Changes in version 1.1.6 (2025-05-15)                  

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).

                  Changes in version 1.1 (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.

                  Changes in version 1.0 (2023-11-24)                   

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.

                         Changes in version 0.2                         

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.

                        Changes in version 0.1.0                        

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