# Niche overlap between each pair of species

`niche.overlap.Rd`

Compute niche overlap between each pair of species.

    niche.overlap(mat, method = c("levins", "schoener",
           "petraitis", "pianka", "czech", "morisita"))

## Arguments

mat | A community matrix with columns representing species, and rows representing plots.
method | A string specifying the name of the index.

## Details

To add.

## Value

A distance matrix contains niche overlap index between each pair of species.

## 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.pair`

## Examples

    data(datasample)
    niche.overlap(datasample, method = "levins")
    #>                         Castanopsis.eyrei Schima.superba Rhododendron.ovatum
    #> Schima.superba                 0.92060290
    #> Rhododendron.ovatum            0.94733410     0.77210028
    #> Cyclobalanopsis.glauca         0.78136218     0.67083329          0.31064433
    #> Daphniphyllum.oldhamii         0.90712368     1.02620020          0.74612792
    #> Loropetalum.chinensis          0.76831186     0.82233431          0.39604740
    #> Pinus.massoniana               0.83822850     1.03077313          0.52217984
    #> Rhododendron.latoucheae        0.72939232     0.62732689          0.70781209
    #> Vaccinium.bracteatum           0.85520794     0.47531617          0.86604862
    #> Lithocarpus.glaber             0.74471678     0.39885806          0.80173563
    #> Syzygium.buxifolium            0.81059630     1.02588320          0.89881966
    #> Castanopsis.tibetana           0.49037500     0.49392988          0.68266608
    #> Castanopsis.fargesii           0.51022451     0.64525500          0.34753237
    #> Photinia.serrulata             0.72601066     0.39296943          0.97143864
    #>                         Cyclobalanopsis.glauca Daphniphyllum.oldhamii
    #> Schima.superba
    #> Rhododendron.ovatum
    #> Cyclobalanopsis.glauca
    #> Daphniphyllum.oldhamii              0.25434174
    #> Loropetalum.chinensis               0.67894492             0.65106204
    #> Pinus.massoniana                    0.18169464             0.72253314
    #> Rhododendron.latoucheae             0.25113670             0.39535997
    #> Vaccinium.bracteatum                0.42946877             0.56531185
    #> Lithocarpus.glaber                  0.60640888             0.30362848
    #> Syzygium.buxifolium                 0.32044781             0.57468308
    #> Castanopsis.tibetana                0.54136905             0.15650821
    #> Castanopsis.fargesii                0.81931925             0.33970714
    #> Photinia.serrulata                  0.08501254             0.46804153
    #>                         Loropetalum.chinensis Pinus.massoniana
    #> Schima.superba
    #> Rhododendron.ovatum
    #> Cyclobalanopsis.glauca
    #> Daphniphyllum.oldhamii
    #> Loropetalum.chinensis
    #> Pinus.massoniana                   0.50551660
    #> Rhododendron.latoucheae            0.42075698       0.51365887
    #> Vaccinium.bracteatum               0.72499084       0.18302898
    #> Lithocarpus.glaber                 0.40257540       0.06820803
    #> Syzygium.buxifolium                0.37303657       0.39534988
    #> Castanopsis.tibetana               0.40264862       0.00000000
    #> Castanopsis.fargesii               1.05521489       0.00000000
    #> Photinia.serrulata                 0.22976010       0.63076385
    #>                         Rhododendron.latoucheae Vaccinium.bracteatum
    #> Schima.superba
    #> Rhododendron.ovatum
    #> Cyclobalanopsis.glauca
    #> Daphniphyllum.oldhamii
    #> Loropetalum.chinensis
    #> Pinus.massoniana
    #> Rhododendron.latoucheae
    #> Vaccinium.bracteatum                 0.73000011
    #> Lithocarpus.glaber                   0.80409253           0.65124182
    #> Syzygium.buxifolium                  0.35815982           0.07622100
    #> Castanopsis.tibetana                 1.04712271           0.36329000
    #> Castanopsis.fargesii                 0.68282125           0.50626395
    #> Photinia.serrulata                   1.22684568           0.82326273
    #>                         Lithocarpus.glaber Syzygium.buxifolium
    #> Schima.superba
    #> Rhododendron.ovatum
    #> Cyclobalanopsis.glauca
    #> Daphniphyllum.oldhamii
    #> Loropetalum.chinensis
    #> Pinus.massoniana
    #> Rhododendron.latoucheae
    #> Vaccinium.bracteatum
    #> Lithocarpus.glaber
    #> Syzygium.buxifolium             0.19529939
    #> Castanopsis.tibetana            0.95103873          0.46091167
    #> Castanopsis.fargesii            0.52956851          0.38730279
    #> Photinia.serrulata              0.82685927          0.00000000
    #>                         Castanopsis.tibetana Castanopsis.fargesii
    #> Schima.superba
    #> Rhododendron.ovatum
    #> Cyclobalanopsis.glauca
    #> Daphniphyllum.oldhamii
    #> Loropetalum.chinensis
    #> Pinus.massoniana
    #> Rhododendron.latoucheae
    #> Vaccinium.bracteatum
    #> Lithocarpus.glaber
    #> Syzygium.buxifolium
    #> Castanopsis.tibetana
    #> Castanopsis.fargesii              0.70061396
    #> Photinia.serrulata                0.31177382           0.00000000