plotTraitgram

<code>plotTraitgram</code> plots a traitgram showing the evolution of a continuous trait.
If node values are not given (i.e. the data is empirical data collected from tips,
rather than simulated data), maximum-likelihood ancestral trait estimation is used
to calculate node values. (Ackerly, 2009) given a tree and a set of continuous trait
values.

Provides tools for transforming, a posteriori time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of
fossil taxa using stratigraphic data. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord, which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.

David Bapst

paleotree

Paleontological and Phylogenetic Analyses of Evolution

plotTraitgram function

<dl><dt>trait</dt>
<dd>A vector of continuous trait values. If the length of <code>trait</code>
is equal to the number of tips and number of nodes, than it is presumed internal
node values are given. If the length of <code>trait</code> is equal to the number of tips
of <code>tree</code> then these will be treated as tip values and ancestral trait reconstruction
will be used to reconstruct the missing ancestral values. If <code>trait</code> is not
named, or if internal node values are given, then values will be presumed to be in
the order of tip/node numbering in <code>tree$edge</code>, which for tips is the same as
the ordering in <code>tree$tip.label</code>.</dd>
<dt>tree</dt>
<dd>A <code>phylo</code> object.</dd>
<dt>main</dt>
<dd>Main title of traitgram plot.</dd>
<dt>conf.int</dt>
<dd>If <code>TRUE</code> (the default), confidence intervals are plotted.</dd>
<dt>lwd</dt>
<dd>The line width used for branches in the figure.</dd></dl>

Arguments

Author

Plot a Traitgram for Continuous Traits — plotTraitgram

<dl>

<dt>trait</dt>
<dd>A vector of continuous trait values. If the length of <code>trait</code>
is equal to the number of tips and number of nodes, than it is presumed internal
node values are given. If the length of <code>trait</code> is equal to the number of tips
of <code>tree</code> then these will be treated as tip values and ancestral trait reconstruction
will be used to reconstruct the missing ancestral values. If <code>trait</code> is not
named, or if internal node values are given, then values will be presumed to be in
the order of tip/node numbering in <code>tree$edge</code>, which for tips is the same as
the ordering in <code>tree$tip.label</code>.</dd>


<dt>tree</dt>
<dd>A <code>phylo</code> object.</dd>


<dt>main</dt>
<dd>Main title of traitgram plot.</dd>


<dt>conf.int</dt>
<dd>If <code>TRUE</code> (the default), confidence intervals are plotted.</dd>


<dt>lwd</dt>
<dd>The line width used for branches in the figure.</dd>

</dl>

plotTraitgram: Plot a Traitgram for Continuous Traits

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples