stratigraph (version 0.66)

oe.rates: Returns origination and extinction rates

Description

Returns the origination and extinctions rates of taxa in a stratigraphic column.

Usage

oe.rates(x, depths = NULL, breaks = NULL, per.capita = FALSE, remove.below = 1, ...)

Arguments

x

an object of class strat.column.

depths

depths, if different from those provided in x.

breaks

breaks from which to calculate interpolated rates.

per.capita

logical. Whether the origination and extinction rates should be given as fractions of the standing diversity.

remove.below

remove species that occur only this number or fewer levels.

...

not currently used.

Value

oe.rates returns a list of $basic, which is a data frame with columns stand.div, orig and ext giving standing diversity, origination and extinction rates at the sampled depths/times; $bx, which are the boundary crossers at each sampled depth/time; $intervals, which gives the lengths of each interval (in depth or time); and $interpol, which gives interpolated rates per time as calculated by Foote(2000b).

Details

If depths is provided, it will clobber x$depths, should x$depths exist.

References

Foote, M. (2000a) `Origination and Extinction Components of Taxonomic Diversity: Paleozoic and Post-Paleozoic Dynamics' Paleobiology 26(4):578--605.

Foote, M. (2000b) `Origination and extinction components of taxonomic diversity: general problems' Paleobiology 26 (supplement to No. 4):74--102.

See Also

plot.strat.column, stratigraph

Examples

data(sI)
sc <- sI[,-1]
rownames(sc) <- sI[,1]
sc <- sc[-c(3, 6, 10, 11, 12)]
oe.rates(sc, depths = sI[,1])

data(mohawk)
oe.rates(mohawk)
oe.rates(as.strat.column(mohawk))
oe.rates(as.strat.column(mohawk), remove.below = 2)
oe.rates(as.strat.column(mohawk), breaks = seq(0, 1500, by = 50))