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Modern R Development Guide

This document captures current best practices for R development, emphasizing modern tidyverse patterns, performance, and style. Last updated: August 2025

Core Principles

1. Use modern tidyverse patterns - Prioritize dplyr 1.1+ features, native pipe, and current APIs
2. Profile before optimizing - Use profvis and bench to identify real bottlenecks
3. Write readable code first - Optimize only when necessary and after profiling
4. Follow tidyverse style guide - Consistent naming, spacing, and structure

rmcelreath

# proxy confounder problem
# cf https://twitter.com/y2silence/status/1251151157264674816

# note that I rename X1,X2 to A,B and A to X
# The DAG:
# X -> Y
# X <- U -> Y
# A <- U -> B

# Can we use A and B to deconfound X->Y?

gaborcsardi

Run usethis::use_pkgdown_travis()

❯ usethis::use_pkgdown_travis()
✔ Setting active project to '/Users/gaborcsardi/works/ps'
✔ Adding 'docs/' to '.gitignore'
● Set up deploy keys by running `travis::use_travis_deploy()`
● Insert the following code in '.travis.yml'
  before_cache: Rscript -e 'remotes::install_cran("pkgdown")'

rmcelreath

# script for examples in Bayes@Lund2017 presentation

# joint model example
notes_max <- 10
rate_max <- 5
pm <- matrix( NA , nrow=rate_max+1 , ncol=notes_max+1 )
for ( i in 1:(rate_max+1) )
    for ( j in 1:(notes_max+1) )
        pm[i,j] <- dpois( j-1 , lambda=i ) * (1/(rate_max+1))

garrettheaver

#!/bin/sh

# mass deskew scanned files via command line
# - requires: ImageMagick and Deskew Tool
# - see http://galfar.vevb.net/wp/tag/deskew

for d in "$@"; do

  file=`basename "$d" .pdf`
  cd "`dirname "$d"`"

rmaia

require(rstan)
require(geiger)
require(MCMCglmm)

# load data
data(geospiza)
dat <- geospiza$geospiza.data

# create fake sample of trees
tr <- drop.tip(geospiza$geospiza.tree, 'olivacea')

timelyportfolio

#almost entirely based on the 02_text and 03_mpg examples provided by RStudio Shiny
#all credit belongs to them


if (!require(PerformanceAnalytics)) {
  stop("This app requires the PerformanceAnalytics package. To install it, run 'install.packages(\"PerformanceAnalytics\")'.\n")
}

if (!require(quantmod)) {
  stop("This app requires the quantmod package. To install it, run 'install.packages(\"quantmod\")'.\n")

ramnathv

Here is how you can make a table in GFM format using knitr + ascii

render_gfm()
gfm_table <- function(x, ...) {
    require(ascii)
    y <- capture.output(print(ascii(x, ...), type = "org"))
 # substitute + with | for table markup

mages

## Markus Gesmann, January 2012
## Please install the following R packages first:
## data.table, doBy, plyr, reshape, sqldf, e.g. via
## install.packages(c("data.table", "doBy", "plyr", "reshape", "sqldf"))

f <- function(x) x^2
sapply(1:10, f)

do.call("rbind", as.list(
  by(iris, list(Species=iris$Species), function(x){

jseabold

"""
Context manager or function to send text messages to your phone when a
process is done.

Edit the global variables. You might be able to find your phone e-mail 
address here: http://tinywords.com/about-old/mobile/

Usage:
with SendText("long running process"):
    do_something()