taxa2phylo: Convert Simulated Taxon Data into a Phylogeny
In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution
taxa2phylo R Documentation
Convert Simulated Taxon Data into a Phylogeny
Description
Converts temporal and ancestor-descendant relationships of taxa into a
dated phylogeny with tips at instantaneous points in time.
Usage
taxa2phylo(taxaData, obs_time = NULL, plot = FALSE)
Arguments
taxaData
A five-column matrix of taxonomic data,
as output by fossilRecord2fossilTaxa via simulations
produced using simFossilRecord. Previously, this was the
default output of the deprecated function simFossilTaxa.
obs_time
A vector of per-taxon times of observation which must be in
the same order of taxa as in the object taxaData.
If obs_time = NULL, the LADs (column 4) in taxaData are used.
plot
If TRUE result the output with ape::plot.phylo.
Details
As described in the documentation for taxa2cladogram, the relationships
among morphotaxa in the fossil record are difficult to describe in terms of
traditional phylogenies. One possibility is to arbitrarily choose particular
instantaneous points of time in the range of some taxa and describe the
temporal relationships of the populations present at those dates. This is
the tactic used by taxa2phylo.
By default, the dates selected (the obs_time argument) are the last occurrences
of the taxon, so a simple use of this function will produce a dated
tree which describes the relationships of the populations present at the
last occurrence time of each taxon in the sampled data.
Alternatively, obs_time can be supplied with different dates within the taxon ranges.
All data relating to when static morphotaxa appear or disappear in the
record is lost. Branching points will be the actual time of speciation,
which (under budding) will often be in the middle of the temporal range of a
taxon.
Cryptic taxa are not dropped or merged as can be done with taxa2cladogram.
The purpose of taxa2phylo is to obtain the 'true' pattern of evolution for
the observation times, independent of what we might actually be able to
recover, for the purpose of comparing in simulation analyses.
As with many functions in the paleotree library, absolute time is always
decreasing, i.e. the present day is zero.
Value
The resulting phylogeny with branch lengths is output as an object
of class phylo. This function will output trees with the element $root.time,
which is the time of the root divergence in absolute time.
The tip labels are the row-names from the simulation input; see the documentation
for simFossilRecord and fossilRecord2fossilTaxa for details.
Note
Do NOT use this function to date a real tree for a real dataset.
It assumes you know the divergence/speciation times of the branching nodes
and relationships perfectly, which is almost impossible given the
undersampled nature of the fossil record. Use timePaleoPhy or
cal3TimePaleoPhy instead.
Do use this function when doing simulations and you want to make a tree of
the 'true' history, such as for simulating trait evolution along
phylogenetic branches.
Unlike taxa2cladogram, this function does not merge cryptic taxa in output
from simFossilRecord (via fossilRecord2fossilTaxa)
and I do not offer an option to secondarily drop them.
The tip labels should provide the necessary information for users to drop
such taxa, however. See simFossilRecord.
Author(s)
David W. Bapst
See Also
simFossilRecord,
taxa2cladogram, fossilRecord2fossilTaxa
Examples
set.seed(444)
record <- simFossilRecord(
p = 0.1,
q = 0.1,
nruns = 1,
nTotalTaxa = c(30,40),
nExtant = 0
)
taxa <- fossilRecord2fossilTaxa(record)
# let's use taxa2cladogram to get the 'ideal' cladogram of the taxa
tree <- taxa2phylo(taxa)
phyloDiv(tree)
# now a phylogeny with tips placed at
# the apparent time of extinction for each taxon
rangesCont <- sampleRanges(taxa,r = 0.5)
tree <- taxa2phylo(taxa,obs_time = rangesCont[,2])
phyloDiv(tree,drop.ZLB = FALSE)
#note that it drops taxa which were never sampled!
