NEWS.md

In tpq/amalgam: Amalgamation-Based Dimension Reduction of Compositional Data

amalgam 0.1.8

• New zero-handling procedure
  • If shrink = TRUE, bin frequencies are estimated by James-Stein-type shrinkage
• New objective functions
  • Add asSLR support to objective.keepWADIST by comparing with Euclidean distance
  • objective.maxDSKL maximizes the RDA of a PCoA of the SKL divergences

amalgam 0.1.7

• New objective function
  • objective.keepSKL preserves the symmetric Kullback-Leibler (SKL) divergences

amalgam 0.1.6

• New objective function
  • objective.keepWADIST preserves the weighted Aitchison distances

amalgam 0.1.5

• Update information objectives
  • objective.keepEntropy now recloses the amalgamation (as it should)
  • objective.maxDEntropy now recloses the amalgamation (as it should)

amalgam 0.1.4

• New backend information functions
  • shannon function calculates Shannon's index
  • uniformity function calculates a normalized Shannon's index
• New objective functions
  • objective.keepEntropy preserves the relative entropy of the amalgams
  • objective.maxDEntropy maximizes the between-group difference in amalgam entropy
• Update amalgam function
  • prepareArgs now forces a re-closure of the data

amalgam 0.1.3

• Switch objective.maxRDA and objective.maxRDA2 (again)

amalgam 0.1.2

• Switch objective.maxRDA and objective.maxRDA2

amalgam 0.1.1

• Update objective.maxRDA and objective.maxRDA2
  • Now sums inertia across all RD axes (as it should)

amalgam 0.1.0

• Update objective.maxRDA2 method
  • Like objective.maxRDA but makes "z" the community matrix

amalgam 0.0.9

• Update objective.maxRDA method
  • Handle rare case when constrained axes explain no variance
  • Add check for "z" argument

amalgam 0.0.8

• Have prepareArgs coerce "z" as a data.frame
• Update objective.maxRDA method
  • Now save the intermediate data to debug

amalgam 0.0.7

• Update objective.maxRDA method
  • Add tryCatch to handle the Lapack routine 'dgesdd' error
  • This error occurs when the SVD fails to converge

amalgam 0.0.6

• New as.slr function turns components into a set of summed log-ratios
• Update amalgam
  • New asSLR argument passed to objective functions
  • Objective functions now support SLRs
  • Update plot method for SLRs

amalgam 0.0.5

• Update amalgam
  • Zeros now replaced with zCompositions::cmultRepl
  • Correctly coerce input as matrix

amalgam 0.0.4

• New scalar product methods
  • New adot computes Aitchison scalar product for two vectors
  • New amat computes Aitchison scalar product for two matrices
  • New unit tests

amalgam 0.0.3

• Update plot.amalgam
  • Add argument to select which amalgams to show in ternary plot

amalgam 0.0.2

• Move zCompositions to Suggests

amalgam 0.0.1

• New int methods
  • int.fromNbit converts a binary vector into integers
• New weight methods
  • weight.Nto1 builds a many-to-one amalgamation matrix
  • weight.NtoN builds a many-to-many amalgamation matrix
• New objective methods
  • objective.keepDist seeks to preserve Aitchison distance
  • objective.maxRDA seeks to maximize constraint of RDA
• New amalgam wrapper
  • This function runs a genetic algorithm for the objective
  • print.amalgam shows the object structure
  • plot.amalgam makes 4-panel figure

tpq/amalgam documentation built on March 14, 2020, 10:27 a.m.