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PlantBiophysics.jl

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

Overview

PlantBiophysics.jl is a Julia package designed to simulate and analyze the biophysical processes of plants. It provides tools for modeling photosynthesis, energy fluxes, and conductances for heat, water vapor, and CO₂. The package is built to support parameter estimation, model comparison, and simulation tasks, offering flexibility and computational efficiency.

Features

  • Parameter Estimation: Fit model parameters using the generic fit function (e.g., the Farquhar et al. 1980 photosynthesis model using A-Cᵢ curves).
  • Model Comparison: Compare different model implementations by providing a list of models, letting PlantBiophysics.jl automatically couple them (e.g., photosynthesis + stomatal conductance + energy balance).
  • Simulation: Run simulations of biophysical processes using selected models, leveraging Julia's computational performance.

Advantages

  • Efficiency: Designed for fast computations.
  • Scalability: Handles simulations from single objects to entire scenes.
  • Extensibility: Allows users to integrate custom models seamlessly, and generically couple them (see Model coupling for more details).
  • Composability: Supports unit propagation with Unitful and error propagation with MonteCarloMeasurements.jl.

Installation

To install the package, enter the Julia package manager mode by pressing ] in the REPL, and execute the following command:

add PlantBiophysics

To use the package, execute this command from the Julia REPL:

using PlantBiophysics

Quick Start

Explore the First simulation section for detailed examples. Here's a quick example:

using PlantBiophysics, PlantSimEngine, PlantMeteo
meteo = Atmosphere(T = 25.0, Wind = 1.0, Rh = 0.5, Ri_SW_f = 400.0) # Example meteorological data
leaf = ModelList(
        Monteith(),
        Fvcb(),
        Medlyn(0.03, 7.0),
        status = (
            Ra_SW_f = meteo[:Ri_SW_f] .* 0.8, aPPFD = meteo[:Ri_SW_f] .* 0.8 .* 0.48 .* 4.57,
            sky_fraction = 1.0, d = 0.03
        )
)
sim = run!(leaf, meteo)
TimeStepTable{Status{(:Ra_SW_f, :sky_fracti...}(1 x 17):
╭─────┬─────────┬──────────────┬─────────┬─────────┬─────────┬───────────┬──────
│ Row │ Ra_SW_f │ sky_fraction │       d │      Tₗ │      Rn │   Ra_LW_f │     ⋯
│     │ Float64 │      Float64 │ Float64 │ Float64 │ Float64 │   Float64 │ Flo ⋯
├─────┼─────────┼──────────────┼─────────┼─────────┼─────────┼───────────┼──────
│   1 │   320.0 │          1.0 │    0.03 │ 25.2317 │ 319.204 │ -0.796481 │ 11. ⋯
╰─────┴─────────┴──────────────┴─────────┴─────────┴─────────┴───────────┴──────
                                                              11 columns omitted

Similar Projects

Other tools for plant biophysics include:

If you know of similar tools not listed here, feel free to make a PR or contact us to add them.

References

Key references for plant biophysics:

  • 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., D. Loustau, et S. Delzon. 2002. "Temperature response of parameters of a biochemically based model of photosynthesis. I. Seasonal changes in mature maritime pine (Pinus pinaster Ait.)." Plant, Cell & Environment 25 (9): 1155‑65.
  • 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.