Getting started with hilldiv3

library(hilldiv3)

Installation

Install hilldiv3 from CRAN:

install.packages("hilldiv3")

For the version in the GitHub repository, which may have changes not yet on CRAN, use devtools::install_github("alberdilab/hilldiv3").

What hilldiv3 does

hilldiv3 measures and compares the diversity of biological communities (OTU/ASV/MAG tables) using Hill numbers, a single family of metrics that unifies richness, Shannon and Simpson diversity through one parameter, the diversity order q.

If Hill numbers are new to you, the key idea is the effective number of taxa: every value answers “how many equally-abundant taxa would give this much diversity?”. A community of 10 taxa where one dominates and the rest are rare behaves, in practice, like far fewer than 10 — and the Hill number says exactly how many. Because all the metrics below share this one currency, you can compare them directly across samples, studies and diversity types.

From the same framework hilldiv3 derives diversity partitioning, (dis)similarity, profiles, evenness and redundancy, for three flavours of diversity:

Flavour	What it accounts for	How you ask for it
Neutral	abundances only	counts
Phylogenetic	evolutionary relatedness	counts + tree
Functional	trait dissimilarity	counts + dist

The diversity type is inferred from the inputs you pass — you call the same functions either way. You can also state it explicitly with type = "neutral" | "phylogenetic" | "functional" to have it validated against your inputs.

The data

Every function takes a count table with taxa (OTUs/ASVs/MAGs) in rows and samples in columns. A matrix is the simplest form:

counts <- matrix(
  c(10, 0, 5,
     2, 8, 1,
     3, 4, 0,
     6, 2, 7),
  nrow = 3, byrow = FALSE,
  dimnames = list(c("t1", "t2", "t3"),
                  c("s1", "s2", "s3", "s4"))
)
counts
#>    s1 s2 s3 s4
#> t1 10  2  3  6
#> t2  0  8  4  2
#> t3  5  1  0  7

Data frames, tibbles, phyloseq objects and TreeSummarizedExperiment objects work too — see Preparing your data.

The package also ships a small simulated gut-microbiome example — gut_counts (a MAG count table), gut_tree (a phylogeny) and gut_traits (a trait table) — used throughout the website articles.

Alpha diversity (within a sample)

hilldiv() returns Hill numbers per sample — the diversity within each community, traditionally called alpha diversity. By default it computes orders q = 0 (richness), q = 1 (Shannon diversity) and q = 2 (Simpson diversity):

hilldiv(counts)
#> Computing "neutral" Hill numbers of "q0", "q1", and "q2".
#> ℹ 3 taxa across 4 samples.
#> <hilldiv3 result: neutral>
#> 12 rows x 3 cols
#> 
#>    q sample    value
#> 1  0     s1 2.000000
#> 2  1     s1 1.889882
#> 3  2     s1 1.800000
#> 4  0     s2 3.000000
#> 5  1     s2 2.137309
#> 6  2     s2 1.753623
#> 7  0     s3 2.000000
#> 8  1     s3 1.979626
#> 9  2     s3 1.960000
#> 10 0     s4 3.000000
#> 11 1     s4 2.693484
#> 12 2     s4 2.528090

Higher q down-weights rare taxa, so qD decreases as q grows unless the sample is perfectly even. Add a tree or a distance matrix to layer on more flavours: a tree adds phylogenetic diversity alongside neutral, and supplying both a tree and a dist returns all three types at once (a type column tells them apart). Restrict the output