Notes from a data witch

A blog by Danielle Navarro

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Greyscale photo of a woman (Lizzo) striking a magnificent pose in front of a brick wall with musical notation painted on it

Pharmacometric simulation with rxode2
R
Pharmacometrics
Basically the same post as the last one. It’s a brief introduction to pharmacometric simulation, but this time I’m using rxode2 instead of mrgsolve
Danielle Navarro
Aug 28, 2023

Pink and blue pill against a blue background

Pharmacometric simulation with mrgsolve
R
Pharmacometrics
Yet another post in the ever-expanding series where Danielle teaches herself pharmacometric modelling, which I’m certain is thrilling to everyone
Danielle Navarro
Aug 14, 2023

Cover art to Paul Simon's 1975 single '50 ways to leave your lover'

Four ways to write assertion checks in R
R
It’s not 50 ways to leave your lover, but spend enough time talking about assertive programming in the bedroom and you’ll only have 49 more to discover
Danielle Navarro
Aug 8, 2023

Hand-drawn scientific diagram from 1937 showing 'blood circulation', 'tissue boundaries', and adding pharamacometric notation

Getting started with Torsten
R
Stan
Torsten
Pharmacometrics
Another small step along the path to Bayesian pharmacometrics
Danielle Navarro
Jul 15, 2023

The Death of Julius Caesar (1806) by Vincenzo Camuccini. A painting depicting, yes, the assassination of Julius Caesar.

Beware the IDEs of Windows (Subsystem for Linux)
Linux
R
Setting up nice developer environments on a Windows / Ubuntu-for-WSL system with the help of RStudio Server and the VS Code WSL extension
Danielle Navarro
Jul 2, 2023

Stylised art showing a balrog riding a dragon. The piece is called 'Gothmog at the Storming of Gondolin', and is CC-BY licenced by Tom Loback

Makefiles. Or, the balrog and the submersible
Reproducibility
Fly, you fools!
Danielle Navarro
Jun 30, 2023

Photo of many small white tables in an outdoor courtyard

Extracting tables from pdf files with tabulizer
R
Data Wrangling
Something nicer than the last post
Danielle Navarro
Jun 16, 2023

A map of the United States with arrows showing movement across states

On living in dark times
R
Statistics
Estimating the number internally displaced transgender people in the United States.
Danielle Navarro
Jun 15, 2023

The LGBT rainbow flag

A little ANSI trickery
R
Fun and games with asciicast and cli. There’s really not much to this one except a little bit of personal entertainment
Danielle Navarro
Jun 14, 2023

An image showing two pieces of paper pinned to a board

Pins and needles
R
Reproducibility
Learning my lessons the hard way
Danielle Navarro
Jun 12, 2023

A photo of numerous pills and capsules in many different colours

Building a population pharmacokinetic model with Stan
Statistics
Pharmacometrics
R
Stan
NONMEM
Bayes
In which the author works her way through the first part of an online tutorial, rewrites some NONMEM code in Stan, and takes notes
Danielle Navarro
Jun 10, 2023

Book cover for 'Software Design by Example'

Software design by example
Software Design
Javascript
R
Regular Expressions
A book review, sort of. Not really. Look, Greg sent me a copy and I had fun reading it. okay?
Danielle Navarro
May 31, 2023

Hex sticker image for the santoku R package

Santoku
R
Data Wrangling
On the small joys of clean, single-purpose R packages.
Danielle Navarro
May 22, 2023

Colourful photo of many pills and tablets

Pharmacokinetic ODE models in Stan
Statistics
Pharmacometrics
Stan
Bayes
MCMC
R
A discussion of one- and two-compartment pharmacokinetic models with model implementations in Stan, covering both first-order dynamics and Michaelis-Menten kinetics.
Danielle Navarro
May 16, 2023

Many white pills shown against a blue background

Non-compartmental analysis
Statistics
Pharmacometrics
R
A heavily oversimplified discussion of a simple pharmacokinetic tool, written as an exercise in teaching myself something new. Learning new things is always fun
Danielle Navarro
Apr 26, 2023

Katy Perry in a wedding dress, looking apprehensive

A personal essay on Bayes factors
Statistics
Bayes
In which the dead return to life and the author has opinions
Danielle Navarro
Apr 12, 2023

Promotional image for the film 'Metropolis'

The Metropolis-Hastings algorithm
Statistics
MCMC
A note that I wrote for a computer science class I taught all the way back in 2010
Danielle Navarro
Apr 12, 2023

Pixellated image of black, white, and grey tiles

How to run R code in the browser with webR
R
WebR
In which the author gets unreasonably excited about a new thing
Danielle Navarro
Apr 9, 2023

