pcps: Principal Coordinates of Phylogenetic Structure

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/pcps.R

Description

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

Usage

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pcps(comm, phylodist, method = "bray", squareroot = TRUE,
  correlations = TRUE)

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

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

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

scores.pcps(x, choices = c(1, 2), ...)

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

Arguments

comm

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

phylodist

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).

correlations

Logical argument (TRUE or FALSE) to specify if are calculed the correlations between each PCPS and each species in matrix P (Default correlations = TRUE).

x

An object of class pcps.

groups

Factor giving the groups (Clades) for each species (Default groups = NULL).

choices

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

display

Display text or points for the sampling units, partial match to "text" or "points" (Default display = "text").

showlabel

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

...

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 summary or the function scores.pcps re-scales the correlation values for obtain the scores for biplot graphics. The function plot 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.

scores

Scores for biplot graphics.

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 <[email protected]>

References

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

See Also

matrix.p, wcmdscale, ordispider, ordilabel

Examples

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data(ADRS)
res<-pcps(ADRS$community, ADRS$phylo)
res
summary(res)
summary(res, choices = c(1, 2))$scores
plot(res, display = "text", groups = c(rep("Clade-A", 2), rep("Clade-B", 4)))

PCPS documentation built on May 24, 2018, 5:04 p.m.

Related to pcps in PCPS...