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Pairwise temporal niche-overlap matrix

temp_overlap_matrix.Rd

Computes all pairwise overlaps among rows (biological identities) using the chosen index.

Usage

temp_overlap_matrix(mat, method = c("pianka", "czekanowski"))

Arguments

mat

Numeric matrix (rows = biological identities, columns = ordered time intervals).

method

Overlap index to use: "pianka" or "czekanowski".

Value

A square symmetric matrix of overlap values with row/colnames copied from mat. The first class of the object is set to the method name.

Details

For Czekanowski, supply a row-rescaled matrix (see rescale_matrix()) or use temp_overlap(), which handles rescaling.

See also

temp_overlap(), rescale_matrix()

Examples

temp_overlap_matrix(ex1, method = "pianka")
#>           spp1      spp2      spp3      spp4      spp5
#> spp1 0.0000000 0.9961896 0.9983251 0.9983618 0.9971781
#> spp2 0.9961896 0.0000000 0.9989437 0.9972414 0.9929789
#> spp3 0.9983251 0.9989437 0.0000000 0.9995934 0.9973623
#> spp4 0.9983618 0.9972414 0.9995934 0.0000000 0.9990181
#> spp5 0.9971781 0.9929789 0.9973623 0.9990181 0.0000000
#> attr(,"class")
#> [1] "pianka" "matrix" "array" 
ex1_rescale <- rescale_matrix(ex1)
temp_overlap_matrix(ex1_rescale, method = "czekanowski")
#>      spp1 spp2 spp3 spp4 spp5
#> spp1 0.00 0.94 0.96 0.95 0.94
#> spp2 0.94 0.00 0.97 0.95 0.92
#> spp3 0.96 0.97 0.00 0.98 0.95
#> spp4 0.95 0.95 0.98 0.00 0.97
#> spp5 0.94 0.92 0.95 0.97 0.00
#> attr(,"class")
#> [1] "czekanowski" "matrix"      "array"