BioCro 
BioCro is a model that predicts plant growth over time given crop-specific parameters and environmental data as input.
It uses models of key physiological and biophysical processes underlying plant growth (Humphries and Long, 1995), and has previously been used for predicting biomass yield and leaf area index of switchgrass and miscanthus (Miguez et al., 2009).
BioCro has also been integrated into a suite of tools that link the model directly to crop trait and yield data (LeBauer et al., 2014). The Predictive Ecosystem Analyzer (PEcAn) couples BioCro to the Biofuel Ecophysiological Traits and Yields database.
An example
The run_biocro() function accepts initial values, parameters, climate variables, and sets of modules to run. It returns the results in a data frame.
library(BioCro)
library(lattice)
result = run_biocro(soybean_initial_values, soybean_parameters, soybean_weather2002, soybean_direct_modules, soybean_differential_modules, soybean_ode_solver)
xyplot(Stem + Leaf ~ TTc, result, type='l')There are parameters and modules for soybean (Glycine max), miscanthus (Miscanthus x giganteus), and willow (Saliceae salix).
Installation
Requirements
- The R environment version 3.2.3 or greater.
- On Windows, Rtools version 3.3 or higher (3.5 is not recommended as of 2019-12-05 since that version is not frozen).
- On Linux, gcc and g++ version 4.9.3 or greater (consult documentation for your distribution for installation instructions).
- On MacOS, Xcode.
Installation steps
Download the BioCro source code from GitHub, unzip the file, and install from the either the command line or from within R using one of the following sets of commands.
Do one of the sets of instruction below. These assume that the source files are in a directory named "biocro".
- From the command line
cd path_to_unzipped_directory
R CMD INSTALL biocro
- Or from within R
setwd('path_to_unzipped_directory')
install.packages('biocro', repos=NULL, type='SOURCE')
Making contributions
Please see the contribution guidelines before submitting changes.
Software Documentation
See the BioCro Documentation Web
Site. There
will be found not only the standard package documentation, but also
documentation of the C++ code, including notes on the biological
models used in BioCro and their implementation. Also included is
documentation for BioCro package developers and maintainers.
References
- Humphries S and Long SP (1995) WIMOVAC - a software package for modeling the dynamics of the plant leaf and canopy photosynthesis. Computer Applications in the Bioscience 11(4):361-371.
- Miguez FE, Zhu XG, Humphries S, Bollero GA, Long SP (2009) A semimechanistic model predicting the growth and production of the bioenergy crop Miscanthus × giganteus: description, parameterization and validation. Global Change Biology Bioenergy 1: 282-296.
- LeBauer D, Wang D, Richter K, Davidson C, Dietze M (2014) Facilitating feedbacks between field measurements and ecosystem models. Ecological Monographs 83(2): 133-154.
- Wang D, Jaiswal D, Lebauer DS, Wertin TM, Bollero GA, Leakey ADB, Long SP (2015) A physiological and biophysical model of coppice willow (Salix spp.) production yields for the contiguous USA in current and future climate scenarios. Plant, Cell & Environment 38(9), 1850-1865.