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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