https://github.com/seananderson/paleobaselines

Paleontological baselines for evaluating extinction risk in the modern oceans
https://github.com/seananderson/paleobaselines

Last synced: 12 days ago
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Paleontological baselines for evaluating extinction risk in the modern oceans

• Host: GitHub
• URL: https://github.com/seananderson/paleobaselines
• Owner: seananderson
• Created: 2013-12-22T17:10:42.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2015-04-30T22:12:23.000Z (over 9 years ago)
• Last Synced: 2024-10-12T01:19:17.266Z (27 days ago)
• Language: TeX
• Homepage:
• Size: 58.3 MB
• Stars: 4
• Watchers: 7
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# 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](http://www.sciencemag.org/content/348/6234/567.abstract). Science. 348 (6234) 675–570. (\*Authors contributed equally)

The analysis is written in the [knitr](http://yihui.name/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](https://github.com/seananderson/paleobaselines/archive/master.zip) and unzip it.

You will need the following R packages installed:

```R

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:

```R

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](http://latex-project.org/). Then, on the Terminal command line, run:

```sh

cd analysis

pdflatex risksupp

bibtex risksupp

pdflatex risksupp

pdflatex risksupp

```

Or, use the `makefile` to run the above steps:

```sh

cd analysis; make

```