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.