Curve of phylogenetic signal at metacommunity level

Share:

Description

The function estimate the phylogenetic signal at metacommunity level and draws a representation curve.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
pcps.curve(comm, dist.spp, trait, method = "bray", squareroot = TRUE,
  null.model.ts = FALSE, null.model.bm = FALSE, tree, runs = 99,
  progressbar = FALSE)

## S3 method for class 'pcpscurve'
plot(x, type = "b", draw.model = c("none", "ts", "bm"),
  probs = c(0.025, 0.975), col = "black", model.col = "black", ...)

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

## S3 method for class 'pcpscurve'
summary(object, probs = c(0.025, 0.975), ...)

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.

trait

Matrix data of species described by traits, with traits as columns and species as rows.

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).

null.model.ts

Logical argument (TRUE or FALSE) to specify if use null model that shuffles terminal tips across the phylogenetic tree to generate null curves. See details (Default null.model.ts = FALSE).

null.model.bm

Logical argument (TRUE or FALSE) to specify if use null model that simulate trait evolving under Brownian motion to generate null curves. See details (Default null.model.bm = FALSE).

tree

Phylogenetic tree, as phylo object.

runs

Number of randomizations.

progressbar

Logical argument (TRUE or FALSE) to specify if display a progress bar on the R console (Default progressbar = FALSE).

x

An object of class pcpscurve.

type

Type of the plot to be drawn (Default type = "b").

draw.model

Type of null model to draw; none (none), taxa shuffle (ts), browian motion model (bm).

probs

Numeric vector of probabilities used by quantile. (Default probs = c(0.025, 0.975)).

col

Plot color.

model.col

Color of lines of null models.

...

Further graphical parameters for points.

object

An object of class pcpscurve.

Details

The PCPS are used, in a sequential manner, as predictors in a linear regression to model the trait averages across the metacommunity. The curve is drawn as the percentage of cumulative eigenvalues in the abscissa and as the determination coefficient of regressions in the ordinate.

Two null models are available. The first one (ts), the null curves are generated shuffling terminal tips across the phylogenetic tree, generates a set of random PCPS and recalculates the curves. The second (bm), the null curves are generated with simulate traits evolving under Brownian motion model.

Value

curve.obs

The cumulative PCPS eigenvalues and the coefficient of determination.

curve.null.ts

The cumulative PCPS eigenvalues and the coefficient of determination for each randomization using the taxa shuffle null model.

curve.null.bm

The cumulative PCPS eigenvalues and the coefficient of determination for each randomization using the Brownian motion null model.

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, pcps

Examples

1
2
3
4
5
6
data(flona)
res_curve<-pcps.curve(flona$community, flona$phylo, flona$trait[,1], method = "bray",
       squareroot = TRUE, null.model.ts = TRUE, runs = 9, progressbar = FALSE)
res_curve
summary(res_curve)
plot(res_curve, type = "b", draw.model = "ts", col = "red")