analog.mult: Multiple analogs comparison

In paleoMAS: Paleoecological Analysis

Description

This function calculates and plots distance or dissimilarity indices (degree of analogy) between all samples in a fossil record and a set of modern or fossil analog samples.

Usage

analog.mult(base, fossil, age, res = 100, method = "euclidean",
           binary = FALSE, plot = TRUE, dimension = TRUE, 
           wire = FALSE, aspect = c(0.5, 0.3), drape = TRUE)

Arguments

base	A matrix containing analog samples with samples in rows and taxa in columns. Rows must be named after each analog sample that they contain (see rownames).
fossil	A matrix with the fossil dataset containing samples in rows and species in columns.
age	A vector with the age or depth of each sample.
res	Temporal resolution for the interpolation needed to plot the results.
method	Corresponds to squared chord distance ("schord") and the 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	Logical indicating whether a transformation of the data into presence/absence is desired. See vegdist (package vegan) for details.
plot	Logical indicating whether or not a plot is desired.
dimension	An indicator of whether or not a three-dimensional plot is desired. If TRUE a 3D figure is plotted according to the argument specified in wire. If FALSE a set of bidimensional panels is produced.
wire	An indicator of the kind of 3D figure that is desired. If TRUE a figure type wireframe (package lattice) is produced. If FALSE a figure type levelplot (package MASS) is produced. Only relevant if dimension=TRUE.
aspect	Argument of the function wireframe. Only relevant if wire=TRUE.
drape	Argument of the function wireframe. Only relevant if wire=TRUE.

Details

When 3D plots are desired, they are based on a grid with a uniform time resolution. Therefore, a linear interpolation is performed, which requires the definition of the desired time resolution through the argument res.

Value

This function returns a list containing:

plot.data	A matrix with distances between fossil samples and analogs interpolated into regular time intervals. The size of the interval was defined in the argument res.
distances	A matrix with the age of fossil samples, and their distance or dissimilarity to each analog sample.

Author(s)

Alexander Correa-Metrio.

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.

See Also

analog.sing. See vegdist for details on the dissimilarity indexes.

Examples

data(quexilchron,quexildepths,quexilper)
#Define chronolgy
age<-quexilchron
ages<-chron(age,quexildepths,max.depth=1957)$chronology[,2]
#If samples are used as representative of time periods
quexilbase<-quexilper[c(1,27,68),]
rownames(quexilbase)<-c("Late Pleistocene","LGM","MIS3")
#comparison of all fossil samples with the three periods 
analog.mult(quexilbase,quexilper,ages,res=500)
#three-dimensional figure
analog.mult(quexilbase,quexilper,ages,res=500,plot=TRUE,dimension=TRUE,wire=TRUE)
#multipanel figure
analog.mult(quexilbase,quexilper,ages,res=500,plot=TRUE,dimension=FALSE)

paleoMAS documentation built on May 2, 2019, 6:46 a.m.