tabula 1.5.1

Bugfixes & changes

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

tabula 1.5.0 (CRAN release date: 2020-01-16)

Internals

• Depend on {arkhe}.

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.

tabula 1.4.0 (release date: 2019-11-25)

• Published in the Journal of Open Source Software.

New classes and methods

• DiversityIndex, HeterogeneityIndex, EvennessIndex and RichnessIndex S4 classes 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

• Deprecate diversity(), evenness() and richness().

Internals

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

tabula 1.3.0 (CRAN release date: 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 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 (CRAN release date: 2018-12-30)

Bugfixes & changes

• similarity() now returns a symmetric matrix.

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 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)

• Beta release.