css: Calculate Corrected Survivorship Scores.

In paleoPhylo: Biodiversity Analyses in a Paleontological and Phylogenetic Context

Description

Currently, calculates Pearson's (1992) corrected survivorship scores to account for variation in variable extinction rates.

Usage

css(pP, lastDate=min(pP$en))

Arguments

pP	An object of class paleoPhylo.
lastDate	The date of the end of the experiment, for use in censoring in survivorship analysis. Defaults to the minumum age in the paleoPhylo object implying that EVERYTHING DIED.

Details

Pearson (1992) criticized survivorship analysis when conducted on the fossil record on the grounds that taxa arising at different periods must have experienced different extinction probabilities and therefore cannot be considered homogeneous, implying that they are inappropriate for survival analysis

Value

An list containing:

nm	A unique identifying ID code for each species lineage, ripped from as.paleoPhylo.
css	The corrected survivorship score (Pearson 1992).
Duration	The raw duration
notExtant	Censorship if nm persists until lastDate.
notExtC	Censorship if nm persists until lastDate or speciates.

Author(s)

Thomas H.G. Ezard [e-mail]

References

Pearson, P. (1992). Survivorship analysis of fossil taxa when real-time extinction rates vary: the paleogene planktonic foraminifera. Paleobiology 18 (2), 115-131.

See Also

pearson93, as.paleoPhylo

Examples

data(pearson93)
p93 <- with(pearson93, as.paleoPhylo(Code, Parent, Start, End, label=Name))
p93css <- css(p93)
with(p93css, plot(css, Duration))

#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*
##NOT RUN
##To do a survivorship analysis, use 
##library(survival)
##m1 <- summary(survfit(Surv(css,notExtant) ~ 1, data=p93css))
##plot(m1)
#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*

paleoPhylo documentation built on May 2, 2019, 6:11 p.m.