Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 9 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (17.0%) to scientific vocabulary
Repository
R package for GRANAR
Basic Info
- Host: GitHub
- Owner: granar
- License: gpl-3.0
- Language: R
- Default Branch: master
- Size: 354 KB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 3
Metadata Files
README.md
Generator of Root ANAtomy in R (GRANAR)
v1.1 --> 
GRANAR is an open-source R package designed to generate root cross-section anatomical networks with ease. Using global parameters, such as mean cell size and number of cell layers, GRANAR simplifies the creation and visualization of virtual monocotyledon root anatomies. This tool is particularly useful for researchers studying root hydraulic conductivity and the impact of anatomical features on water transport.
Features
- Generate Root Anatomies: Create root cross-sections using customizable parameters.
- Visualize Results: Easily plot and explore generated anatomies.
- Save & Share Outputs: Export anatomical data for further analysis.
- Integration with Hydraulic Models: Seamlessly use GRANAR outputs with tools like MECHA for hydraulic property estimations.
- Integration with Biomechanics Models: GRANAR outputs can be coupled with tools like BVPy for stress/strain and deformation pattern.
Installation
Install the latest version of GRANAR directly from GitHub using devtools:
```R
Install devtools if not already installed
install.packages("devtools")
Install GRANAR
devtools::install_github("granar/granar") ```
Getting Started
Below is a quick example to demonstrate how to use GRANAR:
```R
Load GRANAR
library(granar)
Load input parameters
params <- readparamxml(path = system.file("extdata", "root_monocot.xml", package = "granar"))
Generate root anatomy
root <- create_anatomy(parameters = params)
Visualize the generated anatomy
plot_anatomy(root)
Save the generated anatomy to an XML file
writeanatomyxml(sim = root, path = "current_root.xml") ```
Documentation
For detailed documentation and usage examples, please visit the GRANAR website.
Support
If you encounter any issues, have questions, or wish to suggest enhancements, feel free to raise an issue.
Contributing
Contributions are welcome! If you'd like to contribute to GRANAR, please:
- Fork the repository.
- Make your changes in a new branch.
- Submit a pull request with a clear description of your changes.
Citation
If you use GRANAR in your research, please cite the following paper:
Heymans A., Couvreur V., LaRue T., Paez-Garcia A., Lobet G. (2020). GRANAR, a computational tool to better understand the functional importance of monocotyledon root anatomy. Plant Physiology, 182(2), 707-720. doi: 10.1104/pp.19.00617
License
GRANAR is released under a GNU General Public Licence v3.0, which means that distribution and use and binary forms, with or without modification, are permitted under the GNU General Public License v3 and provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
See the LICENSE file for details.
Versioning
v0.9 -->
Owner
- Name: Generator of Root ANAtomy in R [GRANAR]
- Login: granar
- Kind: organization
- Repositories: 3
- Profile: https://github.com/granar
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: >-
GRANAR, a Computational Tool to Better Understand the
Functional Importance of Monocotyledon Root Anatomy
message: >-
If you use this software, please cite the related journal article using the
metadata from this file.
type: article
authors:
- given-names: Adrien
family-names: Heymans
orcid: 'https://orcid.org/0000-0003-3685-2240'
affiliation: 'Earth and Life Institute, UCLouvain, Belgium'
- given-names: Valentin
family-names: Couvreur
orcid: 'https://orcid.org/0000-0002-1087-3978'
affiliation: 'Earth and Life Institute, UCLouvain, Belgium'
- given-names: Therese
family-names: LaRue
affiliation: >-
Department of Biology, Stanford University, Stanford,
California
- family-names: Paez-Garcia
given-names: Ana
orcid: 'https://orcid.org/0000-0002-2006-8681'
affiliation: 'Noble Research Institute, LLC, Ardmore, Oklahoma'
- given-names: Guillaume
family-names: Lobet
orcid: 'https://orcid.org/0000-0002-5883-4572'
affiliation: 'Earth and Life Institute, UCLouvain, Belgium'
identifiers:
- type: doi
value: 10.1104/pp.19.00617
description: Journal article
- type: doi
value: 10.5281/zenodo.3051109
description: v0.9
repository-code: 'https://github.com/granar/granar/tree/master'
url: 'https://granar.github.io/'
abstract: >-
Root hydraulic conductivity is a limiting factor along the
water pathways between the soil and the leaf, and root
radial conductivity is itself defined by cell-scale
hydraulic properties and anatomical features. However,
quantifying the influence of anatomical features on the
radial conductivity remains challenging due to complex
time-consuming experimental procedures. We present an
open-source computational tool, the Generator of Root
Anatomy in R (GRANAR; http://granar.github.io), that can
be used to rapidly generate digital versions of contrasted
monocotyledon root anatomical networks. GRANAR uses a
limited set of root anatomical parameters, easily acquired
with existing image analysis tools. The generated
anatomical network can then be used in combination with
hydraulic models to estimate the corresponding hydraulic
properties. We used GRANAR to reanalyze large maize (Zea
mays) anatomical datasets from the literature. Our model
was successful at creating virtual anatomies for each
experimental observation. We also used GRANAR to generate
anatomies not observed experimentally over wider ranges of
anatomical parameters. The generated anatomies were then
used to estimate the corresponding radial conductivities
with the hydraulic model MECHA (model of explicit
cross-section hydraulic architecture). Our simulations
highlight the large importance of the width of the stele
and the cortex. GRANAR is a computational tool that
generates root anatomical networks from experimental data.
It enables the quantification of the effect of individual
anatomical features on the root radial conductivity.
keywords:
- Root cross-section
- Root hydraulic
license: GPL-3.0
version: v0.9
date-released: '2019-05-20'
GitHub Events
Total
- Issues event: 1
- Issue comment event: 1
- Push event: 8
Last Year
- Issues event: 1
- Issue comment event: 1
- Push event: 8
Dependencies
- R >= 3.3.1 depends
- Hmisc * imports
- alphahull * imports
- deldir * imports
- plyr * imports
- purrr * imports
- retistruct * imports
- sp * imports
- tidyverse * imports
- viridis * imports
- xml2 * imports