dissABC {adiv} | R Documentation |

Coefficients of similarity between communities that rely on the presence/absence of species are generally based on various combinations of the matching/mismatching components of the classical 2 x 2 contingency table. Three of these components are: a=the number of species shared by the two communities; b=the number of species in the first community that are not in the second; c=the number of species in the second community that are not in the first. These coefficients are extended in `dissABC`

to include phylogenetic or functional information on species (Ricotta and Pavoine 2015).

dissABC(comm, dis, option = 1:4, method = c("J", "S", "O", "K", "SS","Si"))

`comm` |
a data frame or a matrix typically with communities as rows, species as columns and relative abundance or absolute abundance as entries. Column labels (species names) should be assigned as in the object |

`dis` |
a matrix (or data frame) of (phylogenetic or functional) dissimilarities among species rescaled in the range [0, 1] or an object of class |

`option` |
a numeric, either 1, 2, 3, or 4 (if several values are given only the first one is considered). See details. |

`method` |
a character or string, either |

To obtain the dissimilarities among plots, one needs to choose the equations to be used for the (phylogenetic or functional) components A, B, and C thanks to argument `option`

and the way the components will be combined, thanks to argument `method`

.

Let *D=(d_ij)* a matrix of (functional, morphological or phylogenetic) dissimilarities between pairs of species with *d_ij = d_ji* and *d_ii = 0*. If the dissimilarity coefficient *d* is in the range [0, 1], it is possible to define a corresponding similarity coefficient *s* as the complement of *d*: *s* = 1 - *d*. Let *x_ik* the abundance of species *i* in community *k*. *S(kh)* is the number of species in the pooled communities *k* and *h* (i.e. the species for which *min(x_ik, x_ih) > 0*). The (absolute) abundance of species similar to *i* in plot *k* is

*Z_ik=sum_j^S(kh) x_jk s_ij*

.

If `option=1`

, equations 6-8 of the main text of Ricotta and Pavoine (2015) are used for calculating components A, B, C:

*A=sum_i^S(kh) min(Z_ik, Z_ih)*

*B=sum_i^S(kh) [max(Z_ik, Z_ih)-Z_ih]*

*C=sum_i^S(kh) [max(Z_ik, Z_ih)-Z_ik]*

If `option=2`

, equations A1-A3 from Appendix S1 of Ricotta and Pavoine (2015) are used.

If `option=3`

, equations A5-A7 from Appendix S1 of Ricotta and Pavoine (2015) are used.

If `option=4`

, equations A10-A12 from Appendix S1 of Ricotta and Pavoine (2015) are used.

If `method="J"`

=the Jaccard index is used:

*A/(A+B+C)*

If `method="S"`

=the Sorensen index is used:

*2A/(2A+B+C)*

If `method="O"`

=the Ochiai index is used:

*A/[sqrt(A+B)sqrt(A+C)]*

If `method="K"`

, the Kulczynski index is used:

*[A/(A+B)+A/(A+C)]/2*

If `method="SS"`

, the Sokal-Sneath index is used:

*A/(A+2B+2C)*

If `method="Si"`

, the Simpson index is used:

*A/(A+min(B,2))*

Function `dissABC`

returns a matrix with the values of the proposed similarities among communities based on interspecies resemblances.

Sandrine Pavoine sandrine.pavoine@mnhn.fr

Ricotta, C. and Pavoine, S. (2015) Measuring similarity among plots including similarity among species: an extension of traditional approaches. *Journal of Vegetation Science*, **26**, 1061–1067.

data(RP15JVS) dissABC(RP15JVS$ab, RP15JVS$D1, method="J", option=1) J <- as.matrix(dissABC(RP15JVS$ab, RP15JVS$D1, method="J", option=1))[, 1] SS <- as.matrix(dissABC(RP15JVS$ab, RP15JVS$D1, method="SS", option=1))[, 1] S <- as.matrix(dissABC(RP15JVS$ab, RP15JVS$D1, method="S", option=1))[, 1] O <- as.matrix(dissABC(RP15JVS$ab, RP15JVS$D1, method="O", option=1))[, 1] K <- as.matrix(dissABC(RP15JVS$ab, RP15JVS$D1, method="K", option=1))[, 1] plot(1:9, J, xlab="Number of the plots which plot 1 is compared to", ylab="Similarity", type="b", ylim=c(0,1), pch=18) lines(1:9, SS, type="b", pch=15) lines(1:9, S, type="b", pch=17) lines(1:9, O, type="b", pch=12) lines(1:9, K, type="b", pch=1) legend("bottomleft", c("Jaccard","Sokal-Sneath","Sorensen","Ochiai","Kulczynski"), pch=c(18,15,17,12,1), lty=1)

[Package *adiv* version 2.1.1 Index]