Remove Gadfly and update dependencies (#85)

StatisticalRethinkingJulia · Sep 8, 2021 · 25bd8c4 · 25bd8c4
1 parent 0437dba
commit 25bd8c4
Show file tree

Hide file tree

Showing 10 changed files with 13 additions and 260 deletions.
diff --git a/Project.toml b/Project.toml
@@ -10,7 +10,6 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Franklin = "713c75ef-9fc9-4b05-94a9-213340da978e"
-Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 RData = "df47a6cb-8c03-5eed-afd8-b6050d6c41da"
@@ -21,15 +20,14 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 
 [compat]
-CSV = "0.8"
-CategoricalArrays = "0.9, 0.10"
-DataFrames = "0.22, 1.1"
+CSV = "0.9"
+CategoricalArrays = "0.10"
+DataFrames = "1"
 DifferentialEquations = "6.16"
-Distributions = "0.24"
+Distributions = "0.25"
 Franklin = "0.10"
-Gadfly = "1.3"
 RData = "0.8"
 StatsFuns = "0.9"
 StatsPlots = "0.14"
-Turing = "0.15, 0.16"
-julia = "1"
+Turing = "0.18"
+julia = "1.6"
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # TuringModels
 
 [![CI][ci-img]][ci-url]
-
+[![Site Analytics](https://img.shields.io/badge/Site-Analytics-blueviolet)](https://app.usefathom.com/share/ovpyqiuq/turingmodels.jl)
 
 ## Introduction
 

diff --git a/_layout/head.html b/_layout/head.html
@@ -8,6 +8,9 @@
  {{if hascode}} {{insert head_highlight.html }} {{end}}
  <link rel="stylesheet" href="/css/franklin.css">
  {{isdef title}} <title>{{fill title}}</title> {{end}}
+
+ <!-- Analytics with a strong focus on privacy. This allows us to know how much attention updating the tutorials should have. -->
+ <script src="https://cdn.usefathom.com/script.js" data-site="OVPYQIUQ" defer></script>
 </head>
 <body>
 

diff --git a/index.md b/index.md
@@ -56,7 +56,6 @@ Before you look at the models below, you might want to look at the [Basic Exampl
 - [m13.1](models/varying-slopes-cafe): Varying slopes cafes
 - [m13.2](models/multinomial-poisson): Multinomial Poisson regression
 - [m13.3](models/varying-intercepts-admission): Varying intercepts admission decisions
-- [m16.5](models/lynx-hare): Lynx and hare populations
 
 ### 1st Edition (2016)
 

diff --git a/models/africa-first-candidate.md b/models/africa-first-candidate.md
@@ -1,6 +1,7 @@
 +++
 title = "Africa first candidate model"
 showall = true
+reeval = true
 +++
 
 In Edition 2 on page 244, McElreath defines the model as

diff --git a/models/lynx-hare.md b/models/lynx-hare.md
diff --git a/scripts/africa-first-candidate.jl b/scripts/africa-first-candidate.jl
@@ -36,6 +36,6 @@ model = model_fn(df.log_gdp, df.rugged_std, mean(df.rugged_std));
 
 chns = sample(model, NUTS(), MCMCThreads(), 1000, 3)
 
-# \defaultgadflyoutput{}
+# \defaultoutput{}
 
 #
diff --git a/scripts/lynx-hare.jl b/scripts/lynx-hare.jl
diff --git a/src/TuringModels.jl b/src/TuringModels.jl
@@ -2,9 +2,8 @@ module TuringModels
 
 using CategoricalArrays
 using DataFrames
-using Gadfly
 
-const project_root = pkgdir(TuringModels)
+const project_root = string(pkgdir(TuringModels))::String
 
 """
  output_dir(name)
@@ -16,29 +15,4 @@ function output_dir(name)
  joinpath(project_root, "__site", "assets", "models", name, "code")
 end
 
-function write_gadfly_svg(output_dir, name, p; width=6inch, height=4inch)
- fig_path = joinpath(output_dir, "$name.svg")
- draw(SVG(fig_path, width, height), p)
-end
-
-function gadfly_plot(chns)
- df = DataFrame(chns)
- params = names(chns, :parameters)
- sdf = DataFrames.stack(df, params, variable_name=:parameter)
- sdf[!, :chain] = categorical(sdf.chain)
-
- p1 = plot(sdf, ygroup=:parameter, x=:iteration, y=:value, color=:chain,
- Geom.subplot_grid(Geom.line, free_x_axis=true, free_y_axis=true),
- Guide.ylabel("sample value"),
- # Key is shown on the right plot, so no need to show it twice.
- Theme(key_position=:none)
- )
- p2 = plot(sdf, ygroup=:parameter, x=:value, color=:chain,
- Geom.subplot_grid(Geom.density, free_x_axis=true, free_y_axis=true,
- Guide.xlabel(orientation=:horizontal)),
- Guide.ylabel("density"))
-
- hstack(p1, p2)
-end
-
 end # module
diff --git a/utils.jl b/utils.jl
@@ -38,42 +38,3 @@ function lx_defaultoutput(com, _)
  \fig{chns.svg}
  """
 end
-
-"""
- \\defaultgadflyoutput{}
-
-Plot `chns` via Gadfly.
-Don't combine this with a call to StatsPlots or `\\defaultoutput` to avoid conflict errors.
-"""
-function lx_defaultgadflyoutput(com, _)
- raw"""
- ```julia:write_helper
- # hideall
- using DataFrames
- using Gadfly
- using TuringModels
-
- output_dir = @OUTPUT
- function write_svg(name, p, width, height)
- fig_path = joinpath(output_dir, "$name.svg")
- draw(SVG(fig_path, width, height), p)
- end;
-
- df = DataFrame(chns)
- params = names(chns, :parameters)
- width = 8inch
- height = length(params) * 2inch
- nothing
- ```
- \output{write_helper}
-
- ```julia:plot
- write_svg("chns", # hide
- TuringModels.gadfly_plot(chns)
- , width, height) # hide
- nothing # hide
- ```
- \output{plot}
- \fig{chns.svg}
- """
-end