This repository contains data and code to reproduce analyses reported in the manuscript "Loss of consumers constrains phenotypic evolution in the resulting food web" (in press at Evolution Letters). The original version of this manuscript was posted on bioRxiv.
For a pretty HTML document displaying all code to reproduce these results, download reproduce_analyses.html from the analyses folder. For an ugly version that is viewable on GitHub, click on the "reproduce_analyses.md" file.
manuscript: contains manuscript.Rmd that knits together manuscript.pdf. It also contains a style file for The American Naturalist (amnat.bst), a bibtex file of references (references.bib), and an intermediate .tex file. Am-Nat-preamble-latex.tex contains useful code for generating a pdf output that resembles the Latex template for The American Naturalist in Rmarkdown.
- prior_versions: contains prior versions of this manuscript.
analyses: contains code to reproduce all analyses. It also contains the figures that are embedded within manuscript.pdf. The main workhorse is reproduce_analyses.Rmd, which is called on when knitting the manuscript together with manuscript.Rmd.
- reproduce_analyses_cache and reproduce_analyses_files: contain all of the components for generating reproduce_analyses.html. This information was stored because it takes greater than 1 h to re-run all of the analyses from scratch.
data: includes the dataset analyzed for this manuscript.
- raw_data_management: contains raw data and code used to generate the final dataset. If content of this folder is not clear after reading finalize_manuscript.dataset.R, gall_contents.info.md, and revising_dataset.R, then please open an issue in this repository to notify me.
The names of all other files should be self-explanatory. If they are not, please open an issue in this repository.