Advanced stats and Open Science

BIO8940

Julien Martin

BIO 8940

2026-01-19

A bit about …

… me

• Evolutionary ecologist

• Not a statisticians by training

• Complex data

• Enjoy coding

• Humour of a 5 years old

… you

• Name

• PI

• Subject

• R knowledge

• Expectation from the course

Structure of the course

Topics

• Intro to github with exercises
• Intro to Open science
• Intro to rmarkdown and to workflowr
• Mixed models
  • Intro, why, when and how
  • Non gaussian, non-linear ?
  • multivariate ?
• p-values and their limits

Teaching style

• Minimum slides from myself
• flipped classroom or learning by problems
• Session = mixed of lecture, discussion and exercises

Schedule

See course website

Assessment

In class (50%)

• participation to discussion (20%)
• presentation on a given topic in small teams (30%)

Project (50%)

• analysis of data using techniques from courses or beyond
• Report written using Quarto
• Oral examination

Software and accounts

Softwares

• R (version 4.0 or higher)
• Text editor: Rstudio or VSCode
• R packages (up to date)
  • open science: quarto
  • mixed models: lme4, gremlin, glmmTMB, MCMCglmm
  • latex: full version or tinytex

Accounts

• github (https://github.com/)
• Open Science Framework (OSF, https://osf.io/)

What is expected from you

What is expected from you

• Weekly Reading

• In class participation

• Do the praticals