timeList2fourDate

fourDateFunctions

fourDate2timeList

Functions for manipulating data where the first and last appearances of taxa
are known from bounded intervals of time. The two main functions listed here
are for converting between (1)
a data structure consisting of a single 'flat' table where each taxon is listed as a
set of four dates (a <code>fourDate</code> data type), and (2) a list format where each taxon
is listed as its first and last intervals, with an associated table of age bounds for
the intervals referred to in the first table (referred to as a <code>timeList</code> data
structure by many <code>paleotree</code> functions).

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

timeList2fourDate function

<dl><dt>timeList</dt>
<dd>A list composed of two matrices with two columns each, the first
giving interval start and end date bounds, and the second giving taxon first and
last interval appearances in reference to the intervals listed in the first matrix.</dd>
<dt>fourDate</dt>
<dd>A four column matrix where each row is a different taxon, the first two columns
are the lower and upper bounds on the time of first appearance for that taxon and the third
and fourth columns are respectively the lower and upper bounds on the time of last appearance
for that taxon, all in time before present.</dd></dl>

Arguments

Author

Converting Datasets of Taxon Ranges in Intervals Between timeList format and fourDate format — timeList2fourDate

<dl>

<dt>timeList</dt>
<dd>A list composed of two matrices with two columns each, the first
giving interval start and end date bounds, and the second giving taxon first and
last interval appearances in reference to the intervals listed in the first matrix.</dd>


<dt>fourDate</dt>
<dd>A four column matrix where each row is a different taxon, the first two columns
are the lower and upper bounds on the time of first appearance for that taxon and the third
and fourth columns are respectively the lower and upper bounds on the time of last appearance
for that taxon, all in time before present.</dd>

</dl>

timeList2fourDate: Converting Datasets of Taxon Ranges in Intervals Between `timeList` format and `fourDate` format

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples