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hillR
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.
Installation
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'))
Examples
dummy = FD::dummy
comm = dummy$abun
traits = dummy$trait
set.seed(123)
tree = ape::rtree(n = ncol(comm), tip.label = paste0("sp", 1:ncol(comm)))
library(hillR)
Calculate taxonomic, functional, and phylogenetic diversity of each site
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
Calculate taxonomic, functional, and phylogenetic diversity across multiple sites
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
Calculate pairwise taxonomic, functional, and phylogenetic diversity
# 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>
Licenses
Licensed under the MIT license. (More information here.)
Citation
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},
}
Reference
- Chao, Anne, Chun-Huo Chiu, and Lou Jost. “Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers.” Annual Review of Ecology, Evolution, and Systematics 45, no. 1 (2014): 297–324. doi:10.1146/annurev-ecolsys-120213-091540.
- Chiu, Chun-Huo, and Anne Chao. “Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers.” PLoS ONE 9, no. 7 (July 7, 2014): e100014. doi:10.1371/journal.pone.0100014.
Contributing
Contributions are welcome. You can provide comments and feedback or ask questions by filing an issue on Github here or making pull requests.