PaleoFidelity: PaleoFidelity: Measuring paleontological fidelity (live-dead...

In MJKowalewski/PaleoFidelity: Analyze and Visualize Agreement between Live and Dead Communities

PaleoFidelity: Measuring paleontological fidelity (live-dead community agreement)

Description

PaleoFidelity package provides common measures of paleontological fidelity used to assess live-dead community agreement. These measures encompass multiple aspects of fidelity, including faunal composition and alpha diversity. Plot functions to visualize fidelity patterns are also provided.

Details

The PaleoFidelity functions are designed to evaluate and visualize congruence (fidelity) between living communities and sympatric death assemblages (the incipient fossil record). The intellectual motivation for live-dead fidelity analyses is the assessments of the informative value of the fossil record ('taphonomy') and the evaluation of recent human-induced ecosystem changes reflected in live-dead disagreements ('conservation paleobiology').

The current version of the package provides functions for assessing 'compositional fidelity' (the agreement in community composition in terms of correlation and similarity measures) and 'diversity fidelity' (offsets in species richness and evenness). The functions include sample standardizations, resampling models, and by-group analyses when grouping factors are provided. Plotting functions designed to visualize compositional and diversity fidelity are included.

Author(s)

Michal Kowalewski [e-mail]

See Also

Useful links:

• https://github.com/mjkowalewski/PaleoFidelity

• Report bugs at https://github.com/mjkowalewski/PaleoFidelity

Examples

# Version and citation
packageVersion('PaleoFidelity')
citation('PaleoFidelity')

# Check if data are compliant and generate basic data summary
data(FidData)
FidelitySummary(live=FidData$live, dead=FidData$dead, gp=FidData$habitat,
n.filters=30, report=TRUE)

# Compositional fidelity analysis with sites grouped by habitat
data(FidData)
out1 <- FidelityEst(live = FidData$live[6:9,], dead = FidData$dead[6:9,],
                    gp = FidData$habitat[6:9], cor.measure='spearman',
                    sim.measure='bray', n.filters=30, iter=99, rm.zero=FALSE, tfsd='none')
SJPlot(out1, gpcol=c('forestgreen', 'coral3'))

# Diversity fidelity analysis with sites grouped by habitat
my.fid <- FidelityDiv(FidData$live[6:9,], FidData$dead[6:9,],
                      FidData$habitat[6:9], n.filters=20,
                       iter=100, CI=0.95)
# site-level estimates of Delta S with 95% CIs and p values
my.fid$x
# p values for means of groups
my.fid$p.gps
AlphaPlot(my.fid, col.gp=c('forestgreen', 'coral1'), bgpt='beige')

MJKowalewski/PaleoFidelity documentation built on Aug. 25, 2024, 8:27 p.m.