Changes in version 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.

                 Changes in version 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.

                        Changes in version 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

                        Changes in version 2.2.0                        

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

                        Changes in version 2.1.0                        

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

                 Changes in version 2.0.0 (2024-11-14)                  

                 Changes in version 1.2.0 (2024-05-11)                  

                        Changes in version 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'.

                     Changes in version 0.0.0.9000                      

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