LeBauer:Notebook/Data

=Overview= This page contains links to data that I work with and data that I have used in my research.

Nitrogen Limitation Meta-analysis (Link)
In addition to the data used in the original publication, this spreadsheet includes additional predictors that were not included in the original paper (LeBauer and Treseder, 2008). These include soil pH, plant community composition, and more - scroll right in the database to see. These data came primarily from the same publication as the NPP data in the meta-analysis; in a few cases from prior site descriptions.

Biofuel Ecophysiological Traits and Yields Database (BETY-db)
The BETY-db can be accessed via the BETY-db web portal

It can also be accessed remotely from the command line, using R, MySQL, or other programs. This requires the user to log in to the ebi-forecast server.

North American Regional Reanalysis (NARR)
Meterological data are downloaded as .h5 files from the NARR server to ebi-cluster:/home/scratch/dietze_lab/NARR

FILE=extract2driver.$1.R cp extract2driver.name.R $FILE mkdir name sed -i 's/FILEROOT/'name'/g' $FILE sed -i 's/SOILAT/'lat'/g' $FILE sed -i 's/SOILON/'lon'/g' $FILE sed -i 's/YEAR0/'year0'/g' $FILE sed -i 's/YEARF/'yearf'/g' $FILE nohup R --vanilla < extract2driver.name.R & where:
 * name is the site name
 * lat lon are the latitude and longitude in decimal degrees
 * year0 and yearf are the start and end year for the data extraction

I have wrapped the above into a shell script (soi.sh) that extracts data from these files for a single site with the command: /home/scratch/dietze_lab/NARR/soi.sh name lat lon year0 yearf

soi.sh is a bash script that modifies the generic extract2driver.template.R, creates a site-specific file named extract2driver. .R, and then runs it.

National Operational Model Archive & Distribution System (NOMADS)
Meterological forecast ensembles are downloaded from the NOMADS server to ebi-cluster:/home/scratch/dietze_lab/NOMADS.