#testing with cryptic speciation
set.seed(444)
record <- simFossilRecord(
p = 0.1,
q = 0.1,
prop.cryptic = 0.5,
nruns = 1,
nTotalTaxa = c(30,40),
nExtant = 0,
count.cryptic = TRUE
)
taxaCrypt <- fossilRecord2fossilTaxa(record)
treeCrypt <- taxa2phylo(taxaCrypt)
layout(1)
plot(treeCrypt)
axisPhylo()
dwbapst/paleotree documentation built on Aug. 30, 2022, 6:44 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| taxa2phylo | R Documentation |
Convert Simulated Taxon Data into a Phylogeny
Description
Converts temporal and ancestor-descendant relationships of taxa into a dated phylogeny with tips at instantaneous points in time.
Usage
taxa2phylo(taxaData, obs_time = NULL, plot = FALSE)
Arguments
taxaData |
A five-column matrix of taxonomic data,
as output by |
obs_time |
A vector of per-taxon times of observation which must be in
the same order of taxa as in the object |
plot |
If |
Details
As described in the documentation for taxa2cladogram, the relationships
among morphotaxa in the fossil record are difficult to describe in terms of
traditional phylogenies. One possibility is to arbitrarily choose particular
instantaneous points of time in the range of some taxa and describe the
temporal relationships of the populations present at those dates. This is
the tactic used by taxa2phylo.
By default, the dates selected (the obs_time argument) are the last occurrences
of the taxon, so a simple use of this function will produce a dated
tree which describes the relationships of the populations present at the
last occurrence time of each taxon in the sampled data.
Alternatively, obs_time can be supplied with different dates within the taxon ranges.
All data relating to when static morphotaxa appear or disappear in the record is lost. Branching points will be the actual time of speciation, which (under budding) will often be in the middle of the temporal range of a taxon.
Cryptic taxa are not dropped or merged as can be done with taxa2cladogram.
The purpose of taxa2phylo is to obtain the 'true' pattern of evolution for
the observation times, independent of what we might actually be able to
recover, for the purpose of comparing in simulation analyses.
As with many functions in the paleotree library, absolute time is always
decreasing, i.e. the present day is zero.
Value
The resulting phylogeny with branch lengths is output as an object
of class phylo. This function will output trees with the element $root.time,
which is the time of the root divergence in absolute time.
The tip labels are the row-names from the simulation input; see the documentation
for simFossilRecord and fossilRecord2fossilTaxa for details.
Note
Do NOT use this function to date a real tree for a real dataset.
It assumes you know the divergence/speciation times of the branching nodes
and relationships perfectly, which is almost impossible given the
undersampled nature of the fossil record. Use timePaleoPhy or
cal3TimePaleoPhy instead.
Do use this function when doing simulations and you want to make a tree of the 'true' history, such as for simulating trait evolution along phylogenetic branches.
Unlike taxa2cladogram, this function does not merge cryptic taxa in output
from simFossilRecord (via fossilRecord2fossilTaxa)
and I do not offer an option to secondarily drop them.
The tip labels should provide the necessary information for users to drop
such taxa, however. See simFossilRecord.
Author(s)
David W. Bapst
See Also
simFossilRecord,
taxa2cladogram, fossilRecord2fossilTaxa
Examples
set.seed(444) record <- simFossilRecord( p = 0.1, q = 0.1, nruns = 1, nTotalTaxa = c(30,40), nExtant = 0 ) taxa <- fossilRecord2fossilTaxa(record) # let's use taxa2cladogram to get the 'ideal' cladogram of the taxa tree <- taxa2phylo(taxa) phyloDiv(tree) # now a phylogeny with tips placed at # the apparent time of extinction for each taxon rangesCont <- sampleRanges(taxa,r = 0.5) tree <- taxa2phylo(taxa,obs_time = rangesCont[,2]) phyloDiv(tree,drop.ZLB = FALSE) #note that it drops taxa which were never sampled! #testing with cryptic speciation set.seed(444) record <- simFossilRecord( p = 0.1, q = 0.1, prop.cryptic = 0.5, nruns = 1, nTotalTaxa = c(30,40), nExtant = 0, count.cryptic = TRUE ) taxaCrypt <- fossilRecord2fossilTaxa(record) treeCrypt <- taxa2phylo(taxaCrypt) layout(1) plot(treeCrypt) axisPhylo()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.