Data

Tools

Indexes

Applications

Experiments

Open Source Science

PlantBiophysics

A Julia package for computing processes related to plant ecophysiology and biophysics

https://github.com/vezy/plantbiophysics.jl

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 10 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.3%) to scientific vocabulary

Keywords from Contributors

pde interpretability numerics matrix-exponential fspm julialang plants flux neural-operator pinns
Last synced: 7 months ago · JSON representation

Repository

A Julia package for computing processes related to plant ecophysiology and biophysics

Basic Info
Statistics
  • Stars: 26
  • Watchers: 4
  • Forks: 7
  • Open Issues: 11
  • Releases: 25
Created over 5 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

PlantBiophysics

Stable Dev Build Status Code Style: Blue ColPrac: Contributor's Guide on Collaborative Practices for Community Packages Aqua QA DOI

A pure Julia package to simulate biophysical processes for plants such as photosynthesis, conductances for heat, water vapor and CO₂, latent, sensible energy fluxes, net radiation and temperature.

The benefits of using this package are:

  • Blazing fast (few μs for the whole energy balance + photosynthesis + conductances)
  • Easy to use and interactive
  • Parameter calibration and simulation in one place, works with DataFrames and MTGs
  • Great composability:
    • easy to extend, add your model for any process, and it just works, with automatic coupling with other models
    • easy to integrate into other models or platforms thanks to Julia's great compatibility with other languages
  • Easy to read, the code implements the equations close to how they are written in the scientific articles (thanks Julia Unicode!)
  • Compatible with other simulation platforms thanks to the MTG format (OpenAlea, ARCHIMED, AMAPStudio...)
  • Error propagation using Measurements.jl or MonteCarloMeasurements.jl

Try it!

Start by creating a new environment for your project using the pkg manager. To enter the package manager, just press ] in the REPL, and it will become blue (press backspace to return to the Julia REPL). Then create the environment using this command:

julia activate .

Don't forget the "."! It is used to tell the pkg manager that you activate the project were you currently are.

You can then install PlantBiophysics using this command (still from the pkg manager):

julia add PlantBiophysics

Examples

Here is an example usage with a simulation of the energy balance and assimilation of a leaf.

