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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 dispRity
crude.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
treats
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.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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.