install.packages(devtools)
library(devtools)
install_github('mobiodiv/mobr', ref = 'dev')
Load mobr and example data
Calculate Whittaker’s beta
## scale index sample_size effort gamma_coverage value
## 1 alpha S 1 NA NA 12.000000
## 2 alpha S 1 NA NA 7.000000
## 3 gamma S 2 NA NA 14.000000
## 4 beta beta_S 2 NA NA 1.473684
Calculate beta for ENS of PIE (beta S_PIE)
## scale index sample_size effort gamma_coverage value
## 1 alpha S_PIE 1 NA NA 6.680108
## 2 alpha S_PIE 1 NA NA 3.512354
## 3 gamma S_PIE 2 NA NA 5.996554
## 4 beta beta_S_PIE 2 NA NA 1.176665
Calculate beta for S given a specific coverage (beta C)
## scale index sample_size effort gamma_coverage value
## 1 alpha S_C 1 142 0.9787356 15.128899
## 2 alpha S_C 1 142 0.9787356 8.786157
## 3 gamma S_C 2 142 0.9787356 13.937069
## 4 beta beta_S_C 2 142 0.9787356 1.165548
Calculate beta for rarefied richness (S_n) for 20 individuals
## scale index sample_size effort gamma_coverage value
## 1 alpha S_n 1 20 NA 7.859347
## 2 alpha S_n 1 20 NA 4.708249
## 3 gamma S_n 2 20 NA 7.431042
## 4 beta beta_S_n 2 20 NA 1.182572
More than two sites can be used at a time
## scale index sample_size effort gamma_coverage value
## 1 alpha S 1 NA NA 12.000000
## 2 alpha S 1 NA NA 7.000000
## 3 alpha S 1 NA NA 11.000000
## 4 alpha S 1 NA NA 11.000000
## 5 alpha S 1 NA NA 5.000000
## 6 alpha S 1 NA NA 5.000000
## 7 alpha S 1 NA NA 4.000000
## 8 alpha S 1 NA NA 11.000000
## 9 alpha S 1 NA NA 7.000000
## 10 alpha S 1 NA NA 9.000000
## 11 gamma S 10 NA NA 38.000000
## 12 beta beta_S 10 NA NA 4.634146
It is also possible to just calculate beta diversity but it is generally not recommended to examine beta without reference to alpha and gamma diversity.
## scale index sample_size effort gamma_coverage value
## 1 beta beta_S 10 NA NA 4.634146