Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 2 3 |
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 |
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 ( |
binary |
Logical indicating whether a transformation of the data into presence/absence is desired. See |
plot |
Logical indicating whether or not a plot is desired. |
dimension |
An indicator of whether or not a three-dimensional plot is desired. If |
wire |
An indicator of the kind of 3D figure that is desired. If |
aspect |
Argument of the function |
drape |
Argument of the function |
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
.
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 |
distances |
A matrix with the age of fossil samples, and their distance or dissimilarity to each analog sample. |
Alexander Correa-Metrio.
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.
analog.sing
. See vegdist
for details on the dissimilarity indexes.
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
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