v1.3.0

New classes and methods

• Matrix this S4 class is now the superclass of all matrix-like classes.
• AbundanceMatrix this virtual S4 class is defined as the superclass of CountMatrix, FrequencyMatrix and IncidenceMatrix.
• SpaceTime this 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.

v1.2.0

• ADD: Belanger and Husi (2006) dating method (#3).
• ADD: binomial co-occurrence assessment method (similarity between types).
• ADD: SimilarityMatrix S4 class to represent a (dis)similarity matrix.
• ADD: plotSpot method for SimilarityMatrix object.
• ADD: plotSpot method for OccurrenceMatrix object.
• ADD: [ methods for several classes.
• FIX: similarity() now returns a SimilarityMatrix object.
• FIX: plotBar() does not add confidence interval by default.
• FIX: add an argument to seriate() to pass a BootCA object (#4).
• FIX: add an optional progress bars with pbapply in long running functions.
• FIX: deprecate useless accessors.
• FiX: OccurrenceMatrix now stores the number of times each pair of taxa occurs together in at least one sample.

v1.1.0

• ADD: Chao1 estimator for abundance data
• ADD: Bias-corrected Chao1 estimator
• ADD: Improved Chao1 estimator
• ADD: Chao2 estimator for replicated incidence data
• ADD: Bias-corrected Chao2 estimator
• ADD: Improved Chao2 estimator
• ADD: Abundance-based Coverage Estimator (ACE)
• ADD: Incidence-based Coverage Estimator (ICE)
• FIX: similarity() now returns a symmetric matrix
• FIX: add references in the 'Description' field of the DESCRIPTION file (#1)
• FIX: split documentation for alpha-diversity measures
• FIX: split documentation for beta-diversity measures

v1.0.0

• ADD: Brainerd-Robinson coefficient of similarity
• ADD: Zuni ceramics dataset
• ADD: Mississippi ceramics dataset
• ADD: BootCA S4 class to store partial bootstrap CA results
• ADD: extract methods for PermutationOrder and BootCA
• ADD: vignette for matrix seriation
• FIX: use stats::rmultinorm() for partial bootstrap CA

v0.9.0

First release.