14.1 BioCro

Model Information
Home Page https://github.com/ebimodeling/biocro/blob/0.951/README.md
Source Code https://github.com/ebimodeling/biocro/tree/0.951
License University of Illinois/NCSA Open Source License
Authors Fernando E. Miguez, Deepak Jaiswal, Justin McGrath, David LeBauer, Scott Rohde, Dan Wang
PEcAn Integration David LeBauer, Chris Black, Kristina Riemer

14.1.1 Introduction

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.

14.1.2 PEcAn configuration file additions

The following sections of the PEcAn XML are relevant to the BioCro model:

  • model
    • revision – Model version number
  • run
    • site/id – ID associated with desired site from BETYdb site entry
    • inputs
      • met/output – Set as BIOCRO
      • met/path – Path to file containing meteorological data

14.1.3 Model specific input files

List of inputs required by model, such as met, etc.

14.1.4 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 call_biocro() function.

BioCro uses a config.xml file similar to ED2. At this time, no other template files are required.

14.1.5 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.

PEcAn works with v. 0.9x and 1.x. Support for v 2.x is not implemented. Support for v 0.9x is most robust and tested.

To install, use

remotes::install_github('ebimodeling/biocro@0.951')