Workshops

Here is the repository of Geek's lunch organization, where students from University Laval (Qc, Canada) store R scripts on tips about coding, packages skills in R statistical software, but sometimes other stuff related to biological sciences

No. 1 - Introduction to GitHub - by E. Champagne.

Some useful pages to install Git, configure GitHub, Rstudio, and connect them :

• https://frousseu.github.io/GHRSP/?fbclid=IwAR0PQvN1E1AjTXMROPDmY_HxbXF8OJuvFoax2M5Rk5l8e0zFAzffIOQ-IRU#introduction
• https://happygitwithr.com/

No. 2 - Dates in R using lubridate and base functions of R - by F. Dery

Details :

• https://lubridate.tidyverse.org/

Potential tutorials :

• https://lubridate.tidyverse.org/articles/lubridate.html

Cheatsheet :

• https://rawgit.com/rstudio/cheatsheets/master/lubridate.pdf

Comparison (page 4, table 3) of lubridate and R functions, and other ways to use it (you can download the article online from URL page) :

• https://www.jstatsoft.org/article/view/v040i03

No.3 - Visualization with base functions of R- by M. Leclerc

Some nice cheatsheets are available :

• htts://www.rstudio.com/resources/cheatsheets/
• http://publish.illinois.edu/johnrgallagher/files/2015/10/BaseGraphicsCheatsheet.pdf
• http://rpubs.com/SusanEJohnston/7953
• https://graphicsprinciples.github.io/

Use smart colours! Colorblind safe + Print version in black & white :

• http://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3

See also Sean Anderson's website :

• https://seananderson.ca/

A goldmine of content he's put together in there :

• https://seananderson.ca/ggplot2-fish554/
• https://seananderson.ca/courses/11-multipanel/multipanel.pdf

See paper titled :

"How can we make better graphs? An initiative to increase the graphical expertise and productivity of quantitative scientists"

• https://doi.org/10.1002/pst.1912

There is a lot of information out there on data visualization :

• https://serialmentor.com/dataviz/

No.4 - Spatial data visualization with R - by A. Brodeur

Useful links :

• https://www.jessesadler.com/post/geocoding-with-r/
• https://www.jessesadler.com/post/gis-with-r-intro/
• https://epsg.io

Packages and vignettes :

• https://r-spatial.github.io/sf/index.html
• https://r-spatial.github.io/mapview/
• https://rstudio.github.io/leaflet/

Books :

• https://geocompr.robinlovelace.net

Cheatsheet :

• sf : https://github.com/rstudio/cheatsheets/raw/master/sf.pdf
• crs : https://www.nceas.ucsb.edu/~frazier/RSpatialGuides/OverviewCoordinateReferenceSystems.pdf
• sp : https://www.maths.lancs.ac.uk/~rowlings/Teaching/UseR2012/cheatsheet.html
• raster: https://rpubs.com/etiennebr/visualraster

No.5 - Code Hygiene for R using Rstudio - by L. De Vriendt

Useful links :

• https://medium.com/@anishmahapatra/code-hygiene-dont-laugh-it-off-2a5aebcdd84b
• https://waterdata.usgs.gov/blog/intro-best-practices/
• https://style.tidyverse.org/syntax.html
• https://www.r-bloggers.com/r-best-practices-r-you-writing-the-r-way/
• https://stat.ethz.ch/Teaching/maechler/R/useR_2014/Maechler-2014-pr.pdf
• https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R/

No.6 - Good and bad practices sample identification and management - by M. Bonin

See the PDF presentation

No.7 - Introduction to Integrated Population Models (IPM) R using R and Winbugs - by B. Vuillaume

The folder contains

• A PDF presentation

No.8 - Random intercepts and interpretation using R and lme4 - by M. Le Moullec

The folder contains

• A .txt file
• An R script that is a guide to mixed models, proper way to look for random intercept, bootstrapped confidence intervals
• A .zip with data from Dryad

No. 9 - How to keep-up with the litterature? - by E. Champagne.

A page of notes (to come) to follow what has been said during the discussion