commit e7ec41c7fa63736ba80e1db50902b000b0e75333
parent 2e6cd442cd49fdc3dffbb16a02408ae5197122e3
Author: Erik Loualiche <eloualic@umn.edu>
Date: Tue, 20 May 2025 11:54:42 -0500
doc
Diffstat:
11 files changed, 1825 insertions(+), 0 deletions(-)
diff --git a/.github/workflows/Documentation.yaml b/.github/workflows/Documentation.yaml
@@ -0,0 +1,57 @@
+name: Documentation
+
+on:
+ push:
+ branches:
+ - main
+ tags: '*'
+ pull_request:
+
+jobs:
+ build:
+ permissions:
+ actions: write
+ contents: write
+ pull-requests: read
+ statuses: write
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: julia-actions/setup-julia@v2
+ with:
+ version: '1'
+ - uses: julia-actions/cache@v2
+ - name: Install dependencies
+ run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+ - name: Build and deploy
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+ GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988
+ run: julia --project=docs/ docs/make.jl
+
+
+
+
+
+
+
+# jobs:
+# doc-preview-cleanup:
+# runs-on: ubuntu-latest
+# steps:
+# - name: Checkout gh-pages branch
+# uses: actions/checkout@v2
+# with:
+# ref: gh-pages
+# - name: Delete preview and history + push changes
+# run: |
+# if [ -d "previews/PR$PRNUM" ]; then
+# git config user.name "EL"
+# git config user.email "EL@EL.com"
+# git rm -rf "previews/PR$PRNUM"
+# git commit -m "delete preview"
+# git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+# git push --force origin gh-pages-new:gh-pages
+# fi
+# env:
+# PRNUM: ${{ github.event.number }}
diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -0,0 +1,51 @@
+# Sample workflow for building and deploying a VitePress site to GitHub Pages
+
+name: Documenter
+
+on:
+ # Runs on pushes targeting the `master` branch. Change this to `main` if you're
+ # using the `main` branch as the default branch.
+ push:
+ branches:
+ - master
+ tags: ['*']
+ pull_request:
+
+ # Allows you to run this workflow manually from the Actions tab
+ workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+ contents: write
+ pages: write
+ id-token: write
+ statuses: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+ group: pages
+ cancel-in-progress: false
+
+jobs:
+ # Build job
+ build:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v4
+ - name: Setup Julia
+ uses: julia-actions/setup-julia@v1
+ - name: Pull Julia cache
+ uses: julia-actions/cache@v1
+ - name: Install documentation dependencies
+ run: julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
+ #- name: Creating new mds from src
+ - name: Build and deploy docs
+ uses: julia-actions/julia-docdeploy@v1
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+ DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+ GKSwstype: "100" # for Plots.jl plots (if you have them)
+ JULIA_DEBUG: "Documenter"
+ DATADEPS_ALWAYS_ACCEPT: true
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -0,0 +1,1404 @@
+# This file is machine-generated - editing it directly is not advised
+
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+
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+[[deps.Xorg_xcb_util_wm_jll]]
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+
+[[deps.Xorg_xkbcomp_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"]
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+[[deps.Xorg_xkeyboard_config_jll]]
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+
+[[deps.Xorg_xtrans_jll]]
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+[[deps.Zlib_jll]]
+deps = ["Libdl"]
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+
+[[deps.Zstd_jll]]
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+[[deps.eudev_jll]]
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+[[deps.fzf_jll]]
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+[[deps.libass_jll]]
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+[[deps.libblastrampoline_jll]]
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+
+[[deps.libdecor_jll]]
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+git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f"
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+[[deps.libinput_jll]]
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+[[deps.p7zip_jll]]
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+
+[[deps.x264_jll]]
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+
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+
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+deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
+git-tree-sha1 = "c950ae0a3577aec97bfccf3381f66666bc416729"
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -0,0 +1,8 @@
+[deps]
+BazerData = "9777a11d-2328-4b97-9b51-b265bb408da6"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
+PalmerPenguins = "8b842266-38fa-440a-9b57-31493939ab85"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
diff --git a/docs/make.jl b/docs/make.jl
@@ -0,0 +1,59 @@
+#!/usr/bin/env julia
+
+
+push!(LOAD_PATH, "../src/")
+import Pkg; Pkg.develop(path="..")
