# Boostrap niche overlap indices

`niche.overlap.boot.Rd`

Bootstrap niche overlap indices

    niche.overlap.boot(mat, method = c("pianka", "schoener", "petraitis",
        "czech", "morisita", "levins"), times = 1000, quant = c(0.025, 0.975))

## Arguments

mat | standard community matrix.
method | character string specifying the index.
times | Interger, representing the number of bootstrap samples to generate.
quant | Quantile of the bootstrap values.

## Details

This function bootstraps the following niche overlap indices between each pair of species: \ `schoener`: Schoener's niche overlap index\ `petraitis`: Petraitis' niche overlap index\ `czech`: Czechanowski index \ `morisita`: Morisita's overlap index\ `levins`: Levin's overlap index\ see more information from Gotelli, N(2009).\

## Value

a data frame with each row for each pair of species the columns are `"Observed", "Boot mean", "Boot std", "Boot CI1", "Boot CI2", "times"`

## References

Zhang Jin-tun,(2004 ) Quantitative Ecology, Science Press, Beijing\

Nicholas J. Gotelli. 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606-2621. http://esapubs.org/archive/ecol/E081/022/EcoSim

## Author

Jinlong Zhang jinlongzhang01@gmail.com

## See also

`niche.overlap.boot.pair`

## Examples

    data(datasample)
    niche.overlap.boot(datasample[,1:4], method = "pianka")
    #>                                            Observed Boot mean Boot std Boot CI1
    #> Castanopsis.eyrei-Schima.superba              0.887     0.894    0.044    0.794
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.820     0.831    0.088    0.633
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.551       NaN       NA    0.273
    #> Schima.superba-Rhododendron.ovatum            0.693     0.725    0.146    0.423
    #> Schima.superba-Cyclobalanopsis.glauca         0.491       NaN       NA    0.295
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.253       NaN       NA    0.090
    #>                                            Boot CI2 times
    #> Castanopsis.eyrei-Schima.superba              0.972  1000
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.972  1000
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.855  1000
    #> Schima.superba-Rhododendron.ovatum            0.940  1000
    #> Schima.superba-Cyclobalanopsis.glauca         0.801  1000
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.577  1000niche.overlap.boot(datasample[,1:4], method = "schoener")
    #>                                            Observed Boot mean Boot std Boot CI1
    #> Castanopsis.eyrei-Schima.superba              0.763     0.785    0.060    0.657
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.725     0.732    0.093    0.515
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.416     0.446    0.123    0.210
    #> Schima.superba-Rhododendron.ovatum            0.645     0.659    0.123    0.399
    #> Schima.superba-Cyclobalanopsis.glauca         0.388       NaN       NA    0.157
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.247       NaN       NA    0.099
    #>                                            Boot CI2 times
    #> Castanopsis.eyrei-Schima.superba              0.900  1000
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.887  1000
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.715  1000
    #> Schima.superba-Rhododendron.ovatum            0.858  1000
    #> Schima.superba-Cyclobalanopsis.glauca         0.750  1000
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.568  1000niche.overlap.boot(datasample[,1:4], method = "czech")
    #>                                            Observed Boot mean Boot std Boot CI1
    #> Castanopsis.eyrei-Schima.superba              0.763     0.786    0.060    0.662
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.725     0.730    0.087    0.525
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.416     0.442    0.130    0.185
    #> Schima.superba-Rhododendron.ovatum            0.645     0.650    0.127    0.370
    #> Schima.superba-Cyclobalanopsis.glauca         0.388     0.427    0.138    0.174
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.247       NaN       NA    0.095
    #>                                            Boot CI2 times
    #> Castanopsis.eyrei-Schima.superba              0.905  1000
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.880  1000
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.706  1000
    #> Schima.superba-Rhododendron.ovatum            0.857  1000
    #> Schima.superba-Cyclobalanopsis.glauca         0.740  1000
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.572  1000niche.overlap.boot(datasample[,1:4], method = "levins")
    #>                                            Observed Boot mean Boot std Boot CI1
    #> Castanopsis.eyrei-Schima.superba              0.921     0.929    0.051    0.823
    #> Castanopsis.eyrei-Rhododendron.ovatum         0.947     0.952    0.045    0.864
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      0.781     0.790    0.163    0.436
    #> Schima.superba-Rhododendron.ovatum            0.772     0.809    0.196    0.432
    #> Schima.superba-Cyclobalanopsis.glauca         0.671       NaN       NA    0.510
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    0.311     0.383    0.209    0.094
    #>                                            Boot CI2 times
    #> Castanopsis.eyrei-Schima.superba              1.022  1000
    #> Castanopsis.eyrei-Rhododendron.ovatum         1.050  1000
    #> Castanopsis.eyrei-Cyclobalanopsis.glauca      1.071  1000
    #> Schima.superba-Rhododendron.ovatum            1.118  1000
    #> Schima.superba-Cyclobalanopsis.glauca         0.926  1000
    #> Rhododendron.ovatum-Cyclobalanopsis.glauca    1.035  1000