BioCro

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 22 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
11 of 36 committers (30.6%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (18.8%) to scientific vocabulary

Keywords from Contributors

ecosystem-models pecan plants trait cyberinfrastructure data-assimilation ecosystem-science meta-analysis national-science-foundation agriculture

Last synced: 6 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: biocro
License: other
Language: C++
Default Branch: main
Homepage: https://biocro.github.io/
Size: 392 MB

Statistics

Stars: 46
Watchers: 16
Forks: 23
Open Issues: 25
Releases: 11

Created about 11 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License

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.

```r library(BioCro) library(lattice)

result <- with(soybean, {runbiocro( initialvalues, parameters, soybeanweather$'2002', directmodules, differentialmodules, odesolver )})

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:

r 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:
1. 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.
2. 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 running git submodule update --init to obtain it.
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 "pathtosourcecodeparent_directory".
1. To install from the command line: cd path_to_source_code_parent_directory R CMD INSTALL biocro
2. To install from within R: setwd('path_to_source_code_parent_directory') install.packages('biocro', repos=NULL, type='SOURCE')

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

Name: BioCro Team
Login: biocro
Kind: organization

Repositories: 7
Profile: https://github.com/biocro

GitHub Events

Total

Create event: 63
Release event: 1
Issues event: 43
Watch event: 4
Delete event: 43
Issue comment event: 419
Push event: 219
Pull request review comment event: 181
Pull request review event: 199
Pull request event: 98
Fork event: 5

Last Year

Create event: 63
Release event: 1
Issues event: 43
Watch event: 4
Delete event: 43
Issue comment event: 419
Push event: 219
Pull request review comment event: 181
Pull request review event: 199
Pull request event: 98
Fork event: 5

Committers

Last synced: 6 months ago

All Time

Total Commits: 3,120
Total Committers: 36
Avg Commits per committer: 86.667
Development Distribution Score (DDS): 0.614

Past Year

Commits: 118
Committers: 5
Avg Commits per committer: 23.6
Development Distribution Score (DDS): 0.331

Top Committers

Name	Email	Commits
eloch216	4**6@u**m	1,205
justinmcgrath	m**b@g**m	560
Scott Rohde	s**e@i**u	282
Justin McGrath	j**h@u**m	219
Scott Rohde	s**e@i**u	164
Megan L. Matthews	5**h@u**m	137
David LeBauer	d**r@g**m	132
Deepak Jaiswal	d**c@g**m	65
ajmann4	a**4@i**u	51
uphone87	y**7@g**m	50
David LeBauer	d**r@i**u	46
leavesandlemmas	6**s@u**m	31
djaiswal	d**l@d**u	28
Ryan Grady	R**6@G**m	19
songqingfeng	s**g@g**m	19
Fernando Miguez	f**z@g**m	18
Dan Wang	d**g@d**)	15
Deepak	d**l@i**u	11
acferris	a**s@s**u	11
Scott Oswald	s**7@g**m	8
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
Justin McGrath	m**d@g**m	4
arjunalal	3**l@u**m	4
David LeBauer	d**r@e**u	3
Venkatraman Srinivasan	v**3@i**u	3
Yufeng He	3**7@u**m	3
Alyssa Ferris	A**s@g**g	2
and 6 more...

Committer Domains (Top 20 + Academic)

illinois.edu: 6 biocluster.igb.illinois.edu: 1 wd-virtualbox.(none): 1 gatesfoundation.org: 1 email.arizona.edu: 1 ubuntu.(none): 1 ckblack.org: 1 stanford.edu: 1 dlebauer-desktop.(none): 1 djaiswal.igb.uiuc.edu: 1 igb.illinois.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 69
Total pull requests: 207
Average time to close issues: 3 months
Average time to close pull requests: 16 days
Total issue authors: 17
Total pull request authors: 10
Average comments per issue: 4.2
Average comments per pull request: 5.21
Merged pull requests: 149
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 26
Pull requests: 104
Average time to close issues: 16 days
Average time to close pull requests: 5 days
Issue authors: 5
Pull request authors: 3
Average comments per issue: 2.81
Average comments per pull request: 5.17
Merged pull requests: 75
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

leavesandlemmas (14)
eloch216 (14)
gsrohde (13)
justinmcgrath (8)
pnlfang (3)
djaiswal (2)
yaron1000 (2)
yufenghe22 (2)
infotroph (2)
dlebauer (2)
uphone87 (1)
yaron-michael (1)
morio1968 (1)
serbinsh (1)
jessicaguo (1)

Pull Request Authors

eloch216 (118)
leavesandlemmas (33)
gsrohde (31)
yufenghe22 (10)
justinmcgrath (4)
uphone87 (4)
dlebauer (3)
infotroph (2)
KristinaRiemer (1)
kimberlyh66 (1)

Top Labels

Issue Labels

enhancement (6) question (5) bug (4) help wanted (2) tabled for now (1) Fixed but not released (1)

Pull Request Labels

wontfix (2) tabled for now (1)

Packages

Total packages: 1
Total downloads:
- cran 222 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
License: MIT + file LICENSE
Latest release: 3.2.0
published about 1 year ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 222 Last month
Docker Downloads: 62,285

Rankings

Dependent packages count: 27.8%

Dependent repos count: 35.7%

Average: 49.5%

Downloads: 84.9%

Maintainers (1)

jmcgrath@illinois.edu

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

stats * imports
knitr * suggests
lattice * suggests
testthat * suggests

.github/actions/build_pkgdown_site/action.yml actions

r-lib/actions/setup-pandoc v2 composite

.github/actions/doxygen-action/action.yml actions

Dockerfile * docker

.github/actions/render_bookdown_book/action.yml actions

r-lib/actions/setup-pandoc v2 composite

.github/actions/run_doxygen/action.yml actions

./.github/actions/doxygen-action * composite

.github/workflows/R-CMD-check-backend.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite
r-lib/actions/setup-tinytex v2 composite

.github/workflows/R-CMD-check.yaml actions

JoshuaTheMiller/conditional-build-matrix 38b0036b90a7f5f1461f446948d156a714e4fa1e composite
actions/checkout v3 composite

.github/workflows/automatically-call-document.yml actions

.github/workflows/document.yml actions

./.github/actions/build_pkgdown_site * composite
./.github/actions/render_bookdown_book * composite
./.github/actions/run_doxygen * composite
actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/document_quantities.yml actions

actions/cache v2 composite
actions/checkout v3 composite
actions/checkout v2 composite
r-lib/actions/setup-r v2 composite

.github/actions/doxygen-action/Dockerfile docker

alpine 3.16 build

BioCro

Science Score: 49.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

BioCro

An example

Simple installation

Installation from source

Requirements

Installation steps

Making contributions

Software Documentation

License

Citing BioCro

References

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: BioCro

Rankings

Maintainers (1)

Dependencies