Package: photosynthesis 2.1.4
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()).
Authors:
photosynthesis_2.1.4.tar.gz
photosynthesis_2.1.4.zip(r-4.5)photosynthesis_2.1.4.zip(r-4.4)photosynthesis_2.1.4.zip(r-4.3)
photosynthesis_2.1.4.tgz(r-4.4-any)photosynthesis_2.1.4.tgz(r-4.3-any)
photosynthesis_2.1.4.tar.gz(r-4.5-noble)photosynthesis_2.1.4.tar.gz(r-4.4-noble)
photosynthesis_2.1.4.tgz(r-4.4-emscripten)photosynthesis_2.1.4.tgz(r-4.3-emscripten)
photosynthesis.pdf |photosynthesis.html✨
photosynthesis/json (API)
NEWS
# Install 'photosynthesis' in R: |
install.packages('photosynthesis', repos = c('https://cdmuir.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cdmuir/photosynthesis/issues
- photo_parameters - Input parameters to simulate C3 photosynthesis using 'photosynthesis()'
Last updated 8 months agofrom:73f32a813f. Checks:OK: 3 NOTE: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 30 2024 |
R-4.5-win | OK | Oct 30 2024 |
R-4.5-linux | OK | Oct 30 2024 |
R-4.4-win | NOTE | Oct 30 2024 |
R-4.4-mac | NOTE | Oct 30 2024 |
R-4.3-win | NOTE | Oct 30 2024 |
R-4.3-mac | NOTE | Oct 30 2024 |
Exports:A_demandA_supplyanalyze_sensitivityaq_responsebakebake_parcalculate_jcalculate_jmaxcompile_datacompute_sensitivityconstantsenviro_parfit_aci_responsefit_aq_responsefit_aq_response2fit_g_mc_variableJfit_gs_modelfit_hydra_vuln_curvefit_manyfit_photosynthesisfit_PV_curvefit_r_light_kokfit_r_light_WalkerOrtfit_r_light_yinfit_r_light2fit_t_responseFvCBget_all_modelsget_default_modelgs_mod_ballberrygs_mod_leuninggs_mod_optigs_mod_optifullJleaf_parmake_bakeparmake_constantsmake_enviroparmake_leafparmarshall_biscoe_1980parameter_namesphotophotosynthesisppm2paprint_graphsread_li6800read_licorrequired_variablessimulate_errort_response_arrheniust_response_arrhenius_kruset_response_arrhenius_medlynt_response_arrhenius_toptt_response_calc_dSt_response_calc_toptt_response_heskelt_response_mmrttemp_resp1temp_resp2W_carboxW_regenW_tpu
Dependencies:backportsbitbit64checkmateclicliprcodetoolscolorspacecpp11crayondigestdplyrfansifarverfurrrfuturegenericsggplot2globalsgluegtablegunithmsisobandlabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvminpack.lmmunsellnlmeparallellypillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangscalesstringistringrtealeavestibbletidyselecttzdbunitsutf8vctrsviridisLitevroomwithr
Fitting CO2 response curves
Rendered fromco2-response.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Fit models to estimate light respiration
Rendered fromlight-respiration.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-19
Started: 2022-11-08
Fitting light response curves
Rendered fromlight-response.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-18
Started: 2022-11-08
Fitting hydraulic vulnerability curves
Rendered fromhydraulic-vulnerability.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Introduction to the photosynthesis package
Rendered fromphotosynthesis-introduction.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2018-11-17
Fitting mesophyll conductance
Rendered frommesophyll-conductance.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Modeling C3 Photosynthesis: recommendations for common scenarios
Rendered frommodeling-recommendations.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Fitting pressure-volume curves
Rendered frompressure-volume.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Sensitivity analysis
Rendered fromsensitivity-analysis.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Fitting stomatal conductance models
Rendered fromstomatal-conductance.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08
Fitting temperature response curves
Rendered fromtemperature-response.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2022-11-08
Started: 2022-11-08