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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "photosynthesis" in publications use:'
type: software
license: MIT
title: 'photosynthesis: Tools for Plant Ecophysiology & Modeling'
version: 2.1.5
doi: 10.1093/aobpla/plab059
identifiers:
- type: doi
  value: 10.32614/CRAN.package.photosynthesis
abstract: 'Contains modeling and analytical tools for plant ecophysiology. MODELING:
  Simulate C3 photosynthesis using the Farquhar, von Caemmerer, Berry (1980) <https://doi.org/10.1007/BF00386231>
  model as described in Buckley and Diaz-Espejo (2015) <https://doi.org/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) <https://doi.org/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)
  <https://doi.org/10.1007/BF00386231>) and AQ curves (Marshall & Biscoe (1980) <https://doi.org/10.1093/jxb/31.1.29>),
  temperature responses (Heskel et al. (2016) <https://doi.org/10.1073/pnas.1520282113>;
  Kruse et al. (2008) <https://doi.org/10.1111/j.1365-3040.2008.01809.x>, Medlyn et
  al. (2002) <https://doi.org/10.1046/j.1365-3040.2002.00891.x>, Hobbs et al. (2013)
  <https://doi.org/10.1021/cb4005029>), respiration in the light (Kok (1956) <https://doi.org/10.1016/0006-3002(56)90003-8>,
  Walker & Ort (2015) <https://doi.org/10.1111/pce.12562>, Yin et al. (2009) <https://doi.org/10.1111/j.1365-3040.2009.01934.x>,
  Yin et al. (2011) <https://doi.org/10.1093/jxb/err038>), mesophyll conductance (Harley
  et al. (1992) <https://doi.org/10.1104/pp.98.4.1429>), pressure-volume curves (Koide
  et al. (2000) <https://doi.org/10.1007/978-94-009-2221-1_9>, Sack et al. (2003)
  <https://doi.org/10.1046/j.0016-8025.2003.01058.x>, Tyree et al. (1972) <https://doi.org/10.1093/jxb/23.1.267>),
  hydraulic vulnerability curves (Ogle et al. (2009) <https://doi.org/10.1111/j.1469-8137.2008.02760.x>,
  Pammenter et al. (1998) <https://doi.org/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:
- family-names: Stinziano
  given-names: Joseph
  email: josephstinziano@gmail.com
  orcid: https://orcid.org/0000-0002-7628-4201
- family-names: Roback
  given-names: Cassaundra
  email: croback@unm.edu
- family-names: Sargent
  given-names: Demi
  email: d.sargent@westernsydney.edu.au
- family-names: Murphy
  given-names: Bridget
  email: bridget.murphy@mail.utoronto.ca
- family-names: Hudson
  given-names: Patrick
  email: hudson.patrick.j@gmail.com
- family-names: Muir
  given-names: Chris
  email: cdmuir@wisc.edu
  orcid: https://orcid.org/0000-0003-2555-3878
preferred-citation:
  type: article
  title: Principles of resilient coding for plant ecophysiologists
  authors:
  - family-names: Stinziano
    given-names: Joseph R
  - family-names: Roback
    given-names: Cassaundra
    email: croback@unm.edu
  - family-names: Gamble
    given-names: Demi
  - family-names: Murphy
    given-names: Bridget K
  - family-names: Hudson
    given-names: Patrick J
  - family-names: Muir
    given-names: Christopher D
  journal: AoB PLANTS
  volume: '13'
  issue: '5'
  year: '2021'
  month: '10'
  issn: 2041-2851
  doi: 10.1093/aobpla/plab059
  url: https://doi.org/10.1093/aobpla/plab059
  notes: plab059
repository: https://CRAN.R-project.org/package=photosynthesis
repository-code: https://github.com/cdmuir/photosynthesis
url: https://github.com/cdmuir/photosynthesis
date-released: '2024-11-23'
contact:
- family-names: Muir
  given-names: Chris
  email: cdmuir@wisc.edu
  orcid: https://orcid.org/0000-0003-2555-3878
references:
- type: generic
  title: 'photosynthesis: tools for plant ecophysiology & modeling'
  authors:
  - family-names: Stinziano
    given-names: Joseph R
  - family-names: Roback
    given-names: Cassaundra
  - family-names: Gamble
    given-names: Demi
  - family-names: Murphy
    given-names: Bridget K
  - family-names: Hudson
    given-names: Patrick J
  - family-names: Muir
    given-names: Christopher D
  notes: R package version 2.1.4
  year: '2023'
  url: https://CRAN.R-project.org/package=photosynthesis