High-Performance Open-Source Archive
### 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."founding"
events tree is now generated from from the input
"modifiers" object rather than arbitrarily.map.traits for very small trees."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.ape (aesthetic).link.traits to link several traits to
each otherdrop.tip and keep.tip
from ape now work on "treats" objectsmap.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.traits internal structure for more
modularity.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).traits now correctly displays multiple traits
with the trait argument (thanks to Dominik Kopčak for
spotting that one)."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.dispRitreats to now work just like
the dispRity function on treats objects.events now generates singleton nodes (and associated
trait values if needed) at the time of the event before applying the
modification.verbose option to treats for when
using the option null.error = integer().treats outputs with
replicates = <integer>.drop.things now works with replicated
treats objects (or multiPhylo)"treats" sub-classestime.condition is now changed to
age.condition.dispRitreats to convert
"treats" output as input for dispRitycrude.bd.est for a crude
estimation of speciation and extinction rates from an input tree.map.traits for mapping a
"traits" onto a tree.transition.matrix for designing
transition matrices for discrete characters.traits process: discrete.process to
generate discrete characters.dads to
treatstreats 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.make.bd.parms utility function for sampling
from distributions (jointly or not).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.BM.process and OU.process to
now be exact (thanks to Rachel Warnock and Louie Rombaut for spotting
that one).bd.params print display when inputs are
numeric.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.
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