ArchaeoPhases 2.0

Bug fixes & changes

ArchaeoPhases 1.x	ArchaeoPhases 2.0
`AgeDepth()`	`bury()`
`CreateMinMaxGroup()`	`phase()`, `as_phases()`
`CredibleInterval()`, `credible_interval()`	`interval_credible()`
`DatesHiatus()`, `dates_hiatus()`	`hiatus()`
`estimate_range()`	`sensitivity()`
`MarginalPlot()`, `marginal_plot()`	`plot()`
`MarginalProba()`	`older()`
`MarginalStatistics()`, `marginal_statistics()`, `multi_marginal_statistics()`	`summary()`
`MultiCredibleInterval()`, `multi_credible_interval()`	`interval_credible()`
`MultiDatesPlot()`, `multi_dates_plot()`	`plot()`
`MultiHPD()`, `multi_hpd()`	`interval_hdr()`
`MultiMarginalPlot()`, `multi_marginal_plot()`	`plot()`
`MultiPhasePlot()`	`plot()`
`MultiPhaseTimeRange()`	`boundaries()`
`MultiPhasesGap()`	`hiatus()`
`MultiPhasesTransition()`	`transition()`
`MultiSuccessionPlot()`	`plot()`
`OccurrencePlot()`, `occurrence_plot()`	`occurrence()` + `plot()`
`PhaseDurationPlot()`	`duration()` + `plot()`
`PhasePlot()`	`plot()`
`PhaseStatistics()`	`summary()`
`PhaseTimeRange()`	`boundaries()`
`PhasesGap()`, `phases_gap()`	`hiatus()`
`PhasesTransition()`	`transition()`
`SuccessionPlot()`	`plot()`
`TempoActivityPlot()`, `tempo_activity_plot()`	`activity()` + `plot()`
`TempoPlot()`, `tempo_plot()`	`tempo()` + `plot()`
`undated_sample()`	`interpolate()`

New functions for Allen’s interval algebra: allen_analyze(), allen_joint_concurrency(), allen_observe_frequency(), allen_illustrate(), allen_observe().

New read functions for MCMC data: read_bcal(), read_oxcal(), read_chronomodel().
- The new read functions return S3 objects that can identify the file that produced them.
- The new read functions are built on read_csv(), which can read data from a file, connection, or the clipboard.
New plot functions: multi_dates_plot(), tempo_activity_plot(), tempo_plot(), marginal_plot(), multi_marginal_plot(), and occurrence_plot().
- The new plot functions are functional replacements for the originals with camelCase names, e.g., TempoPlot() -> tempo_plot().
- The new plot functions return S3 objects with plot() and reproduce() methods.
- The S3 objects inherit from data.frame and can be passed to appropriate statistical functions to summarize the data in the plot.
New statistical functions: credible_interval(), multi_credible_interval(), multi_hpd(), dates_hiatus(), phases_gap(), marginal_statistics(), and phase_statistics().
- The new statistical functions are functional replacements for the originals with camelCase names, e.g., CredibleInterval() -> credible_interval().
- The new statistical functions return lists in canonical R fashion.
- The phase_statistics() function is augmented with a round_to parameter.
New statistical function multi_marginal_statistics().
New statistical function estimate_ranges() that can be used to estimate the sensitivity of calibration results to different model parameters.

Fixed a bug in MultiHPD() that ignored the roundingOfValue parameter.
Fixed a bug in MarginalStatistics() that triggered an error if the function was passed a constant MCMC chain.

Includes an update of the TempoPlot(): optimization of the credible intervals as already done in OccurrencePlot().
Includes a minor update of the vignettes.
Includes an update of the function MarginalPlot() and adds a new function : MultiMarginalPlot().
Includes an update of the function MarginalStatistics() and adds a new function : MultiMarginalMarginalStatistics().
Includes an update of the shiny web application (called by function app_ArchaeoPhases()) that did not work in the previous version.

Includes an update of the function ImportCSV() and a new function for ‘BCal’ users called ImportCSV.BCal().
Includes an update of the MultiDatesPlot(). The graphic is now done with ggplot2.
Includes an update of the TempoPlot() and TempoActivityPlot() functions.
Includes an update of the vignette that describes the main functions of the package.
Includes an update of the shiny web application (called by function app_ArchaeoPhases()).

Includes an update of the vignette that describes the main functions of the package.
Includes an update of the shiny web application (called by function app_ArchaeoPhases()).

Includes a vignette that describes the main functions of the package.
Includes an update of the ImportCSV() function in order to import the raw MCMC generated by ‘BCal’ and to convert the MCMC samples from the date format cal BP (in years before 1950) to the date format BC/AD.
Includes a new dataset of MCMC samples generated by ‘BCal’: Fishpond.RData().
Includes an update of the coda.mcmc() function.
Includes an update of the TempoPlot() function using the package ggplot2.
Includes an update of all graphic functions: it is now possible to export all graphics and to choose the colors associated to the characteristics of groups of dates.
Includes an update of the shiny web application (called by function app_ArchaeoPhases()).

Initial release.
Includes all functions of RChronoModel and their updates.
Includes a function coda.mcm() that creates a MCMC_list in order to use the package coda.
Includes a shiny application and the function app_ArchaeoPhases() to call it from R.
RChronoModel is now obsolete and replaced by ArchaeoPhases.