timeList2fourDate: Converting Datasets of Taxon Ranges in Intervals Between...

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

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

Description

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 fourDate 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 timeList data structure by many paleotree functions).

Usage

timeList2fourDate(timeList)

fourDate2timeList(fourDate)

Arguments

timeList	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.
fourDate	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.

Details

timeList2fourDate is for converting from a timeList format to a fourDate format. fourDate2timeList is for converting from a fourDate format to a timeList format.

Value

A converted data object, respective to the function applied.

Author(s)

David W. Bapst

References

See my recent blog post on temporal datasets in paleontology for some details:

https://nemagraptus.blogspot.com/2015/02/how-do-we-treat-fossil-age-data-dates.html

See Also

bin_timePaleoPhy and taxicDivDisc for common applications; binTimeData for a simulation function for such data objects

Examples

# timeList object from the retiolinae dataset
data(retiolitinae)

str(retioRanges)

taxicDivDisc(retioRanges)

fourDateRet <- timeList2fourDate(retioRanges)

# total uncertainty in retio first and last appearances?
sum(
    (fourDateRet[,1] - fourDateRet[,2]) + 
    (fourDateRet[,3]-fourDateRet[,4])
    )

#convert back
newTimeList <- fourDate2timeList(fourDateRet)
taxicDivDisc(retioRanges)

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