Michael Friendly friendly

## diabetes-pca-tsne.R
#' ---
#' 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)

## measerr_demo.R
#' Demonstrate Effect of Measurement Error in Regression
#'
#' This function takes a variables x and y and demonstrates the effect of adding random normal errors
#' to one or both of the coordinates. For each level of \code{err}, it adds \code{rnorm(0, err * SD)}
#' to the corresponding x and/or y and displays the data points, a data ellipse and the fitted
#' regression line overlaid on the corresponding plot of the un-perturbed data.
#'
#' My thought was to make this general, to be used either in an interactive demonstration or an animated
#' graphic using the \pkg{animate} package. There is something wrong with my logic, because it doesn't
#' work for an interactive demo.

## use_data_doc.R
#' 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 to the file specified
#' by \code{filename}, and a message about this is given.
#'

## Rpackages_bib.R
#' Generate a BibTeX file of all installed packages
#'
#' This function finds all packages installed in your R library and calls
#' `citation()` for each, collecting the BibTeX entries and writing these to
#' a file. It handles situations where there are multiple citations for a package.
#'
#' @param filename  Name of the .bib file to write to.
#' @param header    Include a header giving `sessionInfo()` ?
#' @param preamble  Preamble for the BibTeX file
#' @param prefix    String to prefix the in the bibtex key

## bib-at-end.Rmd
# 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,

## wavelength_to_rgb.R
#' Wavelength to RGB
#'
#' This function converts a given wavelength of light to an
#' approximate RGB color value.
#'
#' @param wavelength A wavelength value, in nanometers, in the human visual range from 380 nm through 750 nm.
#'        These correspond to frequencies in the range from 789 THz through 400 THz.
#' @param gamma The \eqn{\gamma} correction for a given display device. The linear RGB values will require
#'        gamma correction if the display device has nonlinear response.
#' @return a color string, corresponding to the result of \code{\link[grDevices]{rgb}} on the

## term_info.R
#' Extract information about two-way terms in a loglinear model
#'
#' This function is designed for use with an association graph showing the pairwise
#' dependencies among categorical variables in a loglinear model for frequencies
#' fit using \code{\link[MASS]{loglm}} or \code{\link[stats]{glm}} in a poisson family.
#' The goal is to show
#' an association graph diagram with edges indicating the strength of associations
#' between each pair of variables.
#'
#' The weight for two-way terms can be found using the deviance or LRT or AIC statistic

## test-newcommand.html
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.0.37">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


<title>Quarto: Test LaTeX newcommands in HTML doc</title>

## 3d-demo.R
#' ---
#' title: "3D demonstrations of linear transformations and matrix inverse"
#' author: "Michael Friendly"
#' date: "30 Sep 2016"
#' ---

#' Start with a unit cube, representing the identity matrix. Show its transformation
#' by a matrix $A$ as the corresponding transformation of the cube.
#'
#' This also illustrates the determinant, det(A), as the volume of the transformed

## minard-plot.R
#' # Reproduce Minard's March on Moscow Graphic using ggplot2

#' This gist extends the examples given in the HistData package. It explicitly
#' shows the construction of the plot as layers, and adds the plot of temperature
#' vs. longitude below the plot of troop strength.

#' ## Load data and required packages
data(Minard.troops, package="HistData")
data(Minard.cities, package="HistData")
data(Minard.temp, package="HistData")
	#' ---
	#' 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)
	#' Demonstrate Effect of Measurement Error in Regression
	#'
	#' This function takes a variables x and y and demonstrates the effect of adding random normal errors
	#' to one or both of the coordinates. For each level of \code{err}, it adds \code{rnorm(0, err * SD)}
	#' to the corresponding x and/or y and displays the data points, a data ellipse and the fitted
	#' regression line overlaid on the corresponding plot of the un-perturbed data.
	#'
	#' My thought was to make this general, to be used either in an interactive demonstration or an animated
	#' graphic using the \pkg{animate} package. There is something wrong with my logic, because it doesn't
	#' work for an interactive demo.
	#' 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 to the file specified
	#' by \code{filename}, and a message about this is given.
	#'
	#' Generate a BibTeX file of all installed packages
	#'
	#' This function finds all packages installed in your R library and calls
	#' `citation()` for each, collecting the BibTeX entries and writing these to
	#' a file. It handles situations where there are multiple citations for a package.
	#'
	#' @param filename Name of the .bib file to write to.
	#' @param header Include a header giving `sessionInfo()` ?
	#' @param preamble Preamble for the BibTeX file
	#' @param prefix String to prefix the in the bibtex key
	# 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,
	#' Wavelength to RGB
	#'
	#' This function converts a given wavelength of light to an
	#' approximate RGB color value.
	#'
	#' @param wavelength A wavelength value, in nanometers, in the human visual range from 380 nm through 750 nm.
	#' These correspond to frequencies in the range from 789 THz through 400 THz.
	#' @param gamma The \eqn{\gamma} correction for a given display device. The linear RGB values will require
	#' gamma correction if the display device has nonlinear response.
	#' @return a color string, corresponding to the result of \code{\link[grDevices]{rgb}} on the
	#' Extract information about two-way terms in a loglinear model
	#'
	#' This function is designed for use with an association graph showing the pairwise
	#' dependencies among categorical variables in a loglinear model for frequencies
	#' fit using \code{\link[MASS]{loglm}} or \code{\link[stats]{glm}} in a poisson family.
	#' The goal is to show
	#' an association graph diagram with edges indicating the strength of associations
	#' between each pair of variables.
	#'
	#' The weight for two-way terms can be found using the deviance or LRT or AIC statistic
	<!DOCTYPE html>
	<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

	<meta charset="utf-8">
	<meta name="generator" content="quarto-1.0.37">

	<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


	<title>Quarto: Test LaTeX newcommands in HTML doc</title>
	#' ---
	#' title: "3D demonstrations of linear transformations and matrix inverse"
	#' author: "Michael Friendly"
	#' date: "30 Sep 2016"
	#' ---

	#' Start with a unit cube, representing the identity matrix. Show its transformation
	#' by a matrix $A$ as the corresponding transformation of the cube.
	#'
	#' This also illustrates the determinant, det(A), as the volume of the transformed
	#' # Reproduce Minard's March on Moscow Graphic using ggplot2

	#' This gist extends the examples given in the HistData package. It explicitly
	#' shows the construction of the plot as layers, and adds the plot of temperature
	#' vs. longitude below the plot of troop strength.

	#' ## Load data and required packages
	data(Minard.troops, package="HistData")
	data(Minard.cities, package="HistData")
	data(Minard.temp, package="HistData")