ashenoy-cmbi/grafify: Version v2.0.0

This is a major update with some new features, bugfixes, and further cleaning up of code with consistent names of arguments in preparation for CRAN submission. Some previous code may not work because of renaming of some arguments for grouping variables in plot_ functions. But older arguments are retained with deprecation warnings in most cases, so old code should largely work.

a. plot_ functions have a new argument ColSeq (logical TRUE/FALSE) that picks colours sequentially from palette chosen by ColPal when TRUE (default). If set to FALSE, the most distant colours are chosen, as already implemented in scale_..._grafify2 functions. b. Violin plots get a major face-lift with a box-whiskers plot on top of the violin. This gives a clearer picture of data and dispersion than the default quantile lines in geom_violin. They also get new arguments to set thickness of lines (bvthick) and transparency of boxplots (b_alpha). c. There are new functions for fitting linear models with varying slopes and intercepts. These are mixed_model_slopes and mixed_anova_slopes. d. A function for comparing slopes of linear fits posthoc_Trends implements the emmeans::emtrends call.
e. Most plot_ functions now have the ... argument forwarding dots for advanced users to add arguments to ggplot geometries where necessary. f. New plot_grafify_palette function that helps quickly visualise colours in palettes along with their names and hexcodes. g. plot_bar_sd and plot_bar_sd_sc have a new argument bthick to adjust the thickness of lines of the bars.

a. Distribution plots: the The Group grouping argument in plot_density, plot_histogram and plot_qqline is now called group for consistency with other plot_ functions. c. The Factor argument in post-hoc comparisons functions (posthoc_Pairwise, posthoc_vsRes, and posthoc_Levelwise) renamed as Fixed_Factor to be consistent with mixed_model, simple_model, mixed_anova and simple_anova functions. d. The plot_3d_scatterbar and plot_3d_scatterbox now correctly plot one-way ANOVA designs with randomised blocks with shapes mapped to levels of the random factor, and xcol as the grouping factor as originally intended but incorrectly implemented. This complements plot_4d_scatterbar and plot_4d_scatterbox which take two grouping factors and a random factor. e. Examples in help files have arguments explicitly labelled to make them easier to follow. f. groups in before-after plots is now called match as it is a bit more informative when showing matched data. g. For consistency, the argument for controlling opacity in distribution plots is renamed c_alpha in plot_density and plot_histogram (for colour opacity of colours under the density curve or histogram); opacity of symbols in plot_qqline is still called s_alpha.