sj-io

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

jph00

#!/usr/bin/env bash
###
# NB: You probably don't want this gist any more.
#     Instead, use this version from `fastsetup`:
#     https://github.com/fastai/fastsetup/blob/master/setup-conda.sh
###

set -e

cd

wolfv

name: CI

on:
  push:
    branches:
    - main
  pull_request:
    branches:
    - main

jennybc

library(tidyverse)
library(patchwork)

dat_wide <- tibble(
  x = 1:3,
  top = c(4.5, 4, 5.5),
  middle = c(4, 4.75, 5),
  bottom = c(3.5, 3.75, 4.5)
)

mikelove

suppressPackageStartupMessages(library(plyranges))
suppressPackageStartupMessages(library(AnnotationHub))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene))

ah <- AnnotationHub()
query(ah, c("K562","CTCF","unipk"))
peaks <- ah[["AH22543"]]
peaks <- peaks %>% keepStandardChromosomes(pruning.mode="coarse")

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

romainfrancois

library(purrr)
library(dplyr)

na_set <- function(x, p){
  p <- as_mapper(p)
  x[p(x)] <- NA
  x
}

# or something like this using case_when

amorgun

from sqlalchemy.dialects import postgresql

def bulk_upsert(session: Session, 
                items: Sequence[Mapping[str, Any]]):
  session.execute(
    postgresql.insert(MyModel.__table__)
    .values(items)
    .on_conflict_do_update(
      index_elements=[MyModel.id],
      set_={MyModel.my_field.name: 'new_value'},

tomsing1

schemaSpy

Here's how to use it to generate schema relationship diagrams for PostgreSQL databases.

Prerequisites

1. Download the jar file from here (the current version is schemaSpy_5.0.0.jar)
   • Note: There is a release candidate for version 6, but I couldn't get that to play nicely with graphviz on Mac OS 10.13
2. Get the PostgreSQL JDBC driver (either the JDBC3 or JDBC4 jar file is fine)
3. Install graphviz

MarkEdmondson1234

## see also http://blog.revolutionanalytics.com/2017/06/doazureparallel-updated.html on how to run on Azure
## and cloudyr project for AWS https://github.com/cloudyr/aws.ec2


# now also in docs: https://cloudyr.github.io/googleComputeEngineR/articles/massive-parallel.html
library(googleComputeEngineR)
library(future)

## auto auth to GCE via environment file arguments

mfansler

#!/bin/bash

## How to install ascp, in a gist.

## The URI below is not persistent! 
## Check for latest link: https://www.ibm.com/aspera/connect/
wget -qO- https://ak-delivery04-mul.dhe.ibm.com/sar/CMA/OSA/0a07f/0/ibm-aspera-connect_4.1.0.46-linux_x86_64.tar.gz | tar xvz

## run it
chmod +x ibm-aspera-connect_4.1.0.46-linux_x86_64.sh