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:Joseph Stinziano [aut], Cassaundra Roback [aut], Demi Sargent [aut], Bridget Murphy [aut], Patrick Hudson [aut, dtc], Chris Muir [aut, cre]

photosynthesis_2.1.4.tar.gz
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photosynthesis_2.1.4.tgz(r-4.4-any)photosynthesis_2.1.4.tgz(r-4.3-any)
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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'))

Peer review:

Bug tracker:https://github.com/cdmuir/photosynthesis/issues

Datasets:
  • photo_parameters - Input parameters to simulate C3 photosynthesis using 'photosynthesis()'

On CRAN:

7.04 score 34 stars 59 scripts 311 downloads 62 exports 59 dependencies

Last updated 8 months agofrom:73f32a813f. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 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.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Fit models to estimate light respiration

Rendered fromlight-respiration.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-19
Started: 2022-11-08

Fitting light response curves

Rendered fromlight-response.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-18
Started: 2022-11-08

Fitting hydraulic vulnerability curves

Rendered fromhydraulic-vulnerability.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Introduction to the photosynthesis package

Rendered fromphotosynthesis-introduction.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2018-11-17

Fitting mesophyll conductance

Rendered frommesophyll-conductance.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Modeling C3 Photosynthesis: recommendations for common scenarios

Rendered frommodeling-recommendations.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Fitting pressure-volume curves

Rendered frompressure-volume.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Sensitivity analysis

Rendered fromsensitivity-analysis.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Fitting stomatal conductance models

Rendered fromstomatal-conductance.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Fitting temperature response curves

Rendered fromtemperature-response.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-08
Started: 2022-11-08

Readme and manuals

Help Manual

Help pageTopics
'photosynthesis' packagephotosynthesis-package
CO2 supply and demand function (mol / m^2 s)A_demand A_supply
Running 2-parameter sensitivity analysesanalyze_sensitivity
Non-rectangular hyperbolic model of light responsesaq_response
Leaf parameter temperature responsesbake temp_resp1 temp_resp2
S3 class bake_parbake_par
S3 class bakedbaked-class
Inverse non-rectangular hyperbola for J_max calculationcalculate_j calculate_jmax
Get default functions for calculated parameters in photosynthesiscalculated-parameters get_f_parameter
Conductance to CO2 (mol / m^2 / s).get_gbc .get_gmc .get_gsc .get_gtc .get_guc CO2_conductance
Compiling outputs from listscompile_data
Computing measures of sensitivitycompute_sensitivity
S3 class constantsconstants
S3 class enviro_parenviro_par
Fitting ACi curvesfit_aci_response
Fitting light responses of net CO2 assimilationfit_aq_response
Fit photosynthetic light-response curvesfit_aq_response2
Fitting mesophyll conductance with the variable J methodfit_g_mc_variableJ
Fitting stomatal conductance modelsfit_gs_model
Fitting hydraulic vulnerability curvesfit_hydra_vuln_curve
Fitting many functions across groupsfit_many
Fit photosynthetic models with gas-exchange datafit_photosynthesis
Fitting pressure-volume curvesfit_PV_curve
Estimating light respirationfit_r_light_kok fit_r_light_WalkerOrt fit_r_light_yin
Fit models to estimate light respiration (R_\mathrm{d})fit_r_light2
Fitting temperature responsesfit_t_response
Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis modelFvCB W_carbox W_regen W_tpu
Get default modelget_all_models get_default_model marshall_biscoe_1980
Stomatal conductance modelsgs_mod_ballberry gs_mod_leuning gs_mod_opti gs_mod_optifull
J: Rate of electron transport (umol/m^2/s)J
S3 class leaf_parleaf_par
Make lists of parameters for 'photosynthesis'make_bakepar make_constants make_enviropar make_leafpar make_parameters
Get vector of parameter namesparameter_names
Input parameters to simulate C3 photosynthesis using 'photosynthesis()'photo_parameters
Simulate C3 photosynthesisphoto photosynthesis
Convert pressure from PPM to Pascalsppm2pa
Printing graphs to systemprint_graphs
Read a LI-COR fileread_li6800
Read a LI-COR fileread_licor
Variables required for *photosynthesis* modelsrequired_variables
Simulate gas exchange data with measurement errorsimulate_error
Temperature response functionst_response_arrhenius t_response_arrhenius_kruse t_response_arrhenius_medlyn t_response_arrhenius_topt t_response_calc_dS t_response_calc_topt t_response_heskel t_response_mmrt