Package: photosynthesis
Version: 2.1.5
Date: 2024-11-23
Title: Tools for Plant Ecophysiology & Modeling
Authors@R: c(
    person("Joseph", "Stinziano", email = "josephstinziano@gmail.com", role = "aut", comment = c(ORCID = "0000-0002-7628-4201")),
    person("Cassaundra", "Roback", email = "croback@unm.edu", role = "aut"),
    person("Demi", "Sargent", email = "d.sargent@westernsydney.edu.au", role = "aut"),
    person("Bridget", "Murphy", email = "bridget.murphy@mail.utoronto.ca", role = "aut"),
    person("Patrick", "Hudson", email = "hudson.patrick.j@gmail.com", role = c("aut", "dtc")), 
    person("Chris", "Muir", email = "cdmuir@wisc.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2555-3878"))
    )
Depends: R (>= 4.1.0), 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
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()).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/cdmuir/photosynthesis
BugReports: https://github.com/cdmuir/photosynthesis/issues
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: libicu-dev libudunits2-dev libx11-dev
Repository: https://cdmuir.r-universe.dev
Date/Publication: 2025-03-07 18:39:05 UTC
RemoteUrl: https://github.com/cdmuir/photosynthesis
RemoteRef: HEAD
RemoteSha: dee21b23e504f908c1acecbdf11033d8218bad67
NeedsCompilation: no
Packaged: 2026-07-04 00:23:11 UTC; root
Author: Joseph Stinziano [aut] (ORCID: <https://orcid.org/0000-0002-7628-4201>),
  Cassaundra Roback [aut],
  Demi Sargent [aut],
  Bridget Murphy [aut],
  Patrick Hudson [aut, dtc],
  Chris Muir [aut, cre] (ORCID: <https://orcid.org/0000-0003-2555-3878>)
Maintainer: Chris Muir <cdmuir@wisc.edu>