Package: phylloptim
Title: Leaf Gas Exchange with Explicit Plant Hydraulics
Version: 0.36.0
Authors@R: c(
    person("Isaac", "Towers", , "", "aut",
            comment = "Author of the leaf gas exchange and hydraulics model"),
    person("Daniel", "Falster", , "daniel.falster@unsw.edu.au", c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9814-092X")),
    person("Rich", "FitzJohn", , "", "ctb",
            comment = "Root-finding utilities (uniroot.hpp)")
    )
Maintainer: Daniel Falster <daniel.falster@unsw.edu.au>
Description: An implementation of leaf-level gas exchange in which
        stomatal behaviour emerges from hydraulics rather than an
        empirical conductance model. Farquhar-von Caemmerer-Berry
        photosynthesis is coupled to an explicit soil-root-stem-leaf
        water transport path, with Weibull vulnerability curves for
        both xylem and roots, multi-layer soil and gravitational head,
        and the operating point is chosen by Sperry-style gain-risk
        profit maximisation over the root-collar water potential.
        Forward-mode automatic differentiation supplies exact
        derivatives of profit with respect to the collar potential.
        Extracted from the TF24 strategy in the 'plant' package so that
        it can be tested, profiled, extended and embedded
        independently. The model itself is a set of self-contained C++
        headers, under inst/include, that use no R and no 'Rcpp' and
        depend only on Boost and the header-only parts of 'odelia':
        they compile and run with no R present at all, so the model can
        be linked directly into a C++ program or bound to another
        language such as Python without going through this package. R
        users get the same model through an 'RcppR6' layer that sits on
        top of those headers and is never included by them, and R
        packages get it by naming 'phylloptim' in their LinkingTo
        field.
Encoding: UTF-8
License: AGPL (>= 3)
Depends: R (>= 4.2.0)
Imports: graphics, R6, Rcpp, stats, utils
LinkingTo: Rcpp, BH, odelia (>= 0.10.0)
Suggests: codetools, dplyr, ggplot2, knitr, rmarkdown, testthat (>=
        3.0.0), tibble, tidyr, xml2, yaml
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://github.com/traitecoevo/phylloptim,
        https://traitecoevo.github.io/phylloptim/
BugReports: https://github.com/traitecoevo/phylloptim/issues
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
Repository: https://traitecoevo.r-universe.dev
Date/Publication: 2026-11-10 07:34:07 UTC
RemoteUrl: https://github.com/traitecoevo/phylloptim
RemoteRef: HEAD
RemoteSha: af31832bb456a19667882ea8ce15b7c98c8ffd55
NeedsCompilation: yes
Packaged: 2026-11-13 08:31:28 UTC; root
Author: Isaac Towers [aut] (Author of the leaf gas exchange and hydraulics
    model),
  Daniel Falster [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9814-092X>),
  Rich FitzJohn [ctb] (Root-finding utilities (uniroot.hpp))