treats v1.1 (2024-11-11)

NEW FEATURES

• New function: link.traits to link several traits to each other
• New S3 function: drop.tip and keep.tip from ape now work on "treats" objects

MINOR IMPROVEMENTS

• map.traits now can directly save multiple mappings in the same object and can be plotted directly to visualise uncertainty.
• crude.bd.est now calculates the speciation and extinction rates based on the geiger package by default (using the "estimate" method) or just counts the events per time (using the "count" method).
• make.treats can now directly intake dispRity objects with trees and data (e.g. for visualisation).
• plot.treats now plots singletons nodes in light orange when present (with the option added to the manual as well). Thanks for Rob McDonald for the suggestion.
• plot.treats now handles dynamic plot window sizes when plotting multiple trees on top of each other.
• plot.treats now automatically plots any detectable discrete characters using the "phylo" format.
• revamped traits internal structure for more modularity.

BUG FIXES

• Plotting col option is now handled and explained correctly by plot.treats when complex (i.e. when not equal to the number of elements or the number of element categories).
• Plotting traits now correctly displays multiple traits with the trait argument (thanks to Dominik Kopčak for spotting that one).
• Removed bug where some "founding" events lead to an error "crossed_edges not found" when cleaning the treats output.
• discrete.process now works in n dimensions. Thanks to Caleb Scutt for spotting this one.