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photosynthesis

Tools for Plant Ecophysiology & Modeling

v2.1.5 · Nov 24, 2024 · MIT + file LICENSE
CRAN GitHub Mirror

Description

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()).

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NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bake-par.R' 'bake.R' 'calculated-parameters.R' 'conductance.R'
    'constants.R' 'enviro-par.R' 'fit_aq_response.R'
    'fit_aq_response2.Rd' 'fit_photosynthesis.R' 'fit_r_light.R'
    'fit_r_light2.Rd' 'leaf-par.R' 'make_parameters.R' 'models.R'
    'parameter_names.R' 'photosynthesis.R' 'read_licor.R'
    'simulate_error.R' 'simulate_error.Rd' 'utils.R'
NOTE r-oldrel-macos-arm64

installed package size

installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
NOTE r-oldrel-windows-x86_64

installed package size

installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_photosynthesis.R’ ‘fit_r_light.R’ ‘leaf-par.R’
    ‘make_parameters.R’ ‘models.R’ ‘parameter_names.R’ ‘photosynthesis.R’
    ‘read_licor.R’ ‘simulate_error.R’ ‘utils.R’
NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bake-par.R' 'bake.R' 'calculated-parameters.R' 'conductance.R'
    'constants.R' 'enviro-par.R' 'fit_aq_response.R'
    'fit_aq_response2.Rd' 'fit_photosynthesis.R' 'fit_r_light.R'
    'fit_r_light2.Rd' 'leaf-par.R' 'make_parameters.R' 'models.R'
    'parameter_names.R' 'photosynthesis.R' 'read_licor.R'
    'simulate_error.R' 'simulate_error.Rd' 'utils.R'

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bake-par.R' 'bake.R' 'calculated-parameters.R' 'conductance.R'
    'constants.R' 'enviro-
...[truncated]...
ponse.R'
    'fit_aq_response2.Rd' 'fit_photosynthesis.R' 'fit_r_light.R'
    'fit_r_light2.Rd' 'leaf-par.R' 'make_parameters.R' 'models.R'
    'parameter_names.R' 'photosynthesis.R' 'read_licor.R'
    'simulate_error.R' 'simulate_error.Rd' 'utils.R'
NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-
...[truncated]...
ponse.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_photosynthesis.R’ ‘fit_r_light.R’ ‘leaf-par.R’
    ‘make_parameters.R’ ‘models.R’ ‘parameter_names.R’ ‘photosynthesis.R’
    ‘read_licor.R’ ‘simulate_error.R’ ‘utils.R’
NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bake-par.R' 'bake.R' 'calculated-parameters.R' 'conductance.R'
    'constants.R' 'enviro-
...[truncated]...
ponse.R'
    'fit_aq_response2.Rd' 'fit_photosynthesis.R' 'fit_r_light.R'
    'fit_r_light2.Rd' 'leaf-par.R' 'make_parameters.R' 'models.R'
    'parameter_names.R' 'photosynthesis.R' 'read_licor.R'
    'simulate_error.R' 'simulate_error.Rd' 'utils.R'
NOTE r-oldrel-macos-arm64

installed package size

installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
NOTE r-oldrel-windows-x86_64

installed package size

installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb

Reverse Dependencies (1)

suggests

gasanalyzer

Dependency Network

Dependencies Reverse dependencies ggplot2 minpack.lm units checkmate crayon dplyr furrr glue gunit lifecycle magrittr nlme progress purrr readr +3 more dependencies gasanalyzer photosynthesis

Version History

new 2.1.5 Mar 10, 2026
updated 2.1.5 ← 2.1.4 diff Nov 23, 2024
updated 2.1.4 ← 2.1.3 diff Aug 14, 2023
updated 2.1.3 ← 2.1.2 diff May 10, 2023
updated 2.1.2 ← 2.1.1 diff Mar 30, 2023
updated 2.1.1 ← 2.1.0 diff Nov 18, 2022
updated 2.1.0 ← 2.0.3 diff Nov 7, 2022
updated 2.0.3 ← 2.0.1 diff Aug 11, 2022
updated 2.0.1 ← 2.0.0 diff Jun 30, 2021
updated 2.0.0 ← 1.0.2 diff Sep 11, 2020
updated 1.0.2 ← 1.0.0 diff Jun 30, 2020
new 1.0.0 May 8, 2019