Changes in version 2024-05-03 - patch for bug in tree.age.combine() (issue with underscores in taxon names, now automatically removed) Changes in version 2024-05-02 - added two new functions, tree.ages.spp() and tree.age.combine() to facilitate building matrices for time calibration of phylogenies Changes in version 2024-04-05 - improved automatic dimension settings for ts.periods() and ts.stages() Changes in version 2024-03-24 - added parameter 'italicize' to phylo.spindles, allowing automatic italicization of taxa given as indices or taxon names - improved color vector handling by phylo.spindles (color vectors that are too short or long are now cycled or abridged automatically) Changes in version 2024-03-23 - added better customizability for phylo.spindles Two new parameters for controlling y locations for plotting and text x alignment - standard value 0 for pos parameter of viol - fixed bug in setting of cutoff values if no ages are provided - fixed abdistr_() function; previous version erraneously failed to take into account the ab.val data in the calculation of abundance because of a forgotten # sign - improved handling of spindle limits in phylo.spindles (cutoff variable) if no age data are provided Changes in version 2024-03-08 ============== - fixed vignette Changes in version 2024-03-07 ============== - Fixed behaviour when paleobioDB is unavailable; all datasets for examples and vignette are now included in package data, so this code should run error-free even if website is unavailable. Changes in version 2024-03-06 ============== - changed row numbering of output of synonymize() Changes in version 2024-03-05 ============== - changed description and documentation - fixed message output - improved behavior of phylo.spindles; now allows plotting without any phylogeny Changes in version 2024-03-02 ============== - improvement to tree.ages() (if data is not found) and added option for occ.cleanup() to return whole data.frame instead of mere column Changes in version 2024-03-01 ============== - Additional function synonymize() that helps with manual editing of taxon-range tables to remove taxonomic errors ============== - Improved error-handling behaviour of pdb() function and others based on it ============== - txt.y argument of phylo.spindles() now accepts vectorized input Changes in version 2024-02-29 ============== - First version of this package Changes in version 0.4.12 (2026-05-27) - some additions to features of phylo_spindles() when handling matrices or data.frames as occ input; x column can now be automatically converted to conform to phylogenetic tree plotting space, if desired, via the tconv parameter Changes in version 0.4.11 - added "plot" parameter to multijitter(); if plot==FALSE, jitterplot is not plotted and only an invisible object containing all points, in original order, is returned. - updated ts.periods and ts.stages with the most recent version (24/10) of the international stratigraphic chart Changes in version 0.4.10 - fixed incorrect/misleading multiplication of tolerance factors in rmeana() Changes in version 0.4.9 - added option to rmeana to handle empty/missing values Changes in version 0.4.8 - fixed handling of update dataframes by ts.periods Changes in version 0.4.7 - fixed handling of missing values by tree.ages.spp() - improved occ.cleanup filtering presets Changes in version 0.4.6 (2025-03-23) - added weights parameter to violins to enable constructing weighted density spindles Changes in version 0.4.5 - fixed error in violins caused by groups with n<2; such groups are now ignored automatically (but space is left for them in the plot for the plotting of points or jitterplots) Changes in version 0.4.4 - fixed behaviour of multijitter() and violins() when group==NULL and x is a numeric vector (previous version would produce error message) Changes in version 0.4.3 - added unit option to ts.periods() and ts.stages (allows plotting to x axis scales other than millions of years) Changes in version 0.4.1 - multijitter and violins now have a parameter "adj" to specify axis label alignment Changes in version 0.4.0 (2024-10-17) - added three additional functions of general utility: violins() is a wrapper around viol() facilitating its use for general-purpose violin plots, jitterp() plots a simple jitter plot, and multijitter() is a wrapper around jitterp() analogous to violins() around viol(). These offer an advantage over ggplot2:geom_violin() and ggplot2::geom_jitter() when integration with base R graphics is needed or desired. Changes in version 0.3.5 - changed handling of plot limits by phylo.spindles() to make use of the full available plotting space of the active device for the horizontal extent of plotted spindles Changes in version 0.3.4 - added parameters for setting the country/continent and environment type when downloading pdb data Changes in version 0.3.3 - added ylimits parameter to phylo.spindles() to specify vertical plot size is no phylogeny is plotted Changes in version 0.3.2 - patched label placement issue in phylo.spindles() when txt.x==NULL