tabula 1.3.0

New classes and methods

Bugfixes & changes

Enhancements

  • Add the Merzbach ceramics dataset.
  • The plot_date() method for DateModel objects now allows to display an activity or a tempo plot.

Internals

  • Reduce required R version to 3.2.
  • Error handling has been revised and error messages have been harmonized.
  • Refer to {ggplot2} functions using :: (stop importing the entire package).
  • Use {vdiffr} to test graphical output.
  • Replace FactoMinerR::CA() with ca::ca() (this avoids having to install all {FactoMineR} dependencies when only one function is used).
  • Remove {dplyr} from the imported packages, move {magrittr} to suggested packages.

Experimental

  • When a Matrix object is first created, an identifier (UUID v4) is generated with generate_uuid(). This ID is preserved when coercing to another class. This makes it possible to identify objects representing the same initial data and associate them with the results of specific computations.
  • get_coordinates() and set_coordinates<- allow to extract and replace spatial informations in AbundanceMatrix objects.
  • get_features() allows to convert an AbundanceMatrix object to a data.frame. It is intended for compatibility with the {sf} package.

tabula 1.2.0 (release date: 2019-03-20)

New classes and methods

  • The function dateEvent() allows to compute chronological models as described in Bellanger and Husi (2006).
  • DateModel this S4 class stores the results of dateEvent().
  • SimilarityMatrix this S4 class represents a (dis)similarity matrix.
  • plotDate() method for DateModel objects.
  • plotSpot() methods for SimilarityMatrix and OccurrenceMatrix objects.
  • [ operators for several classes.

Bugfixes & changes

  • OccurrenceMatrix now stores the number of times each pair of taxa occurs together in at least one sample.
  • similarity() now returns an object of class SimilarityMatrix.
  • plotBar() no longer add confidence interval by default.
  • Remove useless accessors.

Enhancements

  • similarity() gained a new estimator: binomial co-occurrence assessment method (similarity between types).
  • seriate() gained a new argument to pass a BootCA object.

Internals

  • Add an optional progress bars with {pbapply} in long running functions.

tabula 1.1.0 (release date: 2018-12-30)

Bugfixes & changes

Enhancements

  • richness() gained new estimators:
    • For abundance data: Chao1, bias-corrected Chao1, improved Chao1 and Abundance-based Coverage Estimator (ACE).
    • For replicated incidence data: Chao2, bias-corrected Chao2, improved Chao2 and Incidence-based Coverage Estimator (ICE).

Internals

  • Add references in the Description field of the DESCRIPTION file.
  • Split the documentation for alpha-diversity measures.
  • Split the documentation for beta-diversity measures.

tabula 1.0.0 (release date: 2018-12-03)

  • Initial version on CRAN

New classes and methods

  • BootCA this S4 class stores partial bootstrap CA-based seriation results.
  • [[ operators acting on PermutationOrder and BootCA to extract parts.

Bugfixes & changes

  • refine() method for CountMatrix now use stats::rmultinorm() for partial bootstrap CA.

Enhancements

  • Add the Zuni and Mississippi ceramics datasets.
  • similarity() gained a new estimator: the Brainerd-Robinson coefficient of similarity.

Internals

  • Add a vignette for matrix seriation.

tabula 0.9.0 (release date: 2018-11-16)

  • First release.