Changes in version 3.3.2.9000 Changes in version 3.3.2 (2025-09-04) Bugfixes & changes - Fix plot_ford(): ignore empty rows when calculating relative frequencies. Changes in version 3.3.1 (2025-05-15) Internals - Fix tests. Changes in version 3.3.0 (2025-05-13) New classes and methods - Add diversity() to compute multiple alpha diversity indices. Enhancements - simulate() gained a new seed argument. - bootstrap() gained new interval, seed and rare arguments. Bugfixes & changes - Deprecate index_sorenson() (typo). - Deprecate resample(). Breaking changes - Fix bootstrap() for DiversityIndex objects: revert the change introduced in v1.7.0. By default, bootstrap replicates are drawn from a multinomial distribution. This can be changed by setting the rare argument to TRUE. Changes in version 3.2.1 (2025-04-02) Internals - Update package metadata. Changes in version 3.2.0 (2025-01-10) Enhancements - Translate into French. - occurrence() gained a new method argument. - plot(), plot_rank(), she() and profiles() gained new xlab and ylab arguments. Bugfixes & changes - Fix gradient legend width in plot_spot() and plot_heatmap(). - Replace similarity(x, method = "binomial") with occurrence(x, method = "binomial") for consistency. - Remove all previously deprecated methods. Changes in version 3.1.1 (2024-09-05) New classes and methods - Add observed() to get the number of observed types. - Add singleton() and doubleton() to get the number of singleton and doubleton. Internals - Use palette functions from khroma. Changes in version 3.1.0 (2024-05-16) New classes and methods - Add she() to plot SHE analysis. - Add profiles() to plot diversity profiles. - Add test_shannon() and test_simpson() to compare the Shannon and Simpson diversities in two samples. - Add index_squares() to compute Alroy (2018) richness estimator. Enhancements - plot_heatmap() gained a new argument to use a fixed aspect ratio. - Improve color gradient in plot legends. Bugfixes & changes - Fix ACE species richness estimator. - Deprecate test_diversity(). Changes in version 3.0.1 (2023-11-28) Enhancements - Omit axes labels where they would abut or overlap previously drawn labels. Changes in version 3.0.0 (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. Changes in version 2.0.0 (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 - EPPM argument of plot_ford() is defunct (use seriograph() instead). Breaking changes - Seriation methods are no longer reexported from kairos. Changes in version 1.8.0 (2022-09-08) Seriation methods are now reexported from kairos and will be removed in a future release. New classes and methods - Add index_boone(): Boone heterogeneity index. - Add index_baxter(): Baxter rarefaction index. - Add the cantabria dataset. Bugfixes & changes - Remove all previously deprecated methods. Changes in version 1.7.0 (2022-06-23) Seriation methods are now reexported from kairos and will be removed in a future release. New classes and methods - Add RarefactionIndex: S4 class that represent rarefied species richness. - Add bootstrap(), jackknife() and simulate() methods to perform bootstrap and jackknife resampling and to measure diversity in simulated assemblages. - Add heterogeneity(), evenness(), richness() and composition() methods for matrix and data.frame. - Add simulate() to simulate observations from a multinomial distribution. - Add autoplot() and plot() methods for RarefactionIndex objects. 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. Changes in version 1.6.1 (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. Changes in version 1.6.0 (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(). Changes in version 1.5.1 (2020-03-19) Bugfixes & changes - CRAN pacakge check warning (r-devel) has been fixed (use a stringsAsFactors = FALSE default). Changes in version 1.5.0 (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. Changes in version 1.4.0 - Published in the Journal of Open Source Software. 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 - Deprecate diversity(), evenness() and richness(). Internals - Display progress bars only if interactive() is TRUE and pbapply is installed. Changes in version 1.3.0 (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. Changes in version 1.2.0 (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. Changes in version 1.1.0 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. Changes in version 1.0.0 (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. Changes in version 0.9.0 - Beta release.