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# update-pkgs.R
# 
# Update all installed R packages (CRAN + Bioconductor, if BiocManager is
# installed) in one non-interactive run. Designed to be launched with
# Rscript, e.g. from a background process, instead of RStudio's
# Tools > Check for Package Updates (which is slow and blocks the GUI).
#
# Usage (terminal command line):
#   Rscript.exe path/to/update-pkgs.R
#

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# Pull your GitHub commit history via the GraphQL API
#
# What was I working on, and when? How does work on one project relate to
# others? This pulls commit history for a hand-picked list of repos into one
# tidy dataset, so you can answer that with data instead of memory.
#
# ---------------------------------------------------------------------------
# What it does
# ---------------------------------------------------------------------------
# Pulls commits and their attributes from GitHub directly via `gh api

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# chunks.R
# Parse the R code chunks in a Quarto/knitr book project into a data frame,
# one row per chunk, so you can audit code-folding, find figure chunks that
# still need treatment, spot old-style chunk labels, etc. See "Mind Your
# Chunks" (friendly.github.io) for the full writeup.
#
# Usage: run from the project root. Adapt `chapter_files` / `child_files`
# below to match your own project's file-naming convention -- as written,
# this assumes chapter source files are named like "04-something.qmd" in
# the working directory, with any knitr child documents listed explicitly.

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#' Include an HTML-renderable object in any knitr output format
#'
#' A pipe-friendly helper in Rmarkdown, Quarto, and other documents for objects that render natively in HTML output
#' (RStudio Viewer, HTML documents) but need a convenient image fallback for PDF, Word,
#' and other non-HTML formats. It was designed to solve a problem in rendering the result of `color_table()`,
#' and then generalized to provide for other similar cases.
#'
#' Supported classes (handled internally) solve this problem by saving the image to a file and then inserting it in the document
#' using `knitr::include_graphics()`:
#'   - `"gt_tbl"`     (gt package)       -- saved via \code{\link[gt]{gtsave}}

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# Happy Birthday, R!
# R 1.0.0 was first released on February 29, 2000
# Celebrating 26 years of statistical computing!

out_file <- "r_birthday_cake.png"
png(out_file, width = 800, height = 660, bg = "#FFF0F5")
par(mar = c(0.3, 0.3, 0.3, 0.3), bg = "#FFF0F5")
plot(0, 0, type = "n", xlim = c(0, 10), ylim = c(0, 10),
     axes = FALSE, xlab = "", ylab = "")
rect(-1, -1, 11, 11, col = "#FFF0F5", border = NA)

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#!/usr/bin/env Rscript

# Functions to fix one of the awful things that `Rd2roxygen::Rd2roxygen()` does when it tries to convert 
# a package to use roxygen documentation
#
# * Fixes roxygen2 \item formatting used in \describe{} blocks to document arguments and elements of returned results
# * Changes \item{list("VarName")} to \item{\code{VarName}}
# 
# Usage:
#   From R: source("fix_roxygen_items.R"); fix_roxygen_items("R/data.R")

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---
title: "Distribution of Determinants of 3×3 Matrices from {1,2,...,9}"
author: "Michael Friendly"
date: "`r Sys.Date()`"
output:
  html_document:
    toc: true
    toc_float: true
    code_folding: show
    theme: united

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#' ---
#' title: discriminant analysis demo
#' author: Michael Friendly
#' ---

library(MASS)
library(ggplot2)
#library(candisc)
library(dplyr)

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#' Render text in color for Markdown / Quarto documents using LaTeX or CSS styles
#' 
#' This function uses `\textcolor{}{}` from the `xcolor` package for LaTeX output
#' or a CSS `<span>` for HTML output.
#' 
#' Note that a color not defined in the `xcolor` package will trigger a latex error.
#' e.g., `darkgreen` is not defined but can use:
#'    \definecolor{darkgreen}{RGB}{1,50,32}
#'
#' @param text  Text to display, a character string

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#' ---
#' title: penguin colors
#' author: Michael Friendly
#' ---

# Create consistent sets of colors for penguins examples
# These specific colors are taken from https://github.com/srvanderplas/ggpcp-paper/blob/main/index.R
# See the image at: https://allisonhorst.github.io/palmerpenguins/reference/figures/lter_penguins.png

peng.colors <- function(shade=c("medium", "light", "dark")) {