NEWS

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paleoDiv 2024-05-03

• patch for bug in tree.age.combine() (issue with underscores in taxon names, now automatically removed)

paleoDiv 2024-05-02

• added two new functions, tree.ages.spp() and tree.age.combine() to facilitate building matrices for time calibration of phylogenies

paleoDiv 2024-04-05

• improved automatic dimension settings for ts.periods() and ts.stages()

paleoDiv 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)

paleoDiv 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

paleoDiv 2024-03-08

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• fixed vignette

paleoDiv 2024-03-07

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• 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.

paleoDiv 2024-03-06

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• changed row numbering of output of synonymize()

paleoDiv 2024-03-05

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• changed description and documentation
• fixed message output
• improved behavior of phylo.spindles; now allows plotting without any phylogeny

paleoDiv 2024-03-02

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• improvement to tree.ages() (if data is not found) and added option for occ.cleanup() to return whole data.frame instead of mere column

paleoDiv 2024-03-01

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• Additional function synonymize() that helps with manual editing of taxon-range tables to remove taxonomic errors

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• Improved error-handling behaviour of pdb() function and others based on it

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• txt.y argument of phylo.spindles() now accepts vectorized input

paleoDiv 2024-02-29

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• First version of this package

paleoDiv 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

paleoDiv 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

paleoDiv 0.4.10

• fixed incorrect/misleading multiplication of tolerance factors in rmeana()

paleoDiv 0.4.9

• added option to rmeana to handle empty/missing values

paleoDiv 0.4.8

• fixed handling of update dataframes by ts.periods

paleoDiv 0.4.7

• fixed handling of missing values by tree.ages.spp()
• improved occ.cleanup filtering presets

paleoDiv 0.4.6 (2025-03-23)

• added weights parameter to violins to enable constructing weighted density spindles

paleoDiv 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)

paleoDiv 0.4.4

• fixed behaviour of multijitter() and violins() when group==NULL and x is a numeric vector (previous version would produce error message)

paleoDiv 0.4.3

• added unit option to ts.periods() and ts.stages (allows plotting to x axis scales other than millions of years)

paleoDiv 0.4.1

• multijitter and violins now have a parameter "adj" to specify axis label alignment

paleoDiv 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.

paleoDiv 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

paleoDiv 0.3.4

• added parameters for setting the country/continent and environment type when downloading pdb data

paleoDiv 0.3.3

• added ylimits parameter to phylo.spindles() to specify vertical plot size is no phylogeny is plotted

paleoDiv 0.3.2

• patched label placement issue in phylo.spindles() when txt.x==NULL