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Changelog

Source: NEWS.md

tabula 3.0.1.9000

Enhancements

tabula 3.0.1

CRAN release: 2023-11-28

Enhancements

  • Omit axes labels where they would abut or overlap previously drawn labels.

tabula 3.0.0

CRAN release: 2023-08-22

Bugfixes & changes

  • Fix handling of missing values in heterogeneity index (#27).

Breaking changes

  • *Use graphics instead of ggplot2 for plotting. The internal use of ggplot2** was badly interoperable or composable. This also reduces hard dependencies.

Internals

  • Use tinytest and tinysnapshot instead of testthat and vdiffr.

tabula 2.0.0

CRAN release: 2022-11-06

New classes and methods

  • Add plot_diceleraas() to display a Dice-Lerass diagram.
  • Add matrigraph() to display a heatmap highlighting the deviations from independence.
  • Add seriograph() to display a Ford diagram highlighting the relationships between rows and columns.

Bugfixes & changes

Breaking changes

  • Seriation methods are no longer reexported from kairos.

tabula 1.8.0

CRAN release: 2022-09-08

Seriation methods are now reexported from kairos and will be removed in a future release.

New classes and methods

Bugfixes & changes

  • Remove all previously deprecated methods.

tabula 1.7.0

CRAN release: 2022-06-23

Seriation methods are now reexported from kairos and will be removed in a future release.

New classes and methods

Bugfixes & changes

  • rarefaction() now returns a RarefactionIndex object.
  • Deprecate bootstrap_*(), jackknife_*() and simulate_*().
  • Deprecate index_heterogeneity(), index_evenness(), index_richness() and index_composition().

Breaking changes

  • turnover() no longer accept multiple methods as argument.
  • Fix bootstrap() method for DiversityIndex objects: resample with replacement instead of simulating observations from a multinomial distribution.
  • No longer use classes from arkhe: all methods are now defined for matrix and data.frame.
  • Deprecate seriation methods: seriate_*() and permute() now belong to kairos.

tabula 1.6.1

CRAN release: 2021-05-25

Bugfixes & changes

  • Remove all previously deprecated methods.

Breaking changes

  • Remove dating methods: *_mcd(), *_event(), *_accumulation(), plot_date() now belong to kairos.
  • Remove frequency increment test: test_fit() and plot_time() now belong to kairos.

tabula 1.6.0

CRAN release: 2021-05-11

New classes and methods

  • Add DateEvent: S4 class to store the event and accumulation times of archaeological assemblages.
  • Add CompositionIndex: S4 class that represent an asymptotic species richness.
  • Add IncrementTest: S4 class that represent a Frequency Increment Test results.
  • Add eppm() and pvi() to calculate independence statistics.
  • Add predict_event() and predict_accumulation to estimate the event and accumulation dates of an assemblage.
  • Add bootstrap_*() and jackknife_*() to perform bootstrap and jackknife resampling.
  • Add simulate_evenness() and simulate_richness() to measure diversity in simulated assemblages.
  • seriate_average() replaces seriate_correspondance().
  • seriate_rank() replaces seriate_reciprocal().

Bugfixes & changes

  • Remove all previously deprecated methods.
  • Deprecate seriate_correspondance(), seriate_reciprocal() and refine_dates(),
  • index_composition() now returns a CompositionIndex object.
  • similarity() now returns a dist object.
  • date_mcd() now returns an DateMCD object.
  • test_fit() now returns an IncrementTest object.
  • DiversityIndex lost bootstrap() and jackknife() slots.
  • Rename BootCA to RefineCA.
  • Rename DateModel to DateEvent.
  • RefineCA and DateEvent now inherit from dimensio::CA.

Enhancements

  • date_mcd(), date_event() and plot_time() gained a new dates argument.

Internals

  • Imports arkhe >= 0.3.0
  • Re-export methods from arkhe.
  • Imports dimensio.
  • Use datasets from folio.
  • Remove pbapply from suggested packages.
  • Rewrite plot_ford() and plot_bertin().

tabula 1.5.1

CRAN release: 2020-03-19

Bugfixes & changes

  • CRAN pacakge check warning (r-devel) has been fixed (use a stringsAsFactors = FALSE default).

tabula 1.5.0

CRAN release: 2020-01-16

Bugfixes & changes

  • CRAN package check error with long doubles disabled has been fixed (tested with R-hub debian-gcc-devel-nold).
  • CRAN package check notes have been fixed.

Internals

  • Depend on arkhe.

tabula 1.4.0

New classes and methods

  • DiversityIndex, HeterogeneityIndex, EvennessIndex and RichnessIndex: S4 classes that represent diversity index.
  • index_heterogeneity() replaces diversity().
  • index_evenness() replaces evenness().
  • index_richness() replaces richness().
  • index_composition() allows to estimate asymptotic species richness.
  • plot_diversity() produces a diversity vs sample size graph and allow to compare estimates with simulated assemblages.
  • Add replacement methods for the *Matrix classes.

Bugfixes & changes

Internals

  • Display progress bars only if interactive() is TRUE and pbapply is installed.

tabula 1.3.0

CRAN release: 2019-09-20

New classes and methods

  • Matrix S4 class is now the superclass of all matrix-like classes.
  • AbundanceMatrix virtual S4 class is defined as the superclass of CountMatrix, FrequencyMatrix and IncidenceMatrix.
  • SpaceTime S4 class represents space-time informations.
  • as_*() coerce a matrix or data.frame to a CountMatrix, FrequencyMatrix, IncidenceMatrix, OccurrenceMatrix or SimilarityMatrix.
  • date_event() replaces dateEvent().
  • date_mcd() allows Mean Ceramic Date estimation.
  • get_dates() and set_dates<- allow to extract and replace chronological informations in AbundanceMatrix objects.
  • plot_bertin() and plot_ford() replace plotBar().
  • plot_date() replaces plotDate().
  • plot_date() gained a method for AbundanceMatrix objects.
  • plot_heatmap() replaces plotMatrix().
  • plot_rank() replaces plotRank().
  • plot_spot() replaces plotSpot().
  • plot_time() produces an abundance vs. time graph.
  • refine_dates() and refine_seriation() replace refine().
  • seriate_reciprocal() and seriate_correspondance() replace seriate().
  • test_diversity() allows Shannon diversity test.
  • test_fit() produces a Frequency Increment Test.

Bugfixes & changes

  • CountMatrix, FrequencyMatrix and IncidenceMatrix now also contain the SpaceTime class.
  • Deprecate plotBar(), plotMatrix(), plotRank(), plotSpot(), refine(), seriate().
  • Remove dateEvent().
  • Empty rows/columns are removed prior to CA seriation to avoid error in svd().

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

CRAN release: 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

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

CRAN release: 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

  • Beta release.