cross_entropy).measurement[1]

# ╔═╡ 25a6fd3c-60d1-44dd-9f43-49763e8691a1
md"# Exercise 7 solution"

# ╔═╡ c67079e3-91e2-4507-bb0e-3a45761c733a
md"## 7a"

# ╔═╡ 2fde5672-eefe-4334-b9c0-77f330290364
@load KMeans pkg = Clustering

# ╔═╡ 26ad8aa8-a794-4669-88d0-4281e33ea01b
@load EvoTreeClassifier

# ╔═╡ dc4580d7-bdd0-4321-9979-7044b2f2df33
pipe7 = Standardizer |>
        ContinuousEncoder |>
        KMeans(k=10) |>
        EvoTreeClassifier(nrounds=50)

# ╔═╡ fa50e0ac-0d0c-43ff-b2a1-fbbde543f620
md"## 7b"

# ╔═╡ b9814590-55d4-4fa5-910b-f8a9a217eff2
begin
  mach7 = machine(pipe7, XHorse6, yHorse6)
  evaluate!(mach7, resampling=CV(nfolds=6), measure=cross_entropy)
end

# ╔═╡ e06b315d-1c67-4920-aa36-d2e8546da46a
md"## 7c"

# ╔═╡ ba582b6d-92b7-442f-a852-3294242d99ee
begin
	r7 = range(pipe7, :(evo_tree_classifier.max_depth), lower=1, upper=10)
  	curve7_1 = learning_curve(mach7,
                         range = r7,
                         resampling = CV(nfolds=6),
                         measure = cross_entropy)
end

# ╔═╡ a26c8113-18ff-480c-88a1-a2bf91434413
begin
  plt7 = plot(curve7_1.parameter_values, curve7_1.measurements)
  xlabel!(plt7, "max_depth")
  ylabel!(plt7, "CV estimate of cross entropy")
  savefig("exercise_7c.png")
  plt7
end

# ╔═╡ ac1277e1-dd28-42f6-a1cb-54e34396a855
md"Here's a second curve using a different random seed for the booster:"

# ╔═╡ 9fb31f91-3f46-45de-9f04-2a62c09414d4
begin
	pipe7.evo_tree_classifier.rng = Distributions.MersenneTwister(123)
  	curve7_2 = learning_curve(mach7,
                         range = r7,
                         resampling = CV(nfolds=6),
                         measure = cross_entropy)
end

# ╔═╡ e77629c1-10ee-4527-8037-0de5806e1a54
begin
  plot!(curve7_2.parameter_values, curve7_2.measurements, leg = true)
  savefig("exercise_7c_2.png")
  plt7
end

# ╔═╡ c5a91339-900f-4f82-9961-a09632c33fb0
md"""
One can automate the production of multiple curves with different
seeds in the following way:
"""

# ╔═╡ 175be988-90dc-4b37-95a4-7e7ecbc9ae29
 curves7_3 = learning_curve(mach7,
                          range = r7,
                          resampling = CV(nfolds=6),
                          measure = cross_entropy,
                          rng_name = :(evo_tree_classifier.rng),
                          rngs = 6) # list of RNGs, or num to auto generate

# ╔═╡ 2c4ee7b3-e43e-4269-b7cc-46f4ef988c68
begin
  plt7_2 = plot(curves7_3.parameter_values, curves7_3.measurements)
  savefig("exercise_7c_3.png")
  plt7_2
end

# ╔═╡ e62f9a56-5ddb-4ad3-90fb-7f2721f6fcc7
md"""
If you have multiple threads available in your julia session, you
can add the option `acceleration=CPUThreads()` to speed up this
computation.
"""

# ╔═╡ 5846d352-3641-4754-af65-ccd25ecb9818
md"# Exercise 8 solution"

# ╔═╡ 9f13b374-8918-4bae-8890-979691212d9b
md"From the question statement:"

# ╔═╡ 95642ccf-43dc-4f7c-918b-a672ccdf1c59
yHouse, XHouse = unpack(house, ==(:price), rng=123); # from Exercise 3

# ╔═╡ 6420a5f2-2fea-45b3-b496-095dd6971ed4
@load EvoTreeRegressor

# ╔═╡ f1c10774-befe-48aa-94a6-3b176d4c5343
tree_booster = EvoTreeRegressor(nrounds = 70)

# ╔═╡ 391536d7-1981-4518-a6fa-eaf14df5d44b
begin 
	model8 = ContinuousEncoder |> tree_booster
  	r_nbins = range(model8,
             :(evo_tree_regressor.nbins),
             lower = 2.5,
             upper= 7.5, scale=x->2^round(Int, x))
end

