photosynthesis: Tools for Plant Ecophysiology & Modeling

Contains modeling and analytical tools for plant ecophysiology. MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer, Berry (1980) <doi:10.1007/BF00386231> model as described in Buckley and Diaz-Espejo (2015) <doi:10.1111/pce.12459>. It uses units to ensure that parameters are properly specified and transformed before calculations. Temperature response functions get automatically "baked" into all parameters based on leaf temperature following Bernacchi et al. (2002) <doi:10.1104/pp.008250>. The package includes boundary layer, cuticular, stomatal, and mesophyll conductances to CO2, which each can vary on the upper and lower portions of the leaf. Use straightforward functions to simulate photosynthesis over environmental gradients such as Photosynthetic Photon Flux Density (PPFD) and leaf temperature, or over trait gradients such as CO2 conductance or photochemistry. ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) <doi:10.1007/BF00386231>) and AQ curves (Marshall & Biscoe (1980) <doi:10.1093/jxb/31.1.29>), temperature responses (Heskel et al. (2016) <doi:10.1073/pnas.1520282113>; Kruse et al. (2008) <doi:10.1111/j.1365-3040.2008.01809.x>, Medlyn et al. (2002) <doi:10.1046/j.1365-3040.2002.00891.x>, Hobbs et al. (2013) <doi:10.1021/cb4005029>), respiration in the light (Kok (1956) <doi:10.1016/0006-3002(56)90003-8>, Walker & Ort (2015) <doi:10.1111/pce.12562>, Yin et al. (2009) <doi:10.1111/j.1365-3040.2009.01934.x>, Yin et al. (2011) <doi:10.1093/jxb/err038>), mesophyll conductance (Harley et al. (1992) <doi:10.1104/pp.98.4.1429>), pressure-volume curves (Koide et al. (2000) <doi:10.1007/978-94-009-2221-1_9>, Sack et al. (2003) <doi:10.1046/j.0016-8025.2003.01058.x>, Tyree et al. (1972) <doi:10.1093/jxb/23.1.267>), hydraulic vulnerability curves (Ogle et al. (2009) <doi:10.1111/j.1469-8137.2008.02760.x>, Pammenter et al. (1998) <doi:10.1093/treephys/18.8-9.589>), and tools for running sensitivity analyses particularly for variables with uncertainty (e.g. g_mc(), gamma_star(), R_d()).

Version: 2.1.1
Depends: R (≥ 4.0.0), ggplot2 (≥ 3.4.0), minpack.lm (≥ 1.2-1), units (≥ 0.6.6)
Imports: checkmate (≥ 2.0.0), crayon (≥ 1.3.4), dplyr (≥ 0.8.5), furrr (≥ 0.1.0), glue (≥ 1.4.0), graphics (≥ 4.0.0), grDevices (≥ 4.0.0), gunit (≥ 1.0.2), lifecycle (≥ 1.0.0), magrittr (≥ 1.5.0), methods (≥ 3.5.0), nlme (≥ 3.1-147), purrr (≥ 0.3.3), rlang (≥ 0.4.6), stats (≥ 4.0.0), stringr (≥ 1.4.0), tealeaves (≥ 1.0.5), tibble (≥ 3.0.0), utils (≥ 4.0.0)
Suggests: brms, broom, future, knitr, rmarkdown, testthat, tidyr, tidyselect
Published: 2022-11-19
Author: Joseph Stinziano ORCID iD [aut], Cassaundra Roback [aut], Demi Sargent [aut], Bridget Murphy [aut], Patrick Hudson [aut, dtc], Chris Muir ORCID iD [aut, cre]
Maintainer: Chris Muir <cdmuir at hawaii.edu>
BugReports: https://github.com/cdmuir/photosynthesis/issues
License: MIT + file LICENSE
URL: https://github.com/cdmuir/photosynthesis
NeedsCompilation: no
Citation: photosynthesis citation info
Materials: README NEWS
In views: Agriculture
CRAN checks: photosynthesis results

Documentation:

Reference manual: photosynthesis.pdf
Vignettes: co2-response
hydraulic-vulnerability
Fit models to estimate light respiration
Fitting light response curves
mesophyll-conductance
Modeling C3 Photosynthesis: recommendations for common scenarios
Introduction to the photosynthesis package
pressure-volume
sensitivity-analysis
stomatal-conductance
temperature-response

Downloads:

Package source: photosynthesis_2.1.1.tar.gz
Windows binaries: r-devel: photosynthesis_2.1.1.zip, r-release: photosynthesis_2.1.0.zip, r-oldrel: photosynthesis_2.1.1.zip
macOS binaries: r-release (arm64): photosynthesis_2.1.1.tgz, r-oldrel (arm64): photosynthesis_2.1.1.tgz, r-release (x86_64): photosynthesis_2.1.1.tgz, r-oldrel (x86_64): photosynthesis_2.1.1.tgz
Old sources: photosynthesis archive

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