friendly’s gists

friendly / penguin-colors.R

Created August 10, 2024 02:50

R functions for consistent sets of colors for penguins examples

	#' ---
	#' 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")) {

friendly / diabetes-pca-tsne.R

Created April 3, 2024 13:21

Animation of PCA vs. tSNE dimension reduction

	#' ---
	#' 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)

friendly / measerr_demo.R

Created November 17, 2023 18:09

Measurement error demonstration

	#' 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.

friendly / use_data_doc.R

Last active June 29, 2024 02:36

Generate Outline Documentation for a Data Set in Roxygen Format

	#' 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.
	#'

friendly / Rpackages_bib.R

Created June 14, 2023 20:37

Generate a BibTeX file of all installed packages

	#' 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

friendly / bib-at-end.Rmd

Created June 14, 2023 15:28

Accumulating R package references in a Quarto book

	# 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,

friendly / term_info.R

Last active February 12, 2023 16:36

Extract information about two-way terms in a loglinear model

	#' 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

friendly / test-newcommand.html

Created August 15, 2022 18:23

Quarto: Test LaTeX newcommands in HTML doc

	<!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>

friendly / clark-lord-paradox.R

Created February 7, 2022 19:08

Demonstrate Lord's Paradox example, following Michael Clarke

	# 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
	#'

friendly / phys-models.bib

Created November 28, 2020 17:49

Bibliography for physical analogs of statistical models

	@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},

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