BETYdb Manuscript Code, Figures, and Data

This repository provides code and data used in:

LeBauer, David, Rob Kooper, Patrick Mulrooney, Scott Rohde, Dan Wang, Stephen P. Long, and Michael C. Dietze. "BETYdb: a yield, trait, and ecosystem service database applied to second‐generation bioenergy feedstock production." GCB Bioenergy 10, no. 1 (2018): 61-71. http://onlinelibrary.wiley.com/doi/10.1111/gcbb.12420/full

• The file gcbb_manuscript.Rmd provides all of the code used to query data, perform statistical analyses, and generate the result figures in the manuscript.
  • this analysis requires access to the underlying postgres database.
• The file 'fig4a_with_ropensci_traits_package.Rmd' shows how to reproduce the above queries using the rOpenSci traits package. More information about accessing data can be found in the documentation (go to betydb.org --> docs --> data access).

Installing a copy of BETYdb

Any of these methods will allow you to use the code from the original analysis (gcbb_manuscript.Rmd); only using the VM will give the exact data from the original analysis (although as of Dec 2018 there have been very few changes to the original data).

Using a local Postgres server

See the BETYdb data access documentation https://pecan.gitbook.io/betydb-data-access/installing-your-own-version-of-betydb

Briefly:

Install Postgres on your computer (e.g. for Mac and Windows)

# Setup database with user bety
# you either need to create a user named "postgres" or replace with your own user name
sudo -u postgres createuser -d -l -P -R -S bety
sudo -u postgres createdb -O bety bety
�
# Download load.bety.sh script 
https://raw.githubusercontent.com/PecanProject/pecan/master/scripts/load.bety.sh
chmod +x load.bety.sh
�
# see description
./load.bety.sh -h
�
# create database and load data from remote site 0 (betydb.org)
sudo -u postgres ./load.bety.sh -c YES -u YES -r 0

Using PEcAn VM

Requires that you install VirtualBox and then import the PEcAN virtual machine.

You can access virtual machine images here: https://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN

This will provide the database, Rstudio, and more. To get the same data used in the manuscript, use PEcAn v 1.4.9.

Using docker compose

Not yet fully documented ...

1. Install Docker https://docs.docker.com/install/
2. clone this repository git clone https://github.com/ebimodeling/betydb_manuscript
3. change into this directory cd betydb_manuscript
4. run Docker Componse docker-compose up
5. additional details to come ...