she() to plot SHE analysis.profiles() to plot diversity profiles.test_shannon() and test_simpson() to compare the Shannon and Simpson diversities in two samples.index_squares() to compute Alroy (2018) richness estimator.plot_heatmap() gained a new argument to use a fixed aspect ratio.test_diversity().plot_diceleraas() to display a Dice-Lerass diagram.matrigraph() to display a heatmap highlighting the deviations from independence.seriograph() to display a Ford diagram highlighting the relationships between rows and columns.EPPM argument of plot_ford() is defunct (use seriograph() instead).Seriation methods are now reexported from kairos and will be removed in a future release.
index_boone(): Boone heterogeneity index.index_baxter(): Baxter rarefaction index.cantabria dataset.Seriation methods are now reexported from kairos and will be removed in a future release.
RarefactionIndex: S4 class that represent rarefied species richness.bootstrap(), jackknife() and simulate() methods to perform bootstrap and jackknife resampling and to measure diversity in simulated assemblages.heterogeneity(), evenness(), richness() and composition() methods for matrix and data.frame.simulate() to simulate observations from a multinomial distribution.autoplot() and plot() methods for RarefactionIndex objects.rarefaction() now returns a RarefactionIndex object.bootstrap_*(), jackknife_*() and simulate_*().index_heterogeneity(), index_evenness(), index_richness() and index_composition().turnover() no longer accept multiple methods as argument.bootstrap() method for DiversityIndex objects: resample with replacement instead of simulating observations from a multinomial distribution.matrix and data.frame.seriate_*() and permute() now belong to kairos.*_mcd(), *_event(), *_accumulation(), plot_date() now belong to kairos.test_fit() and plot_time() now belong to kairos.DateEvent: S4 class to store the event and accumulation times of archaeological assemblages.CompositionIndex: S4 class that represent an asymptotic species richness.IncrementTest: S4 class that represent a Frequency Increment Test results.eppm() and pvi() to calculate independence statistics.predict_event() and predict_accumulation to estimate the event and accumulation dates of an assemblage.bootstrap_*() and jackknife_*() to perform bootstrap and jackknife resampling.simulate_evenness() and simulate_richness() to measure diversity in simulated assemblages.seriate_average() replaces seriate_correspondance().seriate_rank() replaces seriate_reciprocal().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.BootCA to RefineCA.DateModel to DateEvent.RefineCA and DateEvent now inherit from dimensio::CA.date_mcd(), date_event() and plot_time() gained a new dates argument.plot_ford() and plot_bertin().stringsAsFactors = FALSE default).debian-gcc-devel-nold).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.*Matrix classes.diversity(), evenness() and richness().interactive() is TRUE and pbapply is installed.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.CountMatrix, FrequencyMatrix and IncidenceMatrix now also contain the SpaceTime class.plotBar(), plotMatrix(), plotRank(), plotSpot(), refine(), seriate().dateEvent().svd().plot_date() method for DateModel objects now allows to display an activity or a tempo plot.:: (stop importing the entire package).FactoMinerR::CA() with ca::ca() (this avoids having to install all {FactoMineR} dependencies when only one function is used).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.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.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.similarity() gained a new estimator: binomial co-occurrence assessment method (similarity between types).seriate() gained a new argument to pass a BootCA object.similarity() now returns a symmetric matrix.richness() gained new estimators:Description field of the DESCRIPTION file.BootCA this S4 class stores partial bootstrap CA-based seriation results.[[ operators acting on PermutationOrder and BootCA to extract parts.refine() method for CountMatrix now use stats::rmultinorm() for partial bootstrap CA.similarity() gained a new estimator: the Brainerd-Robinson coefficient of similarity.