Tests:

This folder provides some simple tests for each model, using the web/workflow.R script. They can be run with the following syntax:

../web/workflow.R --settings <pecanfile>

# for example to run the ed workflow:
../web/workflow.R --settings pecan.ed.xml

Since workflow.R is a simple rscript you can pass in standard R flags, such as --vanilla, etc.

Files:

• workflow.R : Generic workflow to run PEcAn; it will skip previously completed steps.

Settings Files

• pecan.ed.xml : pecan configuration to run ED on ebifarm.
• pecan.sipnet.xml : pecan configuration to run SIPNET on NIWOT.
• pecan.biocro.xml : pecan configuration to run BIOCRO

Debugging:

• add debugonce(somefunction) to workflow.R after PEcAn.all is loaded
• the run will stop when it gets to the specified function, at which point you can step through.
• Do not commit changes to workflow.R used for debugging

For example, you can add debugonce(run.meta.analysis) to workflow.R and then

R --vanilla --settings <pecanfile>

debugonce(run.meta.analysis)
source "workflow.R"