simFossilRecordMethods: Methods for Editing or Converting Output from Simulated...

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

Methods for Editing or Converting Output from Simulated Fossil Record Objects

Description

These are a set of functions available for manipulating, translating and editing the objects of class fossilRecordSimulation output from function simFossilRecord.

Usage

timeSliceFossilRecord(
  fossilRecord,
  sliceTime,
  shiftRoot4TimeSlice = FALSE,
  modern.samp.prob = 1,
  tolerance = 10^-6
)

fossilRecord2fossilTaxa(fossilRecord)

fossilTaxa2fossilRecord(fossilTaxa)

fossilRecord2fossilRanges(
  fossilRecord,
  merge.cryptic = TRUE,
  ranges.only = TRUE
)

Arguments

fossilRecord	A list object output by simFossilRecord, often composed of multiple elements, each of which is data for 'one taxon', with the first element being a distinctive six-element vector composed of numbers, corresponding to the six fields in tables output by the deprecated function simFossilTaxa.
sliceTime	The date to slice the simFossilRecord output at, given in time-units before the modern, on the same scale as the input fossilRecord.
shiftRoot4TimeSlice	Should the dating of events be shifted, so that the date given for sliceTime is now 0, or should the dates not be shifted, so that they remain on the same scale as the input? This argument accepts a logical TRUE or FALSE, but also accepts the string "withExtantOnly", which will only 'shift' the time-scale if living taxa are present, as determined by having ranges that overlap within tolerance of sliceTime.
modern.samp.prob	The probability that a taxon is sampled at the modern time (or, for timeSliceFossilRecord, the time at which the simulation data is slice). Must be a number between 0 and 1. If 1, all taxa that survive to the modern day (to the sliceTime) are sampled, if 0, none are.
tolerance	A small number which sets a range around the sliceTime within which taxa will be considered extant for the purposes of output.
fossilTaxa	A fossilTaxa object, composed of a table containing information on the true first and last appearance times of taxa, as well as their ancestor-descendant relationships.
merge.cryptic	If TRUE, sampling events for cryptic taxon-units (i.e. those in the same cryptic complex) will be merged into sampling events for a single taxon-unit (with the name of the first taxon in that cryptic complex).
ranges.only	If TRUE (the default), fossilRecord2fossilRanges will return the dates of the first and last sampled occurrences of each taxon-unit (i.e. the stratigraphic range of each taxon). If FALSE, instead a list will be output, with each element being a vector of dates for all sampling events of each taxon-unit.

Details

These functions exist to manipulate fossilRecordSimulation objects output from simFossilRecord, particularly so that they can be interfaced with functions in library paleotree in the same way that output from the deprecated 'legacy' simulation function simFossilTaxa was used.

timeSliceFossilRecord takes a given fossilRecordSimulation object and 'slices' the data to remove any events that occur after the given sliceTime and make it so any taxa still alive as of sliceTime are now listed as extant.

fossilRecord2fossilTaxa converts a fossilRecordSimulation object to the flat table format of taxon data as was originally output by deprecated function simFossilTaxa, and can be taken as input by a number of paleotree functions such as sampleRanges, taxa2phylo and taxa2cladogram.

fossilTaxa2fossilRecord does the reverse, converting a simFossilTaxa table into a fossilRecordSimulation list object, but returns a fossilRecordSimulation object that considers each species as unsampled (as sampling information is not contained within a simFossilTaxa table).

fossilRecord2fossilRanges converts a fossilRecordSimulation object to the flat table format of observed taxon ranges, as is typically output by processing simFossilRecord simulation output with paleotree function sampleRanges.

Value

Depends on the function and the arguments given. See Details.

Author(s)

David W. Bapst

See Also

simFossilRecord

Examples

set.seed(44)
record <- simFossilRecord(
    p = 0.1, q = 0.1, r = 0.1, 
    nruns = 1,
    nTotalTaxa = c(20,30),
    nExtant = 0, 
    plot = TRUE
    )

##################################################
# time-slicing simulations at particular dates

# let's try slicing this record at 940 time-units
slicedRecord <- timeSliceFossilRecord(
    fossilRecord = record, 
    sliceTime = 940
    )
# and let's plot it
divCurveFossilRecordSim(slicedRecord)

# now with shiftRoot4TimeSlice = TRUE to shift the root age
slicedRecord <- timeSliceFossilRecord(
    fossilRecord = record, 
    sliceTime = 940,
    shiftRoot4TimeSlice = TRUE
    )
# and let's plot it
divCurveFossilRecordSim(slicedRecord)

# the last two plots look a little different
    # due to how axis limits are treated...
# notice that in both, 'modern' (extant) taxa
    # are sampled with probability = 1
    
########
# let's try it again, make that probability = 0
# now with shiftRoot4TimeSlice = TRUE
    
slicedRecord <- timeSliceFossilRecord(
    fossilRecord = record, 
    sliceTime = 940,
    shiftRoot4TimeSlice = TRUE, 
    modern.samp.prob = 0
    )
    
# and let's plot it
divCurveFossilRecordSim(slicedRecord)

############################

# converting to taxa objects and observed ranges

# convert to taxa data
taxa <- fossilRecord2fossilTaxa(record)
# convert to ranges
ranges <- fossilRecord2fossilRanges(record)

# plot diversity curves with multiDiv
multiDiv(list(taxa,ranges),
    plotMultCurves = TRUE)
# should look a lot like what we got earlier

# get the cladogram we'd obtain for these taxa with taxa2cladogram
cladogram <- taxa2cladogram(taxa,
    plot = TRUE)

# now get the time-scaled phylogenies with taxa2phylo

# first, with tips extending to the true times of extinction
treeExt <- taxa2phylo(taxa,
    plot = TRUE)

# now, with tips extending to the first appearance dates (FADs) of taxa
	# get the FADs from the ranges
FADs <- ranges[,1]
treeFAD <- taxa2phylo(taxa,
    FADs,plot = TRUE)

dwbapst/paleotree documentation built on Aug. 30, 2022, 6:44 a.m.