Lab notebook

The role of climate and competition on tree range distribution: a multi-scale approach from individuals to metapopulation dynamics

Preface

In this book, I present the methods for quantifying the effect of competition and climate on the demographic dynamics of 31 North American forest trees. While I try my best to make this approach as transparent as possible, I will likely miss specific steps. In such cases, you can find the missing information within the accompanying code. If navigating my code was not enough to answer your question, feel free to email me.

This document is a dynamic report generated using R and Quarto. It is designed to ensure the reproducibility of the results, but note that some sections involve intensive computational processing. Rendering the entire document would require several days, mainly due to the Bayesian model fitting and sensitivity analysis of the IPM, which were executed on a cluster.

I have included the code within this document to facilitate reproducibility, but specific code chunks have been turned off (using eval=FALSE). To replicate this vignette, you will need to download the complete dataset and parameters that are stored in the ownCloud server: (https://doc.ielab.usherbrooke.ca/s/83YSAiLAGeLm682. Note that the total size of the folder is approximately 40 GB. Once you have downloaded the parameters, create a file named _data.path and place it at the root of this project (./suppMaterial/_data.path). Inside this file, specify the local path of the downloaded data. For instance, if you download the full content of the server into the folder book_forest-demography-IPM/data/, the content of the _data.path file should be:

data/

Finally, if Quarto and LaTex are installed, compile this document with:

quarto render .