Note that PlantBiophysics is an extension of PlantSimEngine, so we must import both to make a simulation

```julia

Import the packages (you need to install PlantSimEngine first):

using PlantBiophysics, PlantSimEngine

Declare the meteorology for the simulated time-step (also possible to import meteo files):

meteo = Atmosphere(T = 22.0, Wind = 0.8333, Rh = 0.4490995)

Using the model from Medlyn et al. (2011) for Gs and the model of Monteith and Unsworth (2013) for the energy balance:

leaf = ModelList( energybalance = Monteith(), photosynthesis = Fvcb(), stomatalconductance = Medlyn(0.03, 12.0), status = (RaSWf = [13.747, 14.5], sky_fraction = 1.0, aPPFD = 1500.0, d = 0.03) )

run!(leaf, meteo) ```

For more examples, please read the documentation.

Ask Questions

If you have any questions or feedback, open an issue or ask on discourse.

Contributing

Contributions are welcome! If you develop a model for a process, please make a pull request so the community can enjoy it!

See contributor's guide badge for more informations: ColPrac: Contributor's Guide on Collaborative Practices for Community Packages.

Similar projects

References

Baldocchi, Dennis. 1994. « An analytical solution for coupled leaf photosynthesis and stomatal conductance models ». Tree Physiology 14 (7-8‑9): 1069‑79. https://doi.org/10.1093/treephys/14.7-8-9.1069.

Duursma, R. A., et B. E. Medlyn. 2012. « MAESPA: a model to study interactions between water limitation, environmental drivers and vegetation function at tree and stand levels, with an example application to [CO2] × drought interactions ». Geoscientific Model Development 5 (4): 919‑40. https://doi.org/10.5194/gmd-5-919-2012

Farquhar, G. D., S. von von Caemmerer, et J. A. Berry. 1980. « A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species ». Planta 149 (1): 78‑90.

Leuning, R., F. M. Kelliher, DGG de Pury, et E.-D. SCHULZE. 1995. « Leaf nitrogen, photosynthesis, conductance and transpiration: scaling from leaves to canopies ». Plant, Cell & Environment 18 (10): 1183‑1200.

Medlyn, B. E., E. Dreyer, D. Ellsworth, M. Forstreuter, P. C. Harley, M. U. F. Kirschbaum, X. Le Roux, et al. 2002. « Temperature response of parameters of a biochemically based model of photosynthesis. II. A review of experimental data ». Plant, Cell & Environment 25 (9): 1167‑79. https://doi.org/10.1046/j.1365-3040.2002.00891.x.

Monteith, John L., et Mike H. Unsworth. 2013. « Chapter 13 - Steady-State Heat Balance: (i) Water Surfaces, Soil, and Vegetation ». In Principles of Environmental Physics (Fourth Edition), edited by John L. Monteith et Mike H. Unsworth, 217‑47. Boston: Academic Press.

Schymanski, Stanislaus J., et Dani Or. 2017. « Leaf-Scale Experiments Reveal an Important Omission in the Penman–Monteith Equation ». Hydrology and Earth System Sciences 21 (2): 685‑706. https://doi.org/10.5194/hess-21-685-2017.

Vezy, Rémi, Mathias Christina, Olivier Roupsard, Yann Nouvellon, Remko Duursma, Belinda Medlyn, Maxime Soma, et al. 2018. « Measuring and modelling energy partitioning in canopies of varying complexity using MAESPA model ». Agricultural and Forest Meteorology 253‑254 (printemps): 203‑17. https://doi.org/10.1016/j.agrformet.2018.02.005.

Owner

  • Name: Rémi Vezy
  • Login: VEZY
  • Kind: user
  • Location: Montpellier
  • Company: CIRAD

I am a researcher in plant modelling at the AMAP lab in CIRAD.

GitHub Events

Total
  • Create event: 7
  • Commit comment event: 10
  • Issues event: 7
  • Release event: 3
  • Watch event: 1
  • Delete event: 4
  • Issue comment event: 7
  • Member event: 1
  • Push event: 44
  • Pull request event: 11
  • Fork event: 1
Last Year
  • Create event: 7
  • Commit comment event: 10
  • Issues event: 7
  • Release event: 3
  • Watch event: 1
  • Delete event: 4
  • Issue comment event: 7
  • Member event: 1
  • Push event: 44
  • Pull request event: 11
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 419
  • Total Committers: 5
  • Avg Commits per committer: 83.8
  • Development Distribution Score (DDS): 0.103
Past Year
  • Commits: 73
  • Committers: 3
  • Avg Commits per committer: 24.333
  • Development Distribution Score (DDS): 0.151
Top Committers
Name Email Commits
remi.vezy V****Y 376
CompatHelper Julia c****y@j****g 13
SimonTreil s****u@o****r 12
github-actions[bot] 4****] 12
Simon Treillou 6****u 6
Committer Domains (Top 20 + Academic)
orange.fr: 1 julialang.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 20
  • Total pull requests: 56
  • Average time to close issues: 4 months
  • Average time to close pull requests: 19 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.2
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 41
Past Year
  • Issues: 6
  • Pull requests: 10
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 2 months
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.1
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 5
View more stats
Top Authors
Issue Authors
  • VEZY (14)
  • rpaperez (2)
  • Samuel-amap (1)
  • github-actions[bot] (1)
  • JulienLamour (1)
  • bspanoghe (1)
  • JuliaTagBot (1)
Pull Request Authors
  • github-actions[bot] (44)
  • SimonTreillou (9)
  • Samuel-amap (6)
  • VEZY (2)
  • bspanoghe (2)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • julia 5 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 23
juliahub.com: PlantBiophysics

A Julia package for computing processes related to plant ecophysiology and biophysics

  • Versions: 23
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5 Total
Rankings
Dependent repos count: 9.9%
Forks count: 28.1%
Average: 29.2%
Dependent packages count: 38.9%
Stargazers count: 39.8%
Last synced: 8 months ago