evoCA {adiv} | R Documentation |

The function `evoCA`

performs the evolutionary correspondence analysis (evoCA) (Pavoine 2016): an adaptation of the correspondence analysis (CA) to analyse the distributions of lineages among sites and, simultaneously, to analyse the phylogenetic composition of sites. The function `plot.evoCA`

displays the phylogeny on the factorial maps of evoCA.

evoCA(phyl, comm, scannf = TRUE, nf = 2, abundance = TRUE) ## S3 method for class 'evoCA' plot(x, xaxis = 1, yaxis = 2, graph = FALSE, ...)

`phyl` |
an object inheriting the class |

`comm` |
a data frame or a matrix typically with communities (or sites, plots, etc.) as rows, species as columns and presence/absence (1/0) or an index of abundance as entries. Species should be labeled as in the phylogenetic tree where they are the tips. |

`scannf` |
a logical value indicating whether the screeplot (eigenvalues) should be displayed for choosing the number of axes to be kept. |

`nf` |
if |

`abundance` |
a logical value, if |

`x` |
an object of class |

`xaxis` |
the number of the evoCA axis chosen for the x-axis of the 3d plot. |

`yaxis` |
the number of the evoCA axis chosen for the y-axis of the 3d plot. |

`graph` |
a logical value. |

`...` |
other arguments can be added and passed to the function |

`evoCA`

returns an object of class `evoCA`

and of class `dudi`

(see package ade4, `?dudi`

). Graphical tools are associated with class `dudi`

in packages ade4 and adegraphics (see example section below and `?scatter.dudi`

).

The returned object contains the following components:

`tab` |
a data frame with n rows and p columns, with communities as rows and nodes of the phylogeny as columns; the entries of the data frame evaluate the degree of dependence (values that depart from zero)/independence(close-to-zero values) between the occurrence in a community and the position in the phylogeny; |

`cw` |
weights attributed to the nodes of the phylogeny, a vector with p components; |

`lw` |
weights attributed to the communities, a vector with n components; |

`eig` |
vector of eigenvalues; |

`rank` |
integer, number of axes; |

`nf` |
integer, number of kept axes; |

`c1` |
normed scores for the nodes of the phylogeny, data frame with p rows and nf columns; |

`l1` |
normed scores for the communities, data frame with n rows and nf columns; |

`co` |
scores for the nodes of the phylogeny, data frame with p rows and nf columns; |

`li` |
scores for the communities, data frame with n rows and nf columns; |

`call` |
the original call. |

If X is an object of class `evoCA`

, then `attributes(X)$phy`

contains the phylogenetic tree (of class `phylo`

) with names for internal nodes.

`plot.evoCA`

returns a dynamics 3-dimensional plot

Sandrine Pavoine sandrine.pavoine@mnhn.fr

Pavoine, S. (2016) A guide through a family of phylogenetic dissimilarity measures among sites. *Oikos*, **125**, 1719–1732.

`evoNSCA`

, `evopcachord`

, `evopcahellinger`

, `evodiss`

## Not run: if(require(ade4) && require(ape) && require(adegraphics)){ O <- adegpar()$plabels$optim adegpar("plabels.optim" = TRUE) data(batcomm) ab <- batcomm$ab phy <- read.tree(text=batcomm$tre) plot(phy, show.node=TRUE) evoCAbat <- evoCA(phy, ab, scan=FALSE, nf=2) evoCAbat$eig/sum(evoCAbat$eig) s.label(evoCAbat$li) s.label(evoCAbat$co) s.arrow(evoCAbat$co) inertia.dudi(evoCAbat, row=TRUE)$row.abs inertia.dudi(evoCAbat, col=TRUE)$col.abs evoCAbat <- evoCA(phy, ab, scan=FALSE, nf=3) ## All axes are now retained # The Euclidean (canonical) distances among habitat points on the evoCA space is dist(evoCAbat$li) # which is equal to evoDchi2: evodiss(phy, ab, "chi2") # Run the following commands only # if you have graphics support to use # the rgl package on your computer: plot(evoCAbat, graph = TRUE) # With argument "graph = TRUE" # you will be able to vizualize the 3d plot. # See also, plot(evoCAbat, xaxis=1, yaxis=3, graph = TRUE) adegpar("plabels.optim" = O) } ## End(Not run)

[Package *adiv* version 2.1.1 Index]