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:
devtools::install_github("daijiang/hillR")dummy = FD::dummy
comm = dummy$abun
traits = dummy$trait
tree = ape::rtree(n = ncol(comm), tip.label = paste0("sp", 1:ncol(comm)))
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 0.4016663 0.1922618 0.2780442 0.1146261 0.3816159 0.404177 0.2934143
## FDis 0.3481687 0.1670560 0.2375808 0.1146261 0.3211366 0.330233 0.2532751
## D_q 4.0974923 3.6518111 3.2454591 3.0237158 3.0655375 5.233241 3.1470056
## MD_q 1.6458245 0.7021037 0.9023810 0.3465969 1.1698580 2.115156 0.9233765
## FD_q 6.7437533 2.5639502 2.9286406 1.0480104 3.5862436 11.069121 2.9058708
## com8 com9 com10
## Q 0.3343662 0.4156546 0.3844765
## FDis 0.2877931 0.3421687 0.3503927
## D_q 4.3998540 5.2114653 4.1694097
## MD_q 1.4711625 2.1661695 1.6030400
## 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
## 6.587145 5.025573 3.290982 4.113949 4.878235 6.188022 5.099523 5.386479
## com9 com10
## 7.069928 5.751388hill_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
## 1 0 0.4529152 29.66099 14.15941 2.09479 0.9889415
## region_similarity
## 1 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 8.714781 5.339122 1.63225 0.92975 0.5696126hill_taxa_parti_pairwise(comm, q = 0, show.warning = F) # pairwise taxonomic diversity
## # A tibble: 45 x 8
## q site1 site2 TD_gamma TD_alpha TD_beta local_similarity
## <dbl> <fct> <fct> <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 0.400
## 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 0.400
## # ... with 35 more rows, and 1 more variable: region_similarity <dbl>
hill_func_parti_pairwise(comm, traits, q = 0, show.warning = F) # pairwise functional diversity
## # A tibble: 45 x 8
## q site1 site2 FD_gamma FD_alpha FD_beta local_similarity
## <dbl> <fct> <fct> <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
## # ... with 35 more rows, and 1 more variable: region_similarity <dbl>
hill_phylo_parti_pairwise(comm, tree, q = 0, show.warning = F) # pairwise phylogenetic diversity
## # A tibble: 45 x 8
## q site1 site2 PD_gamma PD_alpha PD_beta local_similarity
## <dbl> <fct> <fct> <dbl> <dbl> <dbl> <dbl>
## 1 0 com1 com2 7.63 5.81 1.31 0.685
## 2 0 com1 com3 6.84 4.94 1.39 0.615
## 3 0 com2 com3 6.44 4.16 1.55 0.450
## 4 0 com1 com4 7.54 5.35 1.41 0.590
## 5 0 com2 com4 6.76 4.57 1.48 0.521
## 6 0 com3 com4 5.85 3.70 1.58 0.419
## 7 0 com1 com5 8.33 5.73 1.45 0.546
## 8 0 com2 com5 5.98 4.95 1.21 0.792
## 9 0 com3 com5 7.40 4.08 1.81 0.189
## 10 0 com4 com5 5.66 4.50 1.26 0.742
## # ... with 35 more rows, and 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.