SPecies Association Analysis

Miscellaneous functions for analysing species association and niche overlap.

Details

The DESCRIPTION file: This package was not yet installed at build time.
Index: This package was not yet installed at build time.

Author

Jinlong Zhang [aut, cre]

Maintainer: Jinlong Zhang <jinlongzhang01@gmail.com>

References

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

Examples

  library(vegan)
  data(BCI)
  ## select the top 30 species according to relative frequeny.
  sub <- sub.sp.matrix(BCI, common = 30)
  ## Set the digits to 1
  plotlowertri(cor(sub), size = TRUE, cex = 3, digits = 1)

  ## Niche width and niche overlap
  data(datasample)
  niche.overlap.boot(datasample[,1:3], method = "levins")
#>                                       Observed Boot mean Boot std Boot CI1
#> Castanopsis.eyrei-Schima.superba         0.921     0.930    0.052    0.819
#> Castanopsis.eyrei-Rhododendron.ovatum    0.947     0.955    0.048    0.856
#> Schima.superba-Rhododendron.ovatum       0.772     0.803    0.191    0.446
#>                                       Boot CI2 times
#> Castanopsis.eyrei-Schima.superba         1.022  1000
#> Castanopsis.eyrei-Rhododendron.ovatum    1.063  1000
#> Schima.superba-Rhododendron.ovatum       1.112  1000
  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
  niche.width(datasample[,1:3], method = "shannon")
#>   Castanopsis.eyrei Schima.superba Rhododendron.ovatum
#> 1          2.003976        1.94466            1.776253