occurrence {tabula} | R Documentation |
Co-Occurrence
Description
Co-Occurrence
Usage
occurrence(object, ...)
## S4 method for signature 'matrix'
occurrence(object, method = c("absolute", "relative", "binomial"))
## S4 method for signature 'data.frame'
occurrence(object, method = c("absolute", "relative", "binomial"))
Arguments
object |
A |
... |
Currently not used. |
method |
A |
Details
absolute
Count how many times each pairs of types occur together in at least one sample (absolute frequencies).
relative
Count how many times each pairs of types occur together in at least one sample (relative frequencies).
binomial
Value
A stats::dist object.
Author(s)
N. Frerebeau
See Also
Other diversity measures:
diversity()
,
evenness()
,
heterogeneity()
,
plot.DiversityIndex()
,
plot.RarefactionIndex()
,
profiles()
,
rarefaction()
,
richness()
,
she()
,
similarity()
,
simulate()
,
turnover()
Examples
## Data from Conkey 1980, Kintigh 1989
data("cantabria")
## Plot spot diagram of a co-occurrence matrix
occ_abs <- occurrence(cantabria, method = "absolute") # Absolute frequencies
plot_spot(occ_abs)
occ_rel <- occurrence(cantabria, method = "relative") # Relative frequencies
plot_spot(occ_rel)
## Binomial co-occurrence (similarity between types)
occ_bin <- occurrence(cantabria, method = "binomial")
plot_spot(occ_bin)