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Published May 25, 2023 | Version v0.2
Software Open

TGuillerme/treats: v0.2

Creators

  • 1. University of Sheffield

Description

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

Files

TGuillerme/treats-v0.2.zip

Files (5.7 MB)

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Additional details

Related works

Is supplement to
https://github.com/TGuillerme/treats/tree/v0.2 (URL)