Package: phytoclass
Title: Estimate Chla Concentrations of Phytoplankton Groups
Version: 3.0.0
Authors@R: c(person(
    "Alexander", "Hayward", role = c("aut", "cre", "cph"), email = "phytoclass@outlook.com"
  ), person(
    given="Tylar", family="Murray", role = c("aut")
  ), person(
    given="Sebastian", family="Di Geronimo", role = c("aut")
  ), person(
    given = "Mohd Aasim Maqsood", family = "Khan", role = c("aut")
  ), person(
    given="Andy", family="McKenzie", role = c("aut")
  ))
Description: Determine the chlorophyll a (Chl a) concentrations of
        different phytoplankton groups based on their pigment
        biomarkers. The method uses non-negative matrix factorisation
        and simulated annealing to minimise error between the observed
        and estimated values of pigment concentrations (Hayward et al.
        (2023) <doi:10.1002/lom3.10541>). The approach is similar to
        the widely used 'CHEMTAX' program (Mackey et al. 1996)
        <doi:10.3354/meps144265>, but is more straightforward,
        accurate, and not reliant on initial guesses for the pigment to
        Chl a ratios for phytoplankton groups.
Imports: bestNormalize, dynamicTreeCut, ggplot2, RcppML, stats, tidyr,
        progress
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 3.8)
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), quarto, here
VignetteBuilder: knitr
URL: https://github.com/phytoclass/phytoclass/
BugReports: https://github.com/phytoclass/phytoclass/issues/
Config/testthat/edition: 3
Config/pak/sysreqs: make libicu-dev
Repository: https://phytoclass.r-universe.dev
Date/Publication: 2026-04-10 17:37:06 UTC
RemoteUrl: https://github.com/phytoclass/phytoclass
RemoteRef: HEAD
RemoteSha: 3c2df0d2eaabede0d70ce065cf813addcde4b7e9
NeedsCompilation: no
Packaged: 2026-06-09 06:32:42 UTC; root
Author: Alexander Hayward [aut, cre, cph],
  Tylar Murray [aut],
  Sebastian Di Geronimo [aut],
  Mohd Aasim Maqsood Khan [aut],
  Andy McKenzie [aut]
Maintainer: Alexander Hayward <phytoclass@outlook.com>