jebyrnes / ext-meta

Paleo marine extinction risk meta-analysis for NESCent working group

The folder contains code for a meta-analysis looking at the ecological and environmental determinants of extinction risk for bivalves and gastropods in the fossil record. The code was largely written by Jarrett Byrnes.

The analysis scripts call some R files in the r folder and some data from the data folder.

To re-run the analysis, run the following in an R console:

First, install these packages if you don't have them. It's fine to re-run this line if you aren't sure.

install.packages(c("ggplot2", "gridExtra", "metafor", "RColorBrewer", "AICcmodavg", "knitr", "lme4", "plyr"))

Then set your working directory to the analysis folder. For example, on my computer:

setwd("~/src/ext-meta/analysis/")

Then run these lines of code:

source("../r/proxydata_clean_merge.R")
source("../r/data_clean_merge.r")
library(knitr)
knit2html("final.Rmd")
source("pretty_data_overview.R")
source("plot_effect_sizes.R")