BioCro
A model that predicts plant growth over time given crop-specific parameters and environmental data as input.
https://github.com/biocro/biocro
Category: Biosphere
Sub Category: Plants and Vegetation
Keywords from Contributors
ecosystem-model ecosystem-science pecan plants traits cyberinfrastructure data-assimilation meta-analysis national-science-foundation agriculture
Last synced: about 3 hours ago
JSON representation
Repository metadata
- Host: GitHub
- URL: https://github.com/biocro/biocro
- Owner: biocro
- License: other
- Created: 2015-03-04T02:15:15.000Z (about 10 years ago)
- Default Branch: main
- Last Pushed: 2025-04-24T14:14:03.000Z (6 days ago)
- Last Synced: 2025-04-25T12:11:25.672Z (5 days ago)
- Language: C++
- Homepage: https://biocro.github.io/
- Size: 387 MB
- Stars: 45
- Watchers: 16
- Forks: 21
- Open Issues: 24
- Releases: 11
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
README.md
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). In 2022, BioCro was reorganized to take a truly modular
approach to modeling (Lochocki et al., 2022) and a new soybean model was
developed (Matthews et al., 2022).
BioCro has also been integrated into a suite of tools that link the model
directly to crop trait and yield data (LeBauer et al., 2013). The Predictive
Ecosystem Analyzer (PEcAn) couples
BioCro to the Biofuel Ecophysiological Traits and Yields
database.
See References below for a full list of scientific publications
using the BioCro framework.
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 <- with(soybean, {run_biocro(
initial_values,
parameters,
soybean_weather$'2002',
direct_modules,
differential_modules,
ode_solver
)})
xyplot(Stem + Leaf ~ TTc, data = result, type='l', auto = TRUE)
There are parameters and modules for soybean (Glycine max), miscanthus
(Miscanthus x giganteus), and willow (Saliceae salix).
Simple installation
BioCro is available on CRAN, so it can be installed from R as follows:
install.packages('BioCro')
Installation from source
Requirements
- The R environment version 3.6.0 or greater.
- On Windows, a version of
Rtools appropriate for your
version of R. - On Linux, gcc and g++ version 4.9.3 or greater (consult documentation for your
distribution for installation instructions). - On MacOS, Xcode.
Installation steps
- Obtain a local copy of this repository, making sure to include the Git
submodule code. This can be accomplished using either of two methods:- If you are new to Git, the easiest way to get a local copy is to install
GitHub Desktop and use the "Open with GitHub Desktop" option in the "Code"
dropdown on the GitHub page for this repository. - Alternatively, clone the repository using Git on the command
line in the usual fashion by running
git clone https://github.com/biocro/biocro
The repository
contains a Git submodule, so you will need to take the additional step of
runninggit submodule update --init
to obtain it.
- If you are new to Git, the easiest way to get a local copy is to install
- Install the BioCro R package using one of the following sets of comands.
These assume that the source files are in a directory named "biocro" residing
in a parent directory located at "path_to_source_code_parent_directory".- To install from the command line:
cd path_to_source_code_parent_directory R CMD INSTALL biocro
- To install from within R:
setwd('path_to_source_code_parent_directory') install.packages('biocro', repos=NULL, type='SOURCE')
- To install from the command line:
Making contributions
Please see the contribution guidelines before submitting changes.
These may be found in Chapter One of the Developer's Manual on the
public BioCro Documentation web site.
Software Documentation
See the public BioCro Documentation web
site. There will be found not only the
usual 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.
There is also a separate page that documents all of the quantities
used by the Standard BioCro Module
Library.
License
The BioCro
R package is licensed under the MIT license, while the BioCro C++
framework is licensed under version 3 or greater of the GNU Lesser General
Public License (LGPL). This scheme allows people to freely develop models for
any use (public or private) under the MIT license, but any changes to the
framework that assembles and solves models must make source code changes
available to all users under the LGPL. See LICENSE.note
for more details.
Citing BioCro
Appropriate references for BioCro are
Miguez et al. (2009) and
Lochocki et al. (2022), with details given below. To
cite the package itself, use citation('BioCro')
in R to get details for the
current installed version.
References
- Humphries S and Long SP (1995) WIMOVAC: a software package for modelling the dynamics of plant leaf and canopy photosynthesis. Computer Applications in the Biosciences 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 (2013) 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.
- Larsen S, Jaiswal D, Bentsen NS, Wang D, Long SP (2015) Comparing predicted yield and yield stability of willow and Miscanthus across Denmark. GCB Bioenergy 8(6): 1061-1070.
- Jaiswal D, de Souza AP, Larsen S, LeBauer D, Miguez FE, Sparovek G, Bollero G, Buckeridge MS, Long SP (2017) Brazilian sugarcane ethanol as an expandable green alternative to crude oil use. Nature Climate Change 7(11): 788-792.
- Lochocki EB, Rohde S, Jaiswal D, Matthews ML, Miguez FE, Long SP, McGrath JM (2022) BioCro II: a software package for modular crop growth simulations. in silico Plants 4(1): diac003.
- Matthews ML, Marshall-Colón A, McGrath JM, Lochocki EB, Long SP (2022) Soybean-BioCro: a semi-mechanistic model of soybean growth. in silico Plants 4(1): diab032.
- He Y, Jaiswal D, Liang XZ, Sun C, Long SP (2022) Perennial biomass crops on marginal land improve both regional climate and agricultural productivity. GCB Bioenergy 14(5): 558-571.
- He Y, Matthews ML (2023) Seasonal climate conditions impact the effectiveness of improving photosynthesis to increase soybean yield. Field Crops Research 296: 108907.
