NEWS.md

In TGuillerme/dads: Trees and Traits Simulations

treats v1.1.6 (2025-04-23)

### MINOR IMPROVEMENTS

• make.treats can now directly make multi.treats objects if provided a list of data and trees.
• treats now allows for multiple "founding" events. Thanks to Ruby Redlich for this suggestion.
• The branch leading to the "founding" events tree is now generated from from the input "modifiers" object rather than arbitrarily.

BUG FIXES

• Bug fix in map.traits for very small trees.
• When using "founding" events with "traits", the trait process now correctly uses the founding tree's root trait values rather than the "traits"'s object's default ones (unless specified).
• plot.treats now handles the optional arguments (...) in the right order for multiple trees.
• print change from ape (aesthetic).

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.

treats v1.0 (2023-11-22)

NEW FEATURES

• Completely reworked dispRitreats to now work just like the dispRity function on treats objects.
• The package is now released on CRAN!

MINOR IMPROVEMENTS

• events now generates singleton nodes (and associated trait values if needed) at the time of the event before applying the modification.
• added verbose option to treats for when using the option null.error = integer().
• printing now works for treats outputs with replicates = <integer>.
• drop.things now works with replicated treats objects (or multiPhylo)

BUG FIXES

• Fixed many simulation corner cases (mainly ones for special trees with always only one node, one living and one fossil).
• Fixed printing issues with S3 "treats" sub-classes

DEPRECATED AND DEFUNCT

• time.condition is now changed to age.condition.

treats v0.2 (2023-05-25) CRAN friendly pre-release

NEW FEATURES

• New utility function dispRitreats to convert "treats" output as input for dispRity
• New utility function crude.bd.est for a crude estimation of speciation and extinction rates from an input tree.
• New utility function map.traits for mapping a "traits" onto a tree.
• New utility function transition.matrix for designing transition matrices for discrete characters.
• New traits process: discrete.process to generate discrete characters.
• Changed package name from dads to treats
• Full polished version of the manual!
• treats has now a save.steps option to create internal nodes at regular intervals or specified ones and a replicates option to automatically replicate the simulations.
• Added a make.bd.parms utility function for sampling from distributions (jointly or not).
• Trees can now be generated with birth-death parameters sampled from functions.
• added a list of pre-made modification and condition for events.
• traits can now have a background component that triggers trait generation in the background each time traits are generated.
• events are now fully handled and modular.
• make.events function for helping to make events.
• make.modifiers now has a select.taxa argument.
• make.treats to create "treats" objects from a tree and a dataset (e.g. matrix). This can be useful for using the the plot.treats function on non "treats" objects.
• "events" class objects are now implemented and fully functional with the make.events function and the pre-made mass.extinction and founding.event events.
• drop.things to drop fossils or livings species or internal nodes from "treats" objects.

MINOR IMPROVEMENTS

• Many clarifications and rewording to the manual.

BUG FIXES

• Corrected the BM.process and OU.process to now be exact (thanks to Rachel Warnock and Louie Rombaut for spotting that one).
• Fixed bd.params print display when inputs are numeric.

treats v0.1.0 (2020-11-13) first release

NEW FEATURES

• treats function first release.
• make.traits function first release.
• make.modifiers function first release.
• print and plot functions for "treats" objects.
• parent.traits utility function first release.
• Manual first release

TGuillerme/dads documentation built on July 16, 2025, 9:14 p.m.