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

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
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), ...)
``` |

`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 |

`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. |

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`

).

`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. |

**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`

.

Vanderlei Julio Debastiani <[email protected]>

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

`matrix.p`

, `wcmdscale`

, `ordispider`

, `ordilabel`

1 2 3 4 5 6 |

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

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