aariq/pca-vs-pls

Research compendium for "Using the right tool for the job: understanding the difference between unsupervised and supervised analyses of multivariate ecological data."

Research compendium for "Using the right tool for the job: understanding the difference between unsupervised and supervised analyses of multivariate ecological data."

Research compendium for Scott ER, Crone EE (2021) Using the right tool for the job: the difference between unsupervised and supervised analyses of multivariate ecological data. Oecologia. https://doi.org/10.1007/s00442-020-04848-w

This repository contains the R scripts (.R and .Rmd files) necessary to reproduce results from this paper. Datasets generated by these scripts are found in the "data" directory. To run scripts "1-muir-data-wrangling.R" and "2-muir-analys.Rmd", you will need to download the dataset from Muir et al (2017), from Data Dryad. Unzip the download and place the contents inside "data/muir/". Figures and tables generated by the analysis are found in the "out" directory.

This project uses renv to manage package dependencies. After downloading this (or forking it via GitHub), open the .Rproj file. After installing and loading the renv package, simply run restore() to install the exact configuration of R packages originally used in this analysis.

References

Muir CD, Conesa MÀ, Roldán EJ, et al (2017) Weak coordination between leaf structure and function among closely related tomato species. New Phytol 213:1642–1653. doi: 10.1111/nph.14285