Biostats uOttawa
This site regroup the different resources developed for the biostatistic courses at the university of Ottawa by Julien Martin
Biostatistic courses at uOttawa
Applied biostatistics with R (Bio4x58 / Bio5x58)
- Offered to both undergraduate (Bio4x58) and graduate students (Bio5x58) in english (Bio4158 / Bio5158) and french (Bio4558 / Bio5558)
- Content:
- Foundations of statistics (distributions, CIs, p-values, central limit theorem, Bayesian thinking, …)
- linear models (t-test, ANOVA, regression, ANCOVA, general linear model)
- Intro to R and then everything done in R
- Prerequisite:
- an introduction class to statistics is needed (MAT279 or equivalent is required)
- No (or limited) knowledge of R and no (or limited) knowledge of stats expected.
- Course sites: BioX158: english / BioX558: french
- Book On the R-way to hell / Sur le chemin de l’enf-R is used as course manual with course specific chapters indicated in the table and on course website.
Advanced biostatistics and open science (BIO 8940)
- Bilingual course for graduate students
- Content:
- Brief revision of linear models (assume to be known and a prerequisite)
- Generalized linear model
- Mixed models (lmm and glmm)
- Bayesian approach
- Everything done in R
- Quarto / Rmarkdown
- Prerequisite:
- a functional knowledge of R (loading data, running basic linear models, and making plots)
- a good understanding of linear models
- essentially Bio8940 is a great next steps after completing Bio4x58.
- Course site
- Book On the R-way to hell / Sur le chemin de l’enf-R is used as course manual with course specific chapters indicated in the table and on course website.
Book and tutorials
Statistics with R: On the R-way to hell
This is an introduction to statistics and R book with a multilingual approach. The book is covering an introduction to the basic use of R (data loading, wrangling and plotting), as well as programming, use of github and R markdown /Quarto with R Studio and VS code. It then covers a lot of statistical subjects.
The book (still under development) is available in English and French. I will add more languages later this year hopefully with help of volunteers.
How to fit an animal model
Statistical consulting
As Part of my service in the Biology department, I provide statistical consulting. Please just contact me to book an appointment to discuss your stat problems.
Please bring with you (or send me in advance):
- your data
- your R code (should at least load the data into R)
- a clear working hypothesis
Statistical consulting does not mean that you have to add me as a co-author. I just ask that you add me to the “Acknowledgements” of your thesis and manuscript/article. Repeated consulting on the same problem and my implication on developing project specific coding/analysis might lead to co-authorship, but this usually all comes naturally and is always discussed openly with the student(s) and PI(s). As yet, I have never requested to become a co-author and I was offered co-authorship for 3 manuscripts over > 50 projects discussed.
Quarto templates for reproducible science
A few quarto templates I developed to facilitate open-science for students at uOttawa
bio-uo-proposal:
quarto extension providing 1 new pdf output format (bio-uo-proposal-pdf). I am working on a docx version but tweaking the frontpage is tricky with word document.bio-uo-thesis:
quarto extension providing two new output formats for book projects: an html (bio-uo-thesis-html) and a pdf (bio-uo-thesis-pdf) generating a website (to be hosted on github pages or similar) and a pdf of the thesis adequately formatted for uOttawa (at least biology)