+# locally : julia --color=yes --project make.jl
+
+# --
+using BazerData
+using Documenter
+using DocumenterVitepress
+
+# --
+makedocs(
+ # format = Documenter.HTML(),
+ format = MarkdownVitepress(
+ repo = "https://github.com/eloualiche/BazerData.jl",
+ ),
+ repo = Remotes.GitHub("eloualiche", "BazerData.jl"),
+ sitename = "BazerData.jl",
+ modules = [BazerData],
+ authors = "Erik Loualiche",
+ pages=[
+ "Home" => "index.md",
+ "Manual" => [
+ "man/xtile_guide.md",
+ "man/winsorize_guide.md"
+ ],
+ "Demos" => [
+ "demo/stata_utils.md",
+ ],
+ "Library" => [
+ "lib/public.md",
+ "lib/internals.md"
+ ]
+ ]
+)
+
+
+deploydocs(;
+ repo = "github.com/eloualiche/BazerData.jl",
+ target = "build", # this is where Vitepress stores its output
+ devbranch = "main",
+ branch = "gh-pages",
+ push_preview = true,
+)
+
+
+# deploydocs(;
+# repo = "github.com/eloualiche/BazerData.jl",
+# devbranch = "build",
+# )
+
+# deploydocs(;
+# repo = "github.com/eloualiche/BazerData.jl",
+# target = "build",
+# branch = "gh-pages",
+# )
+
diff --git a/docs/src/demo/stata_utils.md b/docs/src/demo/stata_utils.md
@@ -0,0 +1,16 @@
+# Stata-like utilities
+
+So far I have tried to implement
+1. tabulate
+2. xtile
+3. winsorize
+
+Other stata-like panel stuff are
+panel_fill
+
+Other packages that do similar things
+
+ - See [statar](https://github.com/matthieugomez/statar) for a good package that implements stata feature into R.
+ - See [Binscatters.jl](https://github.com/matthieugomez/Binscatters.jl)
+ - [Douglass](https://github.com/jmboehm/Douglass.jl) to work with DataFrames in Julia using a stata-like syntax.
+ +
\ No newline at end of file
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -0,0 +1,4 @@
+# BazerData.jl
+
+Useful functions for working with data.
+
diff --git a/docs/src/lib/internals.md b/docs/src/lib/internals.md
@@ -0,0 +1,8 @@
+# Package Internals
+
+## `BazerData` Module
+
+```@autodocs
+Modules = [BazerData]
+Public = false
+```
diff --git a/docs/src/lib/public.md b/docs/src/lib/public.md
@@ -0,0 +1,8 @@
+# Public Interface
+
+## `BazerData` Module
+
+```@autodocs
+Modules = [BazerData]
+Private = false
+```
diff --git a/docs/src/man/winsorize_guide.md b/docs/src/man/winsorize_guide.md
@@ -0,0 +1,150 @@
+# Winsorizing
+
+The function `winsorize` tries to emulate stata winsor function.
+
+There is a [`winsor`](https://juliastats.org/StatsBase.jl/stable/robust/#StatsBase.winsor) function in StatsBase.jl but I think it's a little less full-featured.
+
+
+```@setup hist
+import Pkg; Pkg.add("Plots");
+using Plots, Random, BazerData
+gr(); theme(:wong2); Plots.default(display_type=:inline, size=(1250,750), thickness_scaling=1)
+```
+
+
+## Basic usage
+
+Start with a simple distribution to visualize the effect of *winsorizing*
+```@example hist
+Random.seed!(3); x = randn(10_000);
+p1 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution",
+ framestyle=:box, size=(1250,750))
+savefig(p1, "p1.svg"); nothing # hide
+```
+
+
+
+### Replace the outliers based on quantile
+```@example hist;
+x_win = winsorize(x, probs=(0.05, 0.95));
+p2 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution", framestyle=:box);
+histogram!(x_win, bins=-4:0.1:4, color="red", opacity=0.5, label="winsorized")
+savefig(p2, "p2.svg"); nothing # hide
+```
+
+
+
+### One side trim
+```@example hist;
+x_win = winsorize(x, probs=(0, 0.8));
+p3 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution", framestyle=:box);
+histogram!(x_win, bins=-4:0.1:4, color="red", opacity=0.5, label="winsorized");
+savefig(p3, "p3.svg"); nothing # hide
+```
+
+
+
+### Bring your own cutpoints
+Another type of winsorizing is to specify your own cutpoints (they do not have to be symmetric):
+```@example hist
+x_win = winsorize(x, cutpoints=(-1.96, 2.575));
+p4 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution", framestyle=:box);
+histogram!(x_win, bins=-4:0.1:4, color="red", opacity=0.5, label="winsorized");
+savefig(p4, "p4.svg"); nothing # hide
+```
+
+
+
+### Rely on the computer to select the right cutpoints
+If you do not specify either they will specified automatically
+```@example hist
+x_win = winsorize(x; verbose=true);
+p5 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution", framestyle=:box);
+histogram!(x_win, bins=-4:0.1:4, color="red", opacity=0.5, label="winsorized");
+savefig(p5, "p5.svg"); nothing # hide
+```
+
+
+
+### How not to replace outliers
