|University of Illinois/NCSA Open Source License
|Fernando E. Miguez, Deepak Jaiswal, Justin McGrath, David LeBauer, Scott Rohde, Dan Wang
|David LeBauer, Dan Wang
BioCro is a model that estimates photosynthesis at the leaf, canopy, and ecosystem levels and determines plant biomass allocation and crop yields, using underlying physiological and ecological processes to do so.
13.1.2 PEcAn configuration file additions
The following sections of the PEcAn XML are relevant to the BioCro model:
revision– Model version number
site/id– ID associated with desired site from BETYdb site entry
met/output– Set as BIOCRO
met/path– Path to file containing meteorological data
13.1.3 Model specific input files
List of inputs required by model, such as met, etc.
13.1.4 Model configuration files
Genus-specific parameter files are secretly required. These are stored in the PEcAn.BIOCRO package and looked up under the hood.
write.configs.BIOCRO looks for defaults in this order: first any file at a path specified by
settings$pft$constants$file, next by matching the genus name in datasets exported by the BioCro package, and last by matching the genus name in PEcAn.BIOCRO’s extdata/defaults directory.
When adding a new genus, it is necessary to provide a new default parameter file in PEcAn.BIOCRO
inst/extdata/defaults and also (for v<1.0) update the
BioCro uses a config.xml file similar to ED2. At this time, no other template files are required.
13.1.5 Installation notes
BioCro can be run standalone using the model’s R package. Instructions for installing and using the package are in the GitHub repo’s README file.