Spiralling squares and circles in blue, pink, and white

Generative art with grid
Art
R
Grid Graphics
I decided it was time to learn more about the grid package in R, and so naturally used it to make generative art
Danielle Navarro
Mar 31, 2023

Generative art that looks a little like a topographic map of a coastline

Shattered landscapes
Art
R
Using ambient and rayshader to create weird, broken landcape images in R
Danielle Navarro
Mar 13, 2023

A donut shape in brown and white with many criss-crossing lines inside

Fun and games with p5.js and observable.js in quarto
Art
P5
Observable
Javascript
Quarto
Okay it’s a short post in which I teach myself a bit of p5.js, but it does have five different donut examples which seems cool?
Danielle Navarro
Jan 14, 2023

Many tan and white squares arranged in concentric circles against an orange background

Deploying R with kubernetes
R
Docker
Kubernetes
Plumber
In which it is painfully clear that the author is trying to figure it all out as she goes
Danielle Navarro
Jan 10, 2023

A 4x4 grid of cartoon whales, all in the style of the Docker logo

Playing with docker and the github container registry
Linux
R
Docker
In which the author learns how to use docker and, in her usual fashion, goes a little bit overboard. But there are also generative art whales, so that’s nice.
Danielle Navarro
Jan 1, 2023

The Arch Linux logo rendered as ASCII art

btw I use Arch now
Linux
R
There is no reason for this.
Danielle Navarro
Dec 31, 2022

Soft pastel hexagons in a blurry watercolour style

A very strange year
A wrap up of my 2022. Even by the standards of the recent past this has been a very weird year for me. A lot has happened, both professionally and personally. I’m still…
Danielle Navarro
Dec 26, 2022

Many blue and yellow rectangles arranged in concentric circles

Queue
Parallel Computing
R
Object-Oriented Programming
It is a truth universally acknowledged, that a post about multithreading must be in want of an async trick
Danielle Navarro
Dec 22, 2022

Grids of coloured blocks in a vaguely rainbow-like ordering

Crayola crayon colours
R
Data Wrangling
Data Visualisation
Am I bored in the house? Yes. And am I in the house bored? Also yes. But do I have rvest and a stubborn desire not to allow the horrors of ‘data encoded in the CSS style’ to…
Danielle Navarro
Dec 18, 2022

An irregular tiling of rectangles in red, green, and brown.

Unpacking Arrow Datasets
Apache Arrow
R
A comment on how Datasets work in Apache Arrow. I’m not really sure who the audience for this one. Am I just talking to myself? Probably.
Danielle Navarro
Nov 30, 2022

A greyscale image of a mammoth

Everything I know about Mastodon
Mastodon
Social Media
A hastily written guide for data science folks trying to navigate the fediverse.
Danielle Navarro
Nov 3, 2022

Image of a biplane flying towards clouds

Building an Arrow Flight server
Apache Arrow
Networking
R
Python
A step by step walkthrough introducing the reader to Arrow Flight, with examples in R and Python
Danielle Navarro
Oct 18, 2022

Screenshot from an old news paper. Text reads 'The Arrow hits the mark'

Data transfer between Python and R with rpy2 and Apache Arrow
Apache Arrow
R
Python
A Pythonic approach for sharing Arrow Tables between Python and R. This is the second in a two-part series on data transfer. In this post I discuss how the rpy2 Python…
Danielle Navarro
Sep 16, 2022

Close-up of scales on a reticulated python

Passing Arrow data between R and Python with reticulate
Apache Arrow
R
Python
In a multi-language ‘polyglot’ data science world, it becomes important that we are able to pass large data sets efficiently from one language to another without making…
Danielle Navarro
Sep 9, 2022

Image of six open face sandwiches

Sudo ask me a password
Linux
Credentials
R
Resolving a little quirk in managing packages with pak on linux
Danielle Navarro
Sep 4, 2022

Data visualisation that looks like a street map of New York City

How to visualise a billion rows of data in R with Apache Arrow
Apache Arrow
Data Visualisation
R
In which the author grapples with the awkward question of what data visualisation really means when you have a staggering amount of data to work with
Danielle Navarro
Aug 23, 2022

Image of a woman dancing surrounded by tables

Arrays and tables in Arrow
Apache Arrow
R
In which the author discusses arrays, chunked arrays, record batches, tables, and datasets in the R interface to Apache Arrow. Masochism is mentioned, and the music of…
Danielle Navarro
May 25, 2022

A laptop, with a small jug and book adjacent to it

Porting a distill blog to quarto
Quarto
Blogging
Reproducibility

I have moved this blog from distill over to quarto, and taken notes. A year after starting the blog, this promises to be an interesting reproducibility test