# ╔═╡ c67079e3-91e2-4507-8025-5084804a9f6c
md"## 8a"

# ╔═╡ 2bc25e17-89b0-477a-9e90-09023d201062
r_mdepth = range(model8, :(evo_tree_regressor.max_depth), lower=1, upper=12)

# ╔═╡ e06b315d-1c67-4920-b7bb-2f33ef765cc0
md"## 8c"

# ╔═╡ 546c47b0-a0f2-4d48-9625-01172c4a0081
begin
  	tuned_model = TunedModel(model = model8,
                           ranges = [r_nbins, r_mdepth],
                           resampling = Holdout(),
                           measures = mae,
                           tuning = RandomSearch(rng=123),
                           n = 40)
  
  	tuned_mach = machine(tuned_model, XHouse, yHouse) |> fit!
end

# ╔═╡ 07ce36f7-42e0-4f43-af18-aa758659e0d3
begin
	plt8 = plot(tuned_mach)
	xlabel!(plt8[1, 1], "max_depth")
	ylabel!(plt8[1, 1], "mean abs. error")
	xlabel!(plt8[2, 1], "max_depth")
	ylabel!(plt8[2, 1], "nbins")
	xlabel!(plt8[2, 2], "nbins")
	ylabel!(plt8[2, 2], "mean abs. error")
  	savefig("exercise_8c.png")
  	plt8
end

# ╔═╡ d7da0d7d-6776-4614-af4f-11c7de9e21dd
md"## 8d"

# ╔═╡ db1190f8-def5-403a-8dba-241d9b744683
begin
  best_model = report(tuned_mach).best_model
  best_mach = machine(best_model, XHouse, yHouse)
  best_err = evaluate!(best_mach, resampling=CV(nfolds=3), measure=mae)
end

# ╔═╡ f47fee00-3ca4-462c-a6e5-2f0b4dca5c59
tuned_err = evaluate!(tuned_mach, resampling=CV(nfolds=3), measure=mae)

# ╔═╡ 135dac9b-0bd9-4e1d-8550-20498aa03ed0
md"""
---

*This notebook was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
"""

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[[IrrationalConstants]]
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[[IterativeSolvers]]
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[[JSON]]
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[[LibGit2]]
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[[LibSSH2_jll]]
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[[Libffi_jll]]
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[[Libgcrypt_jll]]
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[[Libglvnd_jll]]
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[[Libgpg_error_jll]]
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[[Libmount_jll]]
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[[Measures]]
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[[OpenSSL_jll]]
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[[OpenSpecFun_jll]]
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[[Opus_jll]]
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[[PCRE_jll]]
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[[PDMats]]
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[[Pixman_jll]]
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[[PlotThemes]]
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[[Plots]]
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[[Printf]]
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[[Random123]]
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[[Rmath_jll]]
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[[SHA]]
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[[ScientificTypes]]
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[[ScikitLearnBase]]
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[[Showoff]]
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[[StableRNGs]]
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[[StatsFuns]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"]
git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b"
uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4"
version = "1.4.2+4"

[[Xorg_xkeyboard_config_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"]
git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d"
uuid = "33bec58e-1273-512f-9401-5d533626f822"
version = "2.27.0+4"

[[Xorg_xtrans_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845"
uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
version = "1.4.0+3"

[[Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

[[Zstd_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6"
uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
version = "1.5.0+0"

[[libass_jll]]
deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47"
uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
version = "0.15.1+0"

[[libfdk_aac_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55"
uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
version = "2.0.2+0"

[[libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c"
uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
version = "1.6.38+0"

[[libvorbis_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"]
git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb"
uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
version = "1.3.7+0"

[[nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

[[p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"

[[x264_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2"
uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
version = "2021.5.5+0"

[[x265_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9"
uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
version = "3.5.0+0"

[[xkbcommon_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6"
uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd"
version = "0.9.1+5"
"""

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