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Analysis.rmd
README.md
across_species_fire_data.csv
alba_barplot.R
fire_biplot.R
fire_littersize_manipulation_data.txt
gymno_tree.txt
load_data.R
phylo_trait_figure.R
phylo_trait_figure.r
remake.yml
threshold_fig.R
threshold_fig.r
work_flow.png

README.md

Reproducing the results from Cornwell et al. in press

The contents of this directory should allow you to access the data and recreate--on your own computer from the original data--the graphs from Cornwell et al. in press New Phytologist. Reproducing these results will first require cloning this repository on your computer. If you are brand new to git, it's a good idea to read more about git here.

After you clone the repository, make sure the working directory for R is within the repository then run the following lines of code.

First install the required packages from CRAN:

install.packages(c("R6","yaml","digest","devtools","fields","ape","markdown","knitr","heplots","car"))

Download and install one additional package called "remake" from github.

devtools::install_github("richfitz/remake")

Then run the following command from within R. Make sure the home directory

remake::make()

This script will call R code that loads the data, does various analyses and, makes both the figures and a supplemental file that contains the statistical analysis for Table 2 in the paper. The script will place the figures in a folder called "output/figs" within your working directory.

Here is a visualization of the workflow that produces these figures. The entities across the top row are files, the second row are R data objects, and the third row are the figure files.

image

The names of the functions that do each processing and graphics step can be found within the maker.yml file in the repository. The functions themselves are in the .R files. There is also a knitr--produced file that shows the statistical analysis that goes into Table 2 from the main text.