Danielle Navarro
Sydney Research Bazaar, September 2019
slides.com/djnavarro/workflow
djnavarro
compcogscisydney.org
White space in a filename is a bad idea (partly for historical reasons)
Mistake #1
These are unnecessary copies of existing files
Mistake #2
Unnecessary files generated by MATLAB
Mistake #3
Mistake #4
Irrelevant files generated by the operating system
Mistake #5
Data stored in a format that is hard to work with unless you have a MATLAB licence
My data analysis scripts were in MATLAB so I can't run them anymore
Mistake #6
I honestly don't know why I used .eps graphics and nothing else
Mistake #7
If you don't want "future you" to be embarrassed, maybe think about your file names?
Mistake #8
Everything is dumped in one folder
Mistake #9
There is no README file!!!
Mistake #10
Inconsistent separator characters in file names
Mistake #11
Inconsistent naming scheme
Mistake #12
Names that are not very helpful to the human reader
Mistake #13
Template
Project
A good template should include instructions for how to use it
e.g., https://github.com/djnavarro/newproject
If you use GitHub you can create new projects directly from your template (or from someone elses!)
Okay... so why did I organise my template to produce file structures like this?
My folder structure is organised to mirror the structure of a typical research project
Files and folders use a consistent naming scheme that is easy for humans to read and easy for machines to read
Every folder has a README
(I cannot stress this enough... future you will love you for this)
README.md
Relying on free and open source tools so that other people can use it
Best practice version control using a git repository
Cloud storage for the project using GitHub
github.com
rstudio.com
r-project.org
osf.io
git-scm.com
psyarxiv.com
the gatekeepers' attempts to suppress the number of trans people allowed to transition occurred at virtually every step
indefinite periods of psychotherapy designed to evaluate whether or not they met the psychiatrists criteria
those who were allowed to begin the real-life test often faced additional obstacles as some gender identity clinics required trans people to begin their tests prior to starting hormone replacement therapy
exposed the transsexual to all sorts of discrimination, harassment and potential violence
little more than a hazing period
Fear and anxiety
Exhaustion
Gatekeeping
The in-between problem
All models and code available as documented repositories on GitHub
I am a believer in open science. You should have used OSF
We used a Bayesian approach for exploratory model building, evaluated by checking for robust performance on theoretically meaningful desiderata... blah blah blah
Give me a p-value
We like music?
Your favourite music sucks
"Unlike my cisgender counterparts I was never subject to sexual harassment in maths class, but on the other hand I didn’t attend very many of my classes either because I was too busy [self-harming] ... Looking back, my unwillingness to face up to how I felt about gender looks a lot like a trade-off: purchasing a form of male privilege at the expense of my mental health"
Everybody laughs because learning git is one of the hardest steps. We all go through this stage... and that's OKAY!
https://happygitwithr.com/
Transitioning from Dropbox to git + GitHub was a good exchange for me because it suits the work I do.
Neither system is better in general. Your trade-off will look different to mine!
GitHub issues threads are excellent for this: your commits can link the code changes to the issue thread
You can do this for regular scientific projects as well as software development
Email tends to prioritise other people's needs, especially the loudest people
Manage todo lists and time management explicitly (e.g., via todoist.com) gives you better control
asciify
rainbowr
A cognitive psychologist with some experience with R
A grumpy psychometrician with a limited time budget
A social psychologist who wants to believe
Hello? Was it something I said?
Photo by Sven Scheuermeier on Unsplash
Hey, how would you feel about posting research code to the web?
Oh hell no. People would call me stupid
What? You literally wrote a textbook on latent variable modelling and your Ph.D. research won a best paper award at Multivariate Behavior Research. You are not stupid
Yeah but my code has to be written in 20 minute consults and it's ugly. People are unkind about code
(seriously, you are terrible at sales)
tidyverse
lme
git
BayesFactor
lavaan
car
Shiny
R markdown
learning all the things
It can be hard to find a team within a single applied field...
#rstats
But there are people who will support you
Yay!
#rstats
base R
tidyverse
jsPsych
Matlab
JASP
BayesFactor
.Rmd
SQL
lme
JAGS
Stan
base R
tidyverse
jsPsych
Matlab
JASP
BayesFactor
.Rmd
SQL
lme
JAGS
Stan