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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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# Accumulating R package references in a Quarto book

In writing a book using Quarto, I was looking for a way to automatically
accumulate the packages used in each chapter and write them out to a `pkgs.bib`
file at the end.  (I posted this as a Posit Community question, 
https://community.rstudio.com/t/how-to-accumulate-packages-bib-used-in-a-quarto-book/167619 )

I can easily do this with a `knitr` vignette, where the essence
is to include a chunk at the end,

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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")) {

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#' Generate Outline Documentation for a Data Set in Roxygen Format
#' 
#' Generates a shell of documentation for a data set or other object in roxygen format.
#' This function was created by editing \code{\link[utils]{promptData}} to replace
#' the old style \code{.Rd} formatting with code suitable for processing with \code{\link[devtools]{document}}.
#' 
#' @details
#' Unless \code{filename} is \code{NA}, a documentation shell for \code{object} is written in roxygen format to the file specified 
#' by \code{filename}, and a message about this is given.
#' 

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#' ---
#' title: Animate transition from PCA <--> tsne
#' ---
# idea from: https://jef.works/genomic-data-visualization-2024/blog/2024/03/06/akwok1/

#' ## Load packages and data
library(ggplot2) 
library(gganimate) 
library(Rtsne) 
library(patchwork)