css: Calculate Corrected Survivorship Scores.

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/css.R

Description

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

Usage

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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 [email protected]

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

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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 31, 2017, 4:38 a.m.