Merge branch 'master' of https://github.com/mabarbour/complexity_sele…

…ction

README.md

@@ -1,20 +1,22 @@
 [![DOI](https://zenodo.org/badge/108833263.svg)](https://zenodo.org/badge/latestdoi/108833263)
 
 # complexity_selection
-This repository contains data and code to reproduce analyses reported in the manuscript "Phenotypic evolution is more constrained in simpler food webs".
+This repository contains data and code to reproduce analyses reported in the manuscript "Consumer extinctions constrain phenotypic evolution in the resulting food web".
 
 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.
 
-*Am-Nat-preamble-latex.tex* contains useful code for generating a pdf output that resembles the Latex template for *The American Naturalist*. The names of all other files should be self-explanatory. If they are not, please open an issue in this repository.
-
 # Repository structure
 
-**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 togeher with *manuscript.Rmd*. 
+**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.
+
+**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*.
+
+- **prior_versions**: contain prior versions of this manuscript. So far this contains the first version submitted to bioRxiv and *The American Naturalist* in January of 2019.
 
 - **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. 
 
-**manuscript_cache** and **manuscript_files**: contains all of the components for generating *manuscript.pdf*. . This information was stored because it takes greater than 1 h to re-run all of the analyses from scratch.
+The names of all other files should be self-explanatory. If they are not, please open an issue in this repository.