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: |
2.1.5 |
| 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), progress (≥ 1.2.0), purrr (≥ 0.3.3), readr (≥ 2.0.0), rlang (≥ 0.4.6), stats (≥ 4.0.0), stringr (≥ 1.4.0), tealeaves (≥
1.0.5), utils (≥ 4.0.0) |
| Suggests: |
brms, broom, future, knitr, rmarkdown, testthat, tibble, tidyr, tidyselect |
| Published: |
2024-11-24 |
| DOI: |
10.32614/CRAN.package.photosynthesis |
| 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 wisc.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 (source, R code)
hydraulic-vulnerability (source, R code)
Fit models to estimate light respiration (source, R code)
Fitting light response curves (source, R code)
mesophyll-conductance (source, R code)
Modeling C3 Photosynthesis: recommendations for common scenarios (source, R code)
Introduction to the photosynthesis package (source, R code)
pressure-volume (source, R code)
sensitivity-analysis (source, R code)
stomatal-conductance (source, R code)
temperature-response (source, R code)
|
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