similarity | R Documentation |

Similarity

similarity(object, ...) ## S4 method for signature 'CountMatrix' similarity( object, method = c("brainerd", "bray", "jaccard", "morisita", "sorenson", "binomial"), ... ) ## S4 method for signature 'IncidenceMatrix' similarity(object, method = c("jaccard", "sorenson"), ...)

`object` |
A |

`...` |
Further arguments to be passed to internal methods. |

`method` |
A |

*β*-diversity can be measured by addressing *similarity*
between pairs of samples/cases (Brainerd-Robinson, Jaccard, Morisita-Horn
and Sorenson indices). Similarity between pairs of taxa/types can be
measured by assessing the degree of co-occurrence (binomial co-occurrence).

Jaccard, Morisita-Horn and Sorenson indices provide a scale of similarity
from *0*-*1* where *1* is perfect similarity and *0* is
no similarity. The Brainerd-Robinson index is scaled between *0* and
*200*. The Binomial co-occurrence assessment approximates a Z-score.

`binomial`

Binomial co-occurrence assessment. This assesses the degree of co-occurrence between taxa/types within a dataset. The strongest associations are shown by large positive numbers, the strongest segregations by large negative numbers.

`brainerd`

Brainerd-Robinson quantitative index. This is a city-block metric of similarity between pairs of samples/cases.

`bray`

Sorenson quantitative index (Bray and Curtis modified version of the Sorenson index).

`jaccard`

Jaccard qualitative index.

`morisita`

Morisita-Horn quantitative index.

`sorenson`

Sorenson qualitative index.

`similarity()`

returns a stats::dist object.

N. Frerebeau

Brainerd, G. W. (1951). The Place of Chronological Ordering in
Archaeological Analysis. *American Antiquity*, 16(04), 301-313.
doi: 10.2307/276979.

Bray, J. R. & Curtis, J. T. (1957). An Ordination of the Upland Forest
Communities of Southern Wisconsin. *Ecological Monographs*, 27(4),
325-349. doi: 10.2307/1942268.

Kintigh, K. (2006). Ceramic Dating and Type Associations. In J. Hantman and
R. Most (eds.), *Managing Archaeological Data: Essays in Honor of
Sylvia W. Gaines*. Anthropological Research Paper, 57. Tempe, AZ: Arizona
State University, p. 17-26.

Magurran, A. E. (1988). *Ecological Diversity and its Measurement*.
Princeton, NJ: Princeton University Press. doi: 10.1007/978-94-015-7358-0.

Robinson, W. S. (1951). A Method for Chronologically Ordering Archaeological
Deposits. *American Antiquity*, 16(04), 293-301. doi: 10.2307/276978.

Other diversity:
`heterogeneity`

,
`resample`

,
`richness`

,
`simulate()`

,
`turnover()`

## Data from Huntley 2008 ceramics <- CountMatrix( data = c(16, 9, 3, 0, 1, 13, 3, 2, 0, 0, 9, 5, 2, 5, 0, 14, 12, 3, 0, 0, 0, 26, 4, 0, 0, 1, 26, 4, 0, 0, 0, 11, 3, 13, 0, 0, 0, 17, 0, 16, 0, 0, 18, 0, 14), nrow = 9, byrow = TRUE ) rownames(ceramics) <- c("Atsinna", "Cienega", "Mirabal", "PdMuertos", "Hesh", "LowPesc", "BoxS", "Ojo Bon", "S170") colnames(ceramics) <- c("DLH-1", "DLH-2a", "DLH-2b", "DLH-2c", "DLH-4") ## Brainerd-Robinson measure (count data) C <- similarity(ceramics, "brainerd") plot_spot(C) ## Data from Magurran 1988, p. 166 data("birds", package = "folio") ## Plot spot diagram birds <- as_count(birds) ## Jaccard measure (presence/absence data) similarity(birds, "jaccard") # 0.46 ## Sorenson measure (presence/absence data) similarity(birds, "sorenson") # 0.63 # Jaccard measure (Bray's formula ; count data) similarity(birds, "bray") # 0.44 # Morisita-Horn measure (count data) similarity(birds, "morisita") # 0.81

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