MINOR CHANGES
plot_taxa_ridges():
Changed the rank order of taxa plotted on y-axis to match the rank order of the 2nd quartile (median/50th percentile) of the bootstrap change point estimates. The previous version plotted order of taxa based on the 2nd quartile (median) of the estimated values from the density function, which did not always match the median of the n bootstrap change-point estimates.
Changed the location of the vertical line on x for each taxa to match the 2nd quartile (median/50th percentile) of the bootstrap change point estimates The previous version plotted the location of the vertical line on x based on the 2nd quartile (median) of the estimated values from the density function, which did not always match the median of the n bootstrap change-point estimates.
Added new argument d_lines. Short for “density lines”, a logical determining whether the median change point values estimated from each taxon’s density function, is plotted as a vertical dashed line. When d_lines = TRUE, line is added to the plot but it does not replace the vertical solid line corresponding to the median of the bootstrap change point estimates.
Added new argument breaks. Determines values and labels of breaks (ticks) on the x-axis, allowing the user greater control of appearance of axis ticks, labels, and gridlines.
Removed pur.cut and rel.cut arguments. Plotting function code relies on output from titan(), which is where users specify pur.cut and rel.cut.
plot_taxa():
Changed default plotting of taxa along y to match the median of the bootstrap change point estimates. This aligns with the default plotting in plot_taxa_ridges().
Changed default plotting of locations of symbols (points sized by z-scores) to match the median of the bootstrap change point estimates.This aligns with the default plotting in plot_taxa_ridges().
Changed default cex parameters to smaller values to allow for all taxa names in glades.titan to be plotted in default runs.
plot_sumz_density(): guide = FALSE has been changed to guide = "none" to conform to ggplot2’s changes.
MINOR CHANGES
parallel::makeCluster().MINOR BUG FIXES
plot_taxa_ridges() that rounded the x axis values to the nearest hundredth (round(..., digits = 2)), which had the effect of heaping small-scale data, making it impossible to differentiate different taxa and meaningfully impacting the graphic. This rounding has been removed.MINOR BUG FIXES
For some reason the color "light blue" began erroring in plot_taxa_ridges(). This has been fixed to "lightblue" to provide clean CRAN checks.
The relative heights of the graphics in plot_taxa_ridges() now have better defaults. These can be edited with the new rel_heights argument to that function.