NEWS

---

phytoclass 3.0.0

Functionality-breaking change

Previous version performed "major pigment" checks using a set of hard-coded taxa-pigment pairs. When a major pigment was not included in the sample set, the taxa was dropped.

For phytoclass>=3.0.0, these major pigments are indicated using '2's in the F matrix.

The default behavior, specified by the following matrix:

check_mat <-
  matrix(
    c(
      c(
        "Chlorophytes", "Prasinophytes", "Prasinophytes", "Dinoflagellates-1",
        "Diatoms-1", "Diatoms-2", "Syn", "Cryptophytes", "Haptophytes-H",
        "Haptophytes-L", "Diatoms-1", "Pelagophytes", "Prasinophytes"
      ),
      c(
        "Chl_b", "Chl_b", "Pra", "Per", "Chl_c1", "Fuco", "Zea", "Allo",
        "X19hex", "X19hex", "Fuco", "X19but", "Chl_b"
      )
    ),
    ncol = 2
  )

Is reproduced using an updated default F matrix that includes '2's.

Some very rare edge cases will function differently. Older custom F matrices using only '1's will no longer do the major pigment check for the exact string matches above.

phytoclass 2.3.1 (2026-01-30)

Enhancements

• Updated min_max.rda using new pigment ratio min/max from Simon Wright.
• Improve "custom-example" vignette to use southern ocean min_max.

phytoclass 2.3.0

This version update removes internal functions that became unused once combined into a single function. The sets of functions include "Conduit", "Fac_F_RR", "Minimise_elements" and "Random_neighbor".

New features

• convergence_figure() was added in simulated_annealing_Prochloro()
• Progress bar was added in simulated_annealing_Prochloro()
• Cluster() now accepts a row_ids input vector to name each sample
• Cluster() exports an assigments item that relates the ID to the cluster
• Cluster() checks if data.frame input has a column of strings and removes them prior to clustering

Bug Fixes

• The figure functions would error if the number of colors needed exceeded 11. Now, the figure functions can handle additional colors.
• Cluster() had an issue if given a matrix without rownames and would error, now will convert to data.frame prior to running boxcar normalising

phytoclass 2.2.0

• Add automatic switch to Prochlorococcus function based on dvchl column
• added convergence plot

phytoclass 2.1.0

• performance improvements
• improved documentation
• • continuous integration
• • tests
• improved matrix checks
• improved error messages

phytoclass 2.0.0 (2024-11-14)

phytoclass 1.2.0 (2024-05-11)

phytoclass 1.1.0

Breaking changes

New features

We have added a function which allows for chlorophyll derivations for prochlorococcus.

Minor improvements and fixes

We have improved documentation, and relabelled groups, such as 'Diatom-1' instead of 'Diatom-A'.

phytoclass 0.0.0.9000

• Added a NEWS.md file to track changes to the package.