Principal Coordinates of Phylogenetic Structure

Share:

Description

Function to generate Principal Coordinates of Phylogenetic Structure (PCPS).

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
pcps(comm, dist.spp, method = "bray", squareroot = TRUE)

## S3 method for class 'pcps'
plot(x, display = c("text", "points"), groups,
  showlabel = TRUE, choices = c(1, 2), ...)

## S3 method for class 'pcps'
print(x, ...)

## S3 method for class 'pcps'
scores(x, choices = c(1, 2), ...)

## S3 method for class 'pcps'
summary(object, ...)

Arguments

comm

Community data, with species as columns and sampling units as rows. This matrix can contain either presence/absence or abundance data.

dist.spp

Matrix containing phylogenetic distances between species.

method

Dissimilarity index, as accepted by vegdist (Default dist="bray").

squareroot

Logical argument (TRUE or FALSE) to specify if use square root of dissimilarity index (Default squareroot = TRUE).

x

An object of class pcps.

display

Display text or points for the sampling units.

groups

Factor giving the groups (Clades) for each species.

showlabel

Label the groups by their names in the centroid of the object.

choices

Axes for re-scaling. Choices must have length equal to two (Default choices = c(1,2)).

...

Other parameters for the respective functions.

object

An object of class pcps.

Details

The function obtains a matrix containing phylogeny-weighted species composition (matrix.p) and is submitted to principal coordinates analysis (PCoA). This method generates the principal coordinates of phylogenetic structure (PCPS) (Duarte, 2011).

The function scores.pcps re-scales the correlation values for biplot graphics. The function plot.pcps draws a simple biplot and represent clades as "spider" graphs (see ordispider).

Value

P

Phylogeny-weighted species composition matrix.

values

The eigenvalues, relative eigenvalues and cumulative relative eigenvalues.

vectors

The principal coordinates of phylogenetic structure (PCPS).

correlations

Correlations between a PCPS axis and phylogenetically weighted species abundances or frequencies.

Note

IMPORTANT: The sequence species show up in the community data matrix MUST be the same as they show up in the phylogenetic distance matrix. See organize.syncsa.

Author(s)

Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>

References

Duarte, L.S. (2011). Phylogenetic habitat filtering influences forest nucleation in grasslands. Oikos, 120, 208:215.

See Also

matrix.p, wcmdscale

Examples

1
2
3
4
5
6
data(flona)
res<-pcps(flona$community, flona$phylo)
res
summary(res)
scores(res)
plot(res, display = "text", groups = c(rep("Clade-A", 30), rep("Clade-B", 29)))