perCapitaRates: Instantaneous _per-Capita_ Rates of Origination and...

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

Instantaneous per-Capita Rates of Origination and Extinction from the Fossil Record

Description

Calculates and plots per-capita origination and extinction rates from sequential discrete-time taxon ranges, following Foote (2000).

Usage

perCapitaRates(
  timeList,
  plot = TRUE,
  logRates = FALSE,
  drop.extant = FALSE,
  isExtant = NULL,
  jitter = TRUE,
  legendPosition = "topleft"
)

Arguments

timeList	A list composed of two matrices, giving interval start and end dates and taxon first and last occurrences within those intervals. See details.
plot	If TRUE, the per-capita origination and extinctions rates are plotted for each interval. Rates which cannot be calculated for an interval will not be plotted, thus appearing as a gap in the plotted graph. The author takes no responsibility for the aesthetics of this plot.
logRates	If TRUE, rates plotted on log scale.
drop.extant	Drops all extant taxa from a dataset before calculating per-capita origination and extinction rates.
isExtant	A vector of TRUE and FALSE values, same length as the number of taxa in the second matrix of timeList, where TRUE values indicate taxa that are alive in the modern day (and thus are boundary crossers which leave the most recent interval). By default, this argument is NULL and instead which taxa are extant is inferred based on which taxa occur in an interval with start and end times both equal to zero. See details.
jitter	If TRUE (default) the extinction rate will be plotted slightly ahead of the origination rate on the time axis, so the two can be differentiated.
legendPosition	The position of a legend indicating which line is origination rate and which is extinction rate on the resulting plot. This is given as the possible positions for argument x of the function legend, and by default is "topleft", which will be generally useful if origination and extinction rates are initially low. If legendPosition = NA, then a legend will not be plotted.

Details

This function calculates the per-capita rates of taxonomic origination and extinction from paleontological range data, as described by Foote (2000). These values are the instantaneous rate of either type of event occurring per lineage time-units. Although Foote (2001) also presents a number of alternative rates collected from the prior literature such as the 'Van Valen' rate metrics, these are not implemented here, but could be estimated using the matrix invisibly output by this function (See Foote, 2000, for the relevant equations for calculating these).

The timeList object should be a list composed of two matrices, the first matrix giving by-interval start and end times (in absolute time), the second matrix giving the by-taxon first and last appearances in the intervals defined in the first matrix, numbered as the rows. Absolute time should be decreasing, while the intervals should be numbered so that the number increases with time. Taxa alive in the modern should be either (a) listed in isExtant or (b) listed as last occurring in a time interval that begins at time 0 and ends at time 0. See the documentation for the time-scaling function bin_timePaleoPhy and the simulation function binTimeData for more information on formatting.

Unlike some functions in paleotree, such as the diversity curve functions, intervals must be both sequential and non-overlapping. The diversity curve functions deal with such issues by assuming taxa occur from the base of the interval they are first found in until the end of the last interval they are occur in. This inflation of boundary crossers could badly bias estimates of per-capita diversification rates.

Value

This function will invisibly return a ten column matrix, where the number of rows is equal to the number of intervals. The first two columns are interval start and end times and the third column is interval length. The fourth through eighth column is the four fundamental classes of taxa from Foote (2001): Nbt, NbL, NFt, NFL and their sum, N. The final two columns are the per-capita rates estimated for each interval in units per lineage time-units; the ninth column is the origination rate (pRate) and the tenth column is the extinction rate (qRate).

References

Foote, M. 2000 Origination and extinction components of taxonomic diversity: general problems. Pp. 74–102. In D. H. Erwin, and S. L. Wing, eds. Deep Time: Paleobiology's Perspective. The Paleontological Society, Lawrence, Kansas.

See Also

DiversityCurves, SamplingConv

Examples

#with the retiolinae dataset
data(retiolitinae)
perCapitaRates(retioRanges)

# Simulate some fossil ranges with simFossilRecord
set.seed(444)
record <- simFossilRecord(
    p = 0.1, q = 0.1, nruns = 1, nTotalTaxa = c(80,100), nExtant = 0)
taxa <- fossilRecord2fossilTaxa(record)

#simulate a fossil record with imperfect sampling with sampleRanges()
rangesCont <- sampleRanges(taxa,r = 0.5)

#Now let's use binTimeData() to bin in intervals of 5 time units
rangesDisc <- binTimeData(rangesCont,int.length = 5)

#and get the per-capita rates
perCapitaRates(rangesDisc)

#on a log scale
perCapitaRates(rangesDisc,logRates = TRUE)


#get mean and median per-capita rates
res <- perCapitaRates(rangesDisc,plot = FALSE)

apply(res[,c("pRate","qRate")],2,mean,na.rm = TRUE)

apply(res[,c("pRate","qRate")],2,median,na.rm = TRUE)

##############################
#with modern taxa
set.seed(444)

record <- simFossilRecord(
    p = 0.1, 
    q = 0.1, 
    nruns = 1,
    nExtant = c(10,50)
    )
    
taxa <- fossilRecord2fossilTaxa(record)

#simulate a fossil record with imperfect sampling with sampleRanges()
rangesCont <- sampleRanges(taxa,r = 0.5,,modern.samp.prob = 1)

#Now let's use binTimeData() to bin in intervals of 5 time units
rangesDisc <- binTimeData(rangesCont,int.length = 5)

#and now get per-capita rates
perCapitaRates(rangesDisc)

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