deeptime 2.2.0

This new minor version of deeptime introduces several new features and bug fixes. It also is compatible with version 4 of ggplot2.

New features:

• Added geom_text_phylo() for adding node/tip labels to phylogenies when using coord_geo_radial()
• Updated built-in timescales to 2024/12 version of GTS
• Removed the defaults for the colors argument in facet_grid_color(), facet_wrap_color(), facet_nested_color(), and facet_nested_wrap_color()
  • Added facet_grid_geo(), facet_wrap_geo(), facet_nested_geo(), and facet_nested_wrap_geo() which now serve as aliases for these functions with their original defaults (#81)
• Added legends to the examples in the “Plotting geological/stratigraphical patterns” vignette (#78)
• Added facetting examples to the “Plotting temporal data” vignette (#80)

Deprecation:

• Advanced the deprecation of coord_geo_polar(). Use of this function will result in a warning. This function will be removed in a future version of deeptime.
• Advanced the deprecation of getScaleData(). This function has been fully deprecated from deeptime in favor of get_scale_data().

Bug fixes:

• Fixed gtable_frame2() and ggarrange2() for plots that use theme_void() (#74)
• Fixed disparity_through_time() for rare edge cases (#71)
• Updated GeomPointsRange to use the aesthetic defaults from ggplot2::GeomPointrange
• Updated GeomTextPhylo to use the aesthetic defaults from ggplot2::GeomText

deeptime 2.1.0

This new minor version of deeptime introduces several new features and bug fixes.

New features:

• Added default label color values to all built-in data as a new lab_color column
  • The label colors are either white or black, whichever has better contrast with the background color based on recommendations by the International Telecommunication Union
• get_scale_data() now returns label colors (as above) for Macrostrat timescales
• Varying strip label colors can now be set with the lab_colors argument in facet_wrap_color() and facet_grid_color() (#68)
  • By default, the strip label colors are set to white or black (as above)
• Added facet_nested_color() and facet_nested_wrap_color() to plot nested faceted plots with colored strips (#55)
• get_scale_data() documentation now lists the available Macrostrat timescales (#69)
• get_scale_data() now supports partial matching to Macrostrat timescales (e.g., get_scale_data("mammal") will retrieve the “North American land mammal ages” timescale)

Notable changes:

• The FGDC pattern data added in deeptime 2.0.0 has been moved to a new data R package called deeptimedata to reduce the size of the deeptime package and the footprint of future deeptime updates

Bug fixes:

• Fixed importing some functions from ggplot2 for coord_geo_radial() and coord_geo_polar()

deeptime 2.0.0

deeptime now requires ggplot2 version 3.5.0 or higher.
This new major version of deeptime includes several new features:

• Added FGDC/USGS geologic patterns to internal data (#52)
• Added functions to retrieve and plot FGDC/USGS geologic patterns (#52)
• Added functions to use FGDC/USGS patterns as ggplot2 fills or with the ggpattern package (see new vignette) (#52)
• Added the true_colors option to get_scale_data(), which, when set to FALSE, can be used to retrieve the custom Macrostrat colors that were previously in the built-in datasets (#62)
• Updated built-in timescales to 2023/06 version of GTS
• Added option to coord_geo() to abbreviate interval labels based on only the intervals that are being plotted (#64)
• Added guide_geo() as an alternative to coord_geo(), mostly for use with radial plots (#53)

Bug fixes:

• Fixed the built-in timescale datasets to have true CGMP colors for the Precambrian (#62)

Notable changes:

• The phytools package is no longer required to install deeptime but is required to use the geom_phylomorpho() function
• The geomtextpath package is no longer required to install deeptime but is required to add labels with the coord_geo_polar() or coord_geo_radial() functions
• The gggeo_scale_old() function has been fully deprecated

deeptime 1.1.1

deeptime now requires rlang version 1.1.0 or higher. This patch version includes several bug fixes:

• Fixed several cases where vignette and documentation building and/or unit testing would fail when the Macrostrat API was down
• Fixed coord_geo_polar() and coord_geo_radial() when the r-axis has expansion (#60)
• Improved argument type checking and error handling across the entire package

deeptime 1.1.0

deeptime now requires ggplot2 version 3.4.0 or higher. This version introduces several new features and bug fixes:

• Added geom_points_range(), a function designed for visualizing temporal occurrence data
• Added facet_grid_color() and facet_wrap_color() for changing strip background colors (#50)
• Added coord_geo_radial(), an enhanced version of coord_geo_polar() (only works with ggplot2 version 3.5.0 and higher) (#56)
• Added family and fontface arguments to coord_geo()
• Added the ability to include interval labels with coord_geo_polar() (#48)
• Fixed the interaction between coord_geo() and ggsave() (#49)
• Fixed size = "auto" when center_end_labels = TRUE in coord_geo()
• Updated several functions to work with ggplot2 version 3.5.0

