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: | 2.0.3 |
| Depends: | R (≥ 4.0.0), ggplot2 (≥ 3.3.0), 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 (≥ 1.0.0), magrittr (≥ 1.5.0), methods (≥ 3.5.0), nlme (≥ 3.1-147), pkgnet (≥ 0.4.1), purrr (≥ 0.3.3), rlang (≥ 0.4.6), stats (≥ 4.0.0), stringr (≥ 1.4.0), tealeaves (≥ 1.0.5), tidyselect (≥ 1.0.0), utils (≥ 4.0.0) |
| Suggests: | future, testthat, knitr, rmarkdown, tidyr |
| Published: | 2022-08-12 |
| Author: | Joseph Stinziano 
[aut],
Cassaundra Roback [aut],
Demi Sargent [aut],
Bridget Murphy [aut],
Patrick Hudson [aut, dtc],
Chris Muir [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 |
| CRAN checks: | photosynthesis results |
Documentation:
| Reference manual: | photosynthesis.pdf |
| Vignettes: |
photosynthesis-curve-fitting-sensitivity-analyses Introduction to the photosynthesis package |
Downloads:
| Package source: | photosynthesis_2.0.3.tar.gz |
| Windows binaries: | r-devel: photosynthesis_2.0.3.zip, r-release: photosynthesis_2.0.3.zip, r-oldrel: photosynthesis_2.0.3.zip |
| macOS binaries: | r-release (arm64): photosynthesis_2.0.3.tgz, r-oldrel (arm64): photosynthesis_2.0.3.tgz, r-release (x86_64): photosynthesis_2.0.3.tgz, r-oldrel (x86_64): photosynthesis_2.0.3.tgz |
| Old sources: | photosynthesis archive |
Linking:
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