pcps: Principal Coordinates of Phylogenetic Structure

In PCPS: Principal Coordinates of Phylogenetic Structure

Description

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

Usage

pcps(
  comm,
  phylodist,
  checkdata = TRUE,
  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. Alternatively comm can be an object of class metacommunity.data, an alternative way to set all data.frames/matrices. When you use the class metacommunity.data the argument phylodist must not be specified. See details.
phylodist	Matrix containing phylogenetic distances between species.
checkdata	Logical argument (TRUE or FALSE) to check if species sequence in the community data follows the same order as the one in the phylodist matrix (Default checkdata = TRUE).
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 sequence species show up in the community data matrix must be the same as they show up in the phylogenetic distance matrix. The function organize.pcps organizes the data, placing the matrices of community and phylogenetic distance in the same order. The use of organize.pcps is not requered for run this function, but is recommended. In this way the arguments comm and phylodist can be specified them as normal arguments or by passing them with the object returned by the function organize.pcps using, in this case only the argument comm. Using the object returned by organize.pcps, the comm argument is used as an alternative way of entering to set all data.frames/matrices, and therefore the phylodist argument must not be specified.

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 details and organize.pcps.

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

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

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 Jan. 16, 2020, 1:03 a.m.