+If you do not want to replace the value by the cutoffs, specify `replace_value=missing`:
+```@example hist
+x_win = winsorize(x, cutpoints=(-2.575, 1.96), replace_value=missing);
+p6 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution", framestyle=:box);
+histogram!(x_win, bins=-4:0.1:4, color="red", opacity=0.5, label="winsorized");
+savefig(p6, "p6.svg"); nothing # hide
+```
+
+
+
+### How to choose your replacement
+The `replace_value` command gives you some flexibility to do whatever you want in your outlier data transformation
+```@example hist
+x_win = winsorize(x, cutpoints=(-2.575, 1.96), replace_value=(-1.96, 1.28));
+p7 = histogram(x, bins=-4:0.1:4, color="blue", label="distribution", framestyle=:box);
+histogram!(x_win, bins=-4:0.1:4, color="red", opacity=0.5, label="winsorized");
+savefig(p7, "p7.svg"); nothing # hide
+```
+
+
+
+
+## Within a DataFrame
+
+I try to mimick the `gtools winsor` [example](https://raw.githubusercontent.com/mcaceresb/stata-gtools/master/docs/examples/gstats_winsor.do)
+
+```@setup dataframe
+import Pkg;
+Pkg.add("DataFrames"); Pkg.add("Plots");
+Pkg.add("PalmerPenguins"); ENV["DATADEPS_ALWAYS_ACCEPT"] = true
+using DataFrames, PalmerPenguins, Plots, BazerData
+gr(); theme(:wong2); Plots.default(display_type=:inline, size=(1250,750), thickness_scaling=1)
+```
+
+
+Winsorize one variable
+```@example dataframe
+df = DataFrame(PalmerPenguins.load())
+
+# gstats winsor wage
+transform!(df, :body_mass_g => (x -> winsorize(x, probs=(0.1, 0.9)) ) => :body_mass_g_w)
+
+p8 = histogram(df.body_mass_g, bins=2700:100:6300, color="blue", label="distribution", framestyle=:box);
+histogram!(df.body_mass_g_w, bins=2700:100:6300, color="red", opacity=0.5, label="winsorized");
+savefig(p8, "p8.svg"); nothing # hide
+```
+
+
+
+Winsorize multiple variables
+```@example dataframe
+# gstats winsor wage age hours, cuts(0.5 99.5) replace
+var_to_winsorize = ["bill_length_mm", "bill_depth_mm", "flipper_length_mm"]
+transform!(df,
+ var_to_winsorize .=> (x -> winsorize(x, probs=(0.1, 0.9)) ) .=> var_to_winsorize .* "_w")
+```
+
+Winsorize on one side only
+```@example dataframe
+# left-winsorizing only, at 1th percentile;
+# cap noi gstats winsor wage, cuts(1 100); gstats winsor wage, cuts(1 100) s(_w2)
+transform!(df, :body_mass_g => (x -> winsorize(x, probs=(0.1, 1)) ) => :body_mass_g_w )
+```
+
+Winsorize by groups
+```@example dataframe
+transform!(
+ groupby(df, :sex),
+ :body_mass_g => (x -> winsorize(x, probs=(0.2, 0.8)) ) => :body_mass_g_w)
+p9 = histogram(df[ isequal.(df.sex, "male"), :body_mass_g], bins=3000:100:6300,
+ color="blue", label="distribution", framestyle=:box);
+histogram!(df[ isequal.(df.sex, "male"), :body_mass_g_w], bins=3000:100:6300,
+ color="red", opacity=0.5, label="winsorized");
+savefig(p9, "p9.svg"); nothing # hide
+```
+
+
+
+
+
+
diff --git a/docs/src/man/xtile_guide.md b/docs/src/man/xtile_guide.md
@@ -0,0 +1,59 @@
+# Xtile
+
+The function `xtile` tries to emulate stata [xtile](https://www.stata.com/manuals/dpctile.pdf) function.
+
+There is a [`BinScatter.jl`](https://github.com/matthieugomez/Binscatters.jl) package which already implements these features.
+
+
+```@setup hist
+import Pkg; Pkg.add("Plots");
+using Plots, Random, StatsBase, BazerData
+gr(); theme(:wong2); Plots.default(display_type=:inline, size=(1250,750), thickness_scaling=1)
+```
+
+
+## Basic usage
+
+Start with a simple distribution to visualize the effect of *winsorizing*
+```@example hist
+Random.seed!(3); x = randn(10_000);
+p1 = histogram(x,
+ bins=-4:0.1:4, alpha=0.25, color="grey", label="",
+ framestyle=:box, size=(1250,750))
+savefig(p1, "p1.svg"); nothing # hide
+```
+
+
+
+The quintiles split the distribution:
+```@example hist;
+x_tile = hcat(x, xtile(x, 5))
+p2 = histogram(x, bins=-4:0.1:4, alpha=0.25, color="grey",
+ label="", framestyle=:box);
+[ histogram!(x_tile[ x_tile[:, 2] .== i , 1], bins=-4:0.1:4,
+ alpha=0.75, label="quantile bin $i")
+ for i in 0:4 ];
+savefig(p2, "p2.svg"); nothing # hide
+```
+
+
+
+It is possible to include weights
+```@example hist;
+x_sorted = sort(x)
+x_tile_weights = xtile(x_sorted, 5,
+ weights=Weights([ log(i)/i for i in 1:length(x)]) )
+p3 = histogram(x, bins=-4:0.1:4, alpha=0.25, color="grey",
+ label="", framestyle=:box);
+[ histogram!(x_sorted[x_tile_weights.==i], bins=-4:0.1:4,
+ alpha=0.75, label="quantile bin $i")
+ for i in 0:4 ];
+savefig(p3, "p3.svg"); nothing # hide
+```
+
+
+
+
+
+
+
