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
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
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
paleoDiv 0.3.1 (Release
date: 2024-05-03)
patch for bug in tree.age.combine() (issue with underscores in taxon
names, now automatically removed)
paleoDiv 0.3.0 (Release
date: 2024-05-02)
added two new functions, tree.ages.spp() and tree.age.combine() to
facilitate building matrices for time calibration of phylogenies
paleoDiv 0.2.6 (Release
date: 2024-04-05)
improved automatic dimension settings for ts.periods() and
ts.stages()
paleoDiv 0.2.5 (Release
date: 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 0.2.4 (Release
date: 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 0.2.3
(Release date: 2024-03-08)
fixed vignette
# paleoDiv 0.2.2
(Release date: 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.
# paleoDiv 0.2.1
(Release date: 2024-03-06)
changed row numbering of output of synonymize()
# paleoDiv 0.2.0
(Release date: 2024-03-05)
changed description and documentation
fixed message output
improved behavior of phylo.spindles; now allows plotting without any
phylogeny
# paleoDiv 0.1.1
(Release date: 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
# paleoDiv v0.1.0
(Release date: 2024-03-01)
Additional function synonymize() that helps with manual editing of
taxon-range tables to remove taxonomic errors
# paleoDiv v0.0.7
(Release date: 2024-03-01)
Improved error-handling behaviour of pdb() function and others based
on it
# paleoDiv v0.0.6
(Release date: 2024-03-01)
txt.y argument of phylo.spindles() now accepts vectorized input