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,

## 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>

## clark-lord-paradox.R
# Demonstrate Lord's Paradox example, following Michael Clarke
# https://m-clark.github.io/docs/lord/index.html

library(ggplot2)
library(dplyr)

#' ## Data example: Initial and final weight for boys & girls
#'
#' Make a plot showing the distribution of gain scores perpendicular to the line of slope = 1
#'

## phys-models.bib
@comment{Physical analogs for statistical models}

@article{GainesPalphrey:1932,
 ISSN = {00368075, 10959203},
 URL = {http://www.jstor.org/stable/1658643},
 author = {W. L. Gaines and J. R. Palfrey},
 journal = {Science},
 number = {1977},
 pages = {472--474},
 publisher = {American Association for the Advancement of Science},

## PartySupport-2019.R
# Stacked Barplot of Support for Political Parites by Province in 2019 Canadian Federal Election
# written by Christopher D. Green
# 22 October 2019
# additions by MF 31 Oct 2019

provs<-c("BC","AB","SK","MB","ON","QC","NB","NS","PE","NF") # names of the provinces
pops<-c(5.0,4.3,1.2,1.4,14.4,8.4,0.8,1.0,0.2,0.5)           # populations in millions

con<-c(34.1,69.2,64.3,45.4,33.2,16.0,32.8,25.7,27.4,28.0)   # % support for Conservatives
lib<-c(26.1,13.7,11.6,26.3,41.5,34.2,37.6,41.3,43.6,44.7)   # % support for Liberals
	#' ---
	#' 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,
	#' 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>
	# Demonstrate Lord's Paradox example, following Michael Clarke
	# https://m-clark.github.io/docs/lord/index.html

	library(ggplot2)
	library(dplyr)

	#' ## Data example: Initial and final weight for boys & girls
	#'
	#' Make a plot showing the distribution of gain scores perpendicular to the line of slope = 1
	#'
	@comment{Physical analogs for statistical models}

	@article{GainesPalphrey:1932,
	ISSN = {00368075, 10959203},
	URL = {http://www.jstor.org/stable/1658643},
	author = {W. L. Gaines and J. R. Palfrey},
	journal = {Science},
	number = {1977},
	pages = {472--474},
	publisher = {American Association for the Advancement of Science},
	# Stacked Barplot of Support for Political Parites by Province in 2019 Canadian Federal Election
	# written by Christopher D. Green
	# 22 October 2019
	# additions by MF 31 Oct 2019

	provs<-c("BC","AB","SK","MB","ON","QC","NB","NS","PE","NF") # names of the provinces
	pops<-c(5.0,4.3,1.2,1.4,14.4,8.4,0.8,1.0,0.2,0.5) # populations in millions

	con<-c(34.1,69.2,64.3,45.4,33.2,16.0,32.8,25.7,27.4,28.0) # % support for Conservatives
	lib<-c(26.1,13.7,11.6,26.3,41.5,34.2,37.6,41.3,43.6,44.7) # % support for Liberals