Danielle Navarro
Apr 20, 2022

Photo of dried grass

Using Amazon S3 with R
Amazon S3
R
Somehow I was convinced that using Amazon S3 would be a supremely difficult thing to learn, kind of like learning git and GitHub for the first time. Thankfully, it’s…
Danielle Navarro
Mar 17, 2022

Abstract generative art in red and black

Data types in Arrow and R
Apache Arrow
R
A post describing fundamental data types in R and Apache Arrow, and how data is exchanged between the two systems. It covers conversion of logicals, integers, floats…
Danielle Navarro
Mar 4, 2022

Photo of a phone displaying the twitter logo crossed out

R scripts for twitter mutes and blocks
Twitter
R
Social Media
Social media safety tools like muting and blocking are often misused, but for people who are targeted for harassment they are powerful and important. This is a brief…
Danielle Navarro
Feb 11, 2022

Photo of the cast of The Magicians

Binding Apache Arrow to R
Apache Arrow
R
I’ve been learning how to program with Apache Arrow inside R, and also I have been watching the SyFy show “The Magicians” obsessively. For no sensible reason I wrote a blog…
Danielle Navarro
Jan 18, 2022

Photo of some cranberries spilling out of a glass jar

Setting CRAN repository options
R

A quick post on how to use RStudio public package manager instead of a standard CRAN mirror, and an example of why that can be useful sometimes.

Danielle Navarro
Jan 10, 2022

Green lit signage showing white arrows

Getting started with Apache Arrow
Apache Arrow
R
I’ve been wanting to learn the basics of Apache Arrow a while: this is the story of how an R user learned to stop worrying and love a standardised in-memory columnar data…
Danielle Navarro
Nov 19, 2021

Woman holding a gun

Data serialisation in R
Serialisation
R
A terrifying descent into madness, or, an explanation of how R serialises an in-memory data structure to summon a sequence of bytes that can be saved or transmitted.…
Danielle Navarro
Nov 15, 2021

Abstract generative art with concentric jagged polygons

Unpredictable paintings
Art
R
An example showing how to build a generative art system in R. The post walks through some of the creative and design choices that are involved, and highlights how much of a…
Danielle Navarro
Nov 1, 2021

Generative art that looks like several stylised trees

Generative art resources in R
Art
R

An extremely incomplete (and probably biased) list of resources to help an aspiring generative artist get started making pretty pictures in R

Danielle Navarro
Oct 19, 2021

Abstract generative art in black and white

How to mint digital art on HEN
Art
Not every artist wants to make cryptoart, and that’s okay. Others do, and that’s okay too. But if you want to try it out in a socially responsible way, it takes a bit of…
Danielle Navarro
Sep 26, 2021

Photo of Britney Spears performing

Visualising the hits of Queen Britney
Tidy Tuesday
Data Visualisation
R
A gentle walkthrough of a few data wrangling and visualisation tools using the Billboard 100 data for this weeks Tidy Tuesday. Pitched at beginners looking to refresh their…
Danielle Navarro
Sep 14, 2021

Flowing generative art that looks a little like jasmine flowers

Art, jasmines, and the water colours
Art
R

An essay and tutorial covering a few useful art techniques in R

Danielle Navarro
Sep 7, 2021

Keys hanging from colourful lego-block keyholder

Managing GitHub credentials from R, difficulty level linux
Git
Credentials
Linux
R

A sick sad story in which a humble R user was forced to learn something about how linux stores passwords and, more importantly, got R to use her GitHub credentials properly

Danielle Navarro
Aug 8, 2021

Generative art with swirly yellow hearts against a red background

Generative art in R
Art
R

Comments on an exhibit I contributed to as part of useR!2021

Danielle Navarro
Jul 8, 2021

Cartoon hearts on a grid of rectangles

Bootstrap cards in distill
Blogging
Bootstrap
Distill
R

How to enable bootstrap 4 on a distill website, even though you probably don’t need to. I like it though because I get to add pretty bootstrap cards

Danielle Navarro
Apr 19, 2021

Photo of a page with handwriting repeating 'I must not tell lies'

Pretty little CLIs
Command Line
R
How to make a gorgeous command line interface in R using the cli package. Somewhere along the way I accidentally learned about ANSI control codes, which strikes me as…
Danielle Navarro
Apr 18, 2021

Generative art that looks like a blueish bunch of flowers

Welcome to the jungle
Blogging
Reproducibility
Distill

I have reluctantly decided to create a new blog. Some thoughts on what I hope to achieve, having tried my hand at blogging so very many times before

Danielle Navarro
Apr 5, 2021
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