# Principal Coordinates of Phylogenetic Structure

### 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 |

`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 |