Changelog
Source:NEWS.md
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 2.3.0
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
errorif 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