Paleontological baselines for evaluating extinction risk in the modern oceans

This repository contains the complete analysis for the paper:

Finnegan*, S., S.C. Anderson*, P.G. Harnik*, C. Simpson, D.P. Tittensor, J.E. Byrnes, Z.V. Finkel, D.R. Lindberg, L.H. Liow, R. Lockwood, H.K. Lotze, C.M. McClain, J.L. McGuire, A. O’Dea, J.M. Pandolfi. Paleontological baselines for evaluating extinction risk in the modern oceans. Science. 348 (6234) 675–570. (*Authors contributed equally)

The analysis is written in the knitr file analysis/risksupp.Rnw, which generates the Supporting Materials document and all figures.

To recreate the analysis, first clone the Git repository:

git clone https://github.com/seananderson/paleobaselines.git

Or download the .zip version and unzip it.

You will need the following R packages installed:

x <- c("knitr", "devtools", "plyr", "reshape2", "ggplot2", "gbm", "maps",
  "mapproj", "maptools", "RColorBrewer", "PBSmapping", "fields", "xtable",
  "lmodel2", "pROC", "rgeos", "dplyr", "doParallel", "foreach", "grImport")
install.packages(x)

Then in an R console (version 3.1.3 or higher) run:

setwd("analysis")
knitr::knit("risksupp.Rnw")

(Warning — this may take a long time to run: ~1 to 3 hours.)

Running knit() on the .Rnw file will generate the LaTeX file analysis/risksupp.tex and all the figures in the figs folder. To generate the Supporting Materials PDF, you will need a LaTeX installation. Then, on the Terminal command line, run:

cd analysis
pdflatex risksupp
bibtex risksupp
pdflatex risksupp
pdflatex risksupp

Or, use the makefile to run the above steps:

cd analysis; make