Notable changes:

• The names for the theme elements that are used for coord_geo_polar() are now prepended with “deeptime.” (e.g., deeptime.axis.line.r) (#51)
• ggplot2 version 3.5.0 has broken several edge cases of coord_trans_xy(). See the documentation for more details. This will be fixed in a future deeptime release.

deeptime 1.0.1

• Fixed the bounds of the Kungurian stage in the built-in stages data
• Updated License to GPL >= 3
• Changed tidyverse to dplyr and magrittr in Suggests and vignettes

deeptime 1.0.0

• Updated built-in timescales to 2022/10 version of GTS
• Added a geom for making phylomorphospaces (geom_phylomorpho())
• Added vignettes
• Renamed getScaleData() to get_scale_data()
• Soft deprecated gggeo_scale() and gggeo_scale_old()

deeptime 0.3.0

deeptime now requires ggplot2 version 3.3.0 or higher. Several new features and fixed compatibility with various ggplot2 versions.

• Added coord_geo_polar(), for adding timescales to polar plots (#33)
• Added color and fill discrete scales that use the GTS colors (#43)
• Fixed coord_geo_polar() and coord_trans_xy() for ggplot2 version 3.4.0 (#44)
• Fixed coord_geo() for ggplot2 version 3.4.0
• Added tests for both ggplot2 version 3.3.6 and 3.4.0
• Removed uses of getFromNamespace() (#45)

deeptime 0.2.3

• Updated built-in timescales to 2022/02 version of GTS
• Better name handling and documentation for getScaleData() (#42)

deeptime 0.2.2

• Skip tests when suggested packages are unavailable
• Added the ability to specify label color (#40)

deeptime 0.2.1

Updated built-in timescales

• Updated the built-in timescales using the Macrostrat API (#39)
• Fixed CRAN checks when ggtree is missing (#38)

deeptime 0.2.0

Several new features and bug fixes.

• coord_geo() now works with discrete axes (#32 and #35)
• Fixed a bug that prevented the use of custom interval data
• Added option to use ggfittext to automatically resize labels (#19)
• Added coord_trans_flip() (#20)
• Fixed axis labels for coord_trans_xy() (#36)
• Added tests with testthat (#34)

deeptime 0.1.0

First minor release (released on CRAN!)

• Fixed ability to use text transformations (from scales) in coord_geo() (#30)
• Added automatic R CMD check Github Actions
• Fixed S3 method consistency and other R CMD check warnings and notes
• Fixed coord_geo() when axis breaks were reversed or NULL (#23 and #29)
• Added packages from examples and README to Suggests

deeptime 0.0.6

Several bug fixes and minor features.

• Added ability to specify a layout for ggarrange2() (#21)
• Added ability to center labels for time intervals that are broken by axis limits (#18)
• Fixed gggeo_scale() for ggplot2>=3.3.0 (#22)
• Replaced README examples with examples using real data (#28)
• Fixed using first letters for the pos argument
• Fixed label order (#26)
• Switched from Travis to Github Actions (#27)
• Fixed handling of axis tick labels for coord_trans_xy (#31)

deeptime 0.0.5

Added coord_geo(), which is a coordinate system for ggplot2 that allows for adding highly customized timescales to ggplot objects. Both gggeo_scale() and gggeo_scale_old are preserved but will receive notably less maintenance moving forward.

• Updated examples and documentation to use coord_geo()
• Added coord_trans_xy(), which is a coordinate system for ggplot2 that is similar to coord_trans() but allows for 2-dimensional transformations
• Added disparity_through_time() which allows for plotting 2-dimensional data across a 3rd dimension (using lattice)

deeptime 0.0.4

ggarrange2() now accepts geo_scale objects and other grobified ggplots

• Fixed missing axes and axis titles

deeptime 0.0.3

Minor release for bug fixes

• Added options to customize borders and line width
• Fixed abbreviations for stages named “Series X” (#9)
• Fixed scale when x-axis crosses 0 (#10, #12)
• Preserve margins of original plots (#13)
• Fixed scale for plots with multiple panels

deeptime 0.0.2

Complete redesign of gggeo_scale() that adds the scale outside of the plotting space using gtable. The old version of gggeo_scale() is preserved as gggeo_scale_old().

• Can now pull timescales from the Macrostrat API (#8)

deeptime 0.0.1

First full release. Adds scale onto the bottom of a ggplot.

• Depends on R>3.4 (#1)
• Fixed adding scales to faceted plots (#2)
• Added timescale data from PBDB API (#3)
• Fixed the use of ggtree when a geom has its own data (#5)
• Fixed the stacking of multiple scales (#6)
• Fixed documentation spelling (#7)