PlantBiophysics.jl

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

Overview

PlantBiophysics is a package to deal with biophysical processes of plants such as photosynthesis, conductances for heat, water vapor and CO₂, latent, sensible energy fluxes, net radiation and temperature. It has two main use-cases:

  • fit the parameters of the models using the generic fit function
  • simulate the processes using the corresponding models

The benefits of PlantBiophysics over existing tools are mainly:

  • (very) fast yet interactive
  • easily scalable: from single objects to whole scenes, one time step to many.
  • easily extendable: make your own model, PlantBiophysics handles its coupling with others automatically
  • composable: use Unitful to propagate units, use MonteCarloMeasurements.jl to propagate measurement error

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

Examples

See the First simulation section for examples.

Similar projects

A lot of similar tools exist in the wild, pick yours from this list:

If you develop such tools and it is not on the list, please make a PR or contact me so we can add it! 😃

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.