This package contains R functions to calculate taxonomic, functional, and phylogenetic diversity and site similarity through Hill Numbers. The underlying methods are based on Chao, Chiu and Jost 2014 and Chiu & Chao 2014.
To install this package, run the following code:
install.packages("hillR")
# or install from Github
install.packages("hillR", repos = c('https://daijiang.r-universe.dev', 'https://cloud.r-project.org'))
= FD::dummy
dummy = dummy$abun
comm = dummy$trait
traits set.seed(123)
= ape::rtree(n = ncol(comm), tip.label = paste0("sp", 1:ncol(comm)))
tree library(hillR)
hill_taxa(comm, q = 0) # taxonomic alpha diversity
## com1 com2 com3 com4 com5 com6 com7 com8 com9 com10
## 4 3 3 2 3 5 3 4 5 4
hill_func(comm, traits, q = 0) # functional alpha diversity
## com1 com2 com3 com4 com5 com6 com7
## Q 0.4214846 0.2848834 0.3254045 0.2620026 0.3984715 0.4427648 0.3228745
## FDis 0.3481687 0.1670560 0.2375808 0.1146261 0.3211366 0.3302330 0.2532751
## D_q 4.0000000 3.0000000 3.0000000 2.0000000 3.0000000 5.0000000 3.0000000
## MD_q 1.6859383 0.8546501 0.9762135 0.5240052 1.1954145 2.2138241 0.9686236
## FD_q 6.7437533 2.5639502 2.9286406 1.0480104 3.5862436 11.0691207 2.9058708
## com8 com9 com10
## Q 0.4045563 0.4515567 0.4177331
## FDis 0.2877931 0.3421687 0.3503927
## D_q 4.0000000 5.0000000 4.0000000
## MD_q 1.6182251 2.2577835 1.6709326
## FD_q 6.4729004 11.2889174 6.6837303
hill_phylo(comm, tree, q = 0) # phylogenetic alpha diversity
## com1 com2 com3 com4 com5 com6 com7 com8
## 5.430079 4.684280 4.461773 2.551395 5.830078 6.088533 4.763594 6.046474
## com9 com10
## 6.262164 5.080340
hill_taxa_parti(comm, q = 0) # taxonomic diversity across all sites
## q TD_gamma TD_alpha TD_beta M_homog local_similarity region_similarity
## 1 0 8 3.6 2.222222 0.45 0.8641975 0.3888889
hill_func_parti(comm, traits, q = 0) # functional diversity across all sites
## q raoQ_gamma FD_gamma FD_alpha FD_beta local_similarity region_similarity
## 1 0 0.4529152 29.66099 14.15941 2.09479 0.9889415 0.4720957
hill_phylo_parti(comm, tree, q = 0) # phylogenetic diversity across all sites
## q PD_gamma PD_alpha PD_beta local_similarity region_similarity
## 1 0 8.292885 5.119871 1.619745 0.9311395 0.574868
# pairwise taxonomic diversity
hill_taxa_parti_pairwise(comm, q = 0, show_warning = FALSE, .progress = FALSE)
## # A tibble: 45 × 8
## q site1 site2 TD_gamma TD_alpha TD_beta local_similarity
## <dbl> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 0 com1 com2 6 3.5 1.71 0.286
## 2 0 com1 com3 5 3.5 1.43 0.571
## 3 0 com2 com3 5 3 1.67 0.333
## 4 0 com1 com4 5 3 1.67 0.333
## 5 0 com2 com4 5 2.5 2 0
## 6 0 com3 com4 4 2.5 1.6 0.4
## 7 0 com1 com5 6 3.5 1.71 0.286
## 8 0 com2 com5 4 3 1.33 0.667
## 9 0 com3 com5 6 3 2 0
## 10 0 com4 com5 4 2.5 1.6 0.4
## # ℹ 35 more rows
## # ℹ 1 more variable: region_similarity <dbl>
# pairwise functional diversity
hill_func_parti_pairwise(comm, traits, q = 0, show_warning = FALSE, .progress = FALSE)
## # A tibble: 45 × 8
## q site1 site2 FD_gamma FD_alpha FD_beta local_similarity
## <dbl> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 0 com1 com2 15.9 10.3 1.54 0.821
## 2 0 com1 com3 10.7 7.96 1.35 0.883
## 3 0 com2 com3 11.1 7.03 1.58 0.807
## 4 0 com1 com4 11.6 7.90 1.47 0.843
## 5 0 com2 com4 11.7 6.85 1.70 0.765
## 6 0 com3 com4 6.60 4.45 1.48 0.839
## 7 0 com1 com5 17.3 11.3 1.54 0.821
## 8 0 com2 com5 7.86 5.92 1.33 0.891
## 9 0 com3 com5 16.2 9.72 1.66 0.780
## 10 0 com4 com5 8.00 5.32 1.50 0.832
## # ℹ 35 more rows
## # ℹ 1 more variable: region_similarity <dbl>
# pairwise phylogenetic diversity
hill_phylo_parti_pairwise(comm, tree, q = 0, show_warning = FALSE, .progress = FALSE)
## # A tibble: 45 × 8
## q site1 site2 PD_gamma PD_alpha PD_beta local_similarity
## <dbl> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 0 com1 com2 6.79 5.06 1.34 0.657
## 2 0 com1 com3 6.14 4.95 1.24 0.759
## 3 0 com2 com3 6.75 4.57 1.48 0.523
## 4 0 com1 com4 6.38 3.99 1.60 0.400
## 5 0 com2 com4 7.13 3.62 1.97 0.0284
## 6 0 com3 com4 5.42 3.51 1.54 0.455
## 7 0 com1 com5 7.04 5.63 1.25 0.750
## 8 0 com2 com5 6.44 5.15 1.25 0.751
## 9 0 com3 com5 7.71 5.15 1.50 0.502
## 10 0 com4 com5 6.42 4.19 1.53 0.467
## # ℹ 35 more rows
## # ℹ 1 more variable: region_similarity <dbl>
Licensed under the MIT license. (More information here.)
Please cite this package if you use it. The citation information can
be obtained by running citation('hillR')
in R.
Li, (2018). hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers. Journal of Open Source Software, 3(31), 1041. https://doi.org/10.21105/joss.01041
@Article{,
title = {hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers},
author = {Daijiang Li},
journal = {Journal of Open Source Software},
year = {2018},
volume = {3},
number = {31},
pages = {1041},
url = {https://doi.org/10.21105/joss.01041},
}
Contributions are welcome. You can provide comments and feedback or ask questions by filing an issue on Github here or making pull requests.