Package index
Adding geological timescales to plots
The original purpose of deeptime, coord_geo() adds a highly customizable timescale to any ggplot2 plot. Other functions now supplement it to aid in the visualization of data over long time scales.
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coord_geo() - Transformed coordinate system with geological timescale
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scale_color_geo()scale_fill_geo()scale_discrete_geo() - Geological Time Scale color scales
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get_scale_data() - Get geological timescale data
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guide_geo() - Geological timescale axis guide
Built-in interval data
deeptime includes a selection of built-in interval data from the most up-to-date Geological Time Scale. These dataframes include name, max age, min age, abbreviation, and color columns.
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eons - Eon data from the International Commission on Stratigraphy (v2024/12)
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eras - Era data from the International Commission on Stratigraphy (v2024/12)
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periods - Period data from the International Commission on Stratigraphy (v2024/12)
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epochs - Epoch data from the International Commission on Stratigraphy (v2024/12)
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stages - Stage data from the International Commission on Stratigraphy (v2024/12)
Deprecated functions
The following function(s) represent early iterations of what is now coord_geo(). These function(s) still work but are considered “deprecated”. They will be removed in a future version of deeptime, and users are strongly encouraged to use coord_geo() instead, which has more features and is still under active development.
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gggeo_scale()print(<geo_scale>)deprecated - Add a geologic scale below ggplots using grid
Adding geological timescales to phylogenies
These functions can be used to add timescales specifically to phylogenies that are plotted with ggtree.
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coord_geo() - Transformed coordinate system with geological timescale
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coord_geo_radial() - Enhanced polar coordinate system with geological timescale
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coord_geo_polar()deprecated - Polar coordinate system with geological timescale
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scale_color_geo()scale_fill_geo()scale_discrete_geo() - Geological Time Scale color scales
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get_scale_data() - Get geological timescale data
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guide_geo() - Geological timescale axis guide
Adding text labels to phylogenies
When using deeptime coordinate systems, this geom may work better than geoms from ggtree.
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geom_text_phylo() - Label nodes on a phylogenetic tree plotted with ggtree
Transforming coordinate systems
These functions can be used to modify the way that your data is plotted by ggplot2.
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coord_trans_flip() - Transformed and flipped Cartesian coordinate system
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coord_trans_xy() - Transformed XY Cartesian coordinate system
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geom_phylomorpho() - Plot a 2-D phylomorphospace in ggplot2
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disparity_through_time() - Disparity through time plot using lattice
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panel.disparity() - Combined wireframe and cloud panel
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coord_trans_xy() - Transformed XY Cartesian coordinate system
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geom_points_range()stat_points_range() - Display points and their range
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facet_grid_color()facet_grid_geo() - Lay out panels in a grid with colored strips
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facet_wrap_color()facet_wrap_geo() - Wrap a 1d ribbon of panels into 2d with colored strips
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facet_nested_color()facet_nested_geo() - Layout panels in a grid with nested colored strips
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facet_nested_wrap_color()facet_nested_wrap_geo() - Ribbon of panels with nested colored strips
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grid.pattern_geo() - Plot an individual FGDC pattern using grid
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geo_pattern()geo_grob() - Get a FGDC geologic plotting pattern
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scale_fill_geopattern() - Geologic pattern fill scale
Combining and arranging plots
These functions can be used to combine and arrange plots into publishable-quality figures.
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ggarrange2() - Combine and arrange multiple ggplot-like objects
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gtable_frame2() - Decompose a ggplot gtable