- Holland B, Matthews ML, Bota P, Sweetlove LJ, Long SP, diCenzo GC (2023) A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost–benefit of nitrogen fixation. New Phytologist 240(2): 744-756.
Owner metadata
- Name: BioCro Team
- Login: biocro
- Email:
- Kind: organization
- Description:
- Website:
- Location:
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/108023099?v=4
- Repositories: 7
- Last ynced at: 2024-04-23T11:36:40.544Z
- Profile URL: https://github.com/biocro
GitHub Events
Total
- Create event: 49
- Release event: 1
- Issues event: 28
- Watch event: 4
- Delete event: 39
- Issue comment event: 351
- Push event: 165
- Pull request review comment event: 161
- Pull request review event: 172
- Pull request event: 78
- Fork event: 3
Last Year
- Create event: 49
- Release event: 1
- Issues event: 28
- Watch event: 4
- Delete event: 39
- Issue comment event: 351
- Push event: 165
- Pull request review comment event: 161
- Pull request review event: 172
- Pull request event: 78
- Fork event: 3
Committers metadata
Last synced: 8 days ago
Total Commits: 3,120
Total Committers: 29
Avg Commits per committer: 107.586
Development Distribution Score (DDS): 0.614
Commits in past year: 232
Committers in past year: 5
Avg Commits per committer in past year: 46.4
Development Distribution Score (DDS) in past year: 0.319
Name | Commits | |
---|---|---|
eloch216 | 4****6 | 1205 |
justinmcgrath | m****b@g****m | 560 |
Scott Rohde | s****e@i****u | 446 |
Justin McGrath | j****h | 223 |
David LeBauer | d****r@g****m | 181 |
Megan L. Matthews | 5****h | 137 |
Deepak Jaiswal | d****c@g****m | 76 |
ajmann4 | a****4@i****u | 51 |
uphone87 | y****7@g****m | 50 |
leavesandlemmas | 6****s | 39 |
djaiswal | d****l@d****u | 28 |
Ryan Grady | R****6@G****m | 20 |
songqingfeng | s****g@g****m | 19 |
Fernando Miguez | f****z@g****m | 18 |
Dan Wang | d****g@d****) | 15 |
acferris | a****s@s****u | 11 |
Chris Black | c****s@c****g | 7 |
djaiswal | d****l@u****) | 7 |
Dan Wang | d****g@i****u | 5 |
Jeremy Kemball | j****l@g****m | 4 |
arjunalal | 3****l | 4 |
Venkatraman Srinivasan | v****3@i****u | 3 |
Yufeng He | 3****7 | 3 |
wd | wd@w****) | 2 |
Alyssa Ferris | A****s@g****g | 2 |
Deepak Jaiswal | d****c@g****m | 1 |
Justin McGrath | j****h@b****u | 1 |
Justin McGrath | j****h@c****l | 1 |
alexandriatran | 1****p@g****m | 1 |
Committer domains:
- illinois.edu: 4
- biocluster.igb.illinois.edu: 1
- gatesfoundation.org: 1
- wd-virtualbox.(none): 1
- ubuntu.(none): 1
- ckblack.org: 1
- stanford.edu: 1
- dlebauer-desktop.(none): 1
- djaiswal.igb.uiuc.edu: 1
Issue and Pull Request metadata
Last synced: 1 day ago
Total issues: 89
Total pull requests: 166
Average time to close issues: 3 months
Average time to close pull requests: 25 days
Total issue authors: 18
Total pull request authors: 10
Average comments per issue: 5.94
Average comments per pull request: 5.78
Merged pull request: 125
Bot issues: 0
Bot pull requests: 0
Past year issues: 27
Past year pull requests: 58
Past year average time to close issues: 19 days
Past year average time to close pull requests: 12 days
Past year issue authors: 7
Past year pull request authors: 4
Past year average comments per issue: 4.56
Past year average comments per pull request: 6.57
Past year merged pull request: 43
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- gsrohde (23)
- eloch216 (15)
- justinmcgrath (9)
- leavesandlemmas (8)
- pnlfang (6)
- infotroph (4)
- djaiswal (3)
- dlebauer (3)
- morio1968 (2)
- serbinsh (2)
- yufenghe22 (2)
- jessicaguo (2)
- sruthi162114001 (2)
- yaron1000 (2)
- istfer (2)
Top Pull Request Authors
- eloch216 (85)
- gsrohde (42)
- leavesandlemmas (13)
- justinmcgrath (7)
- dlebauer (5)
- yufenghe22 (4)
- infotroph (4)
- KristinaRiemer (2)
- kimberlyh66 (2)
- uphone87 (2)
Top Issue Labels
- enhancement (14)
- question (8)
- bug (6)
- help wanted (4)
- tabled for now (2)
- Fixed but not released (2)
Top Pull Request Labels
- tabled for now (2)
- wontfix (2)
Package metadata
- Total packages: 1
-
Total downloads:
- cran: 315 last-month
- Total docker downloads: 62,285
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
cran.r-project.org: BioCro
Modular Crop Growth Simulations
- Homepage: https://github.com/biocro/biocro
- Documentation: http://cran.r-project.org/web/packages/BioCro/BioCro.pdf
- Licenses: MIT + file LICENSE
- Latest release: 3.2.0 (published about 2 months ago)
- Last Synced: 2025-04-29T14:11:31.128Z (1 day ago)
- Versions: 2
- Dependent Packages: 0
- Dependent Repositories: 0
- Downloads: 315 Last month
- Docker Downloads: 62,285
-
Rankings:
- Dependent packages count: 27.794%
- Dependent repos count: 35.698%
- Average: 49.466%
- Downloads: 84.905%
- Maintainers (1)
Dependencies
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Score: 18.64595484004336