analog.sing: Single analog comparison

Description

This function calculates and plots distance or dissimilarity indexes (analogy degree) between all samples in a fossil record and a single sample from the same record.

Usage

analog.sing(fossil, base, age, dca = FALSE, method = "euclidean", binary = FALSE)

Arguments

fossil

A matrix of fossil data containing samples in rows and species in columns.

base

Row number where the analog sample is.

age

A vector with samples ages.

dca

Logical indicating whether or not distances should be calculated based on detrended correspondence analysis scores (DCA performed according to decorana of vegan). If dca=TRUE, the dissimilarity between samples is calculated using scores of the firt 4 axes of a DCA. Some DCA scores are negative, therefore caution is needed to select an appropriate dissimilarity method when dca=TRUE. If method="schord" DCA cannot be used.

method

Corresponds to squared chord distance ("schord"), and methods available in vegdist of vegan. Available methods are "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "morisita", "horn", "mountford", "raup" , "binomial" or "chao". See vegdist (package vegan) for details.

binary

Argument of the function vegdist (package vegan) that standardizes the data into presence/absence before calculating dissimilarities or distances.

Value

Returns a matrix with sample ages and resulting distance or dissimilarity index between each sample and the selected analog.

References

Correa-Metrio, A. 2010. Climate and vegetation of the Yucatan Peninsula during the late Pleistocene. PhD Dissertation, Florida Institute of Technology, Melbourne, FL. 194 p. Overpeck, J.T. T.I. Webb, and I.C. Prentice. 1985, Quantitative interpretation of fossil pollen spectra: Dissimilarity coefficients and the method of modern analogs. Quaternary Research 23: 87-708.

Examples

Run this code

data(quexilper,quexilchron,quexildepths)
age<-quexilchron
d<-quexildepths
ages<-chron(age,d,max.depth=1957,dates="bars")$chronology[,2]
#distance to the first sample without DCA, using canberra metric
analog.sing(quexilper,base=1,ages,method="canberra")
#distance to the first sample with DCA, using euclidean distance
analog.sing(quexilper,base=1,ages,dca=TRUE)