HomogenFishOntario

📖 Cazelles et al. (2019) DOI:10.1111/gcb.14829 - research compendium

Analysis pipeline used in "Homogenization of freshwater lakes: recent compositional shifts in fish communities are explained by gamefish movement and not climate change" by Cazelles et al. (2019) DOI:10.1111/gcb.14829.

⚠️ We are not allowed to share the exact lake locations, therefore, the context map and 3 supplementary figures cannot be reproduced with this research compendium. The data included in this package are released under CC BY NC.

How to reproduce the analysis?

Two options:

1. use the binder;
2. install and use this package.

Moreover the vignettes "Reproduce the analysis carried out in Cazelles et. al (2019)" guides you through the different functions included in the package.

Using the binder

You can use Binder by clicking on the following badge: which sets up an R environment (takes 15-20min ⌛) and then a launches an RStudio instance. Once done, one can simply run:

# this first step is quick cause all packages required are already installed!
library(devtools)
load_all()
pipeline()

NB: the binder was created with the great R package holepunch!

Install and use this R package

First, install the package:

install.packages("remotes")
remotes::install_github("McCannLab/HomogenFishOntario")

This should install all dependencies, but in case you are encountering difficulties with the R packages available on GitHub, use the following:

remotes::install_github(
  c("KevCaz/ecoocc", "inSileco/graphicsutils", "inSileco/inSilecoMisc")
)

Once installed, you can simply reproduce the analysis like so:

HomogenFishOntario::pipeline()

An R 📦?

The form of an R package in a GitHub repository is quite convenient:

• to share of the analysis pipeline;
• to check code quality (even without a proper set of test, several aspects are covered when the package is checked);
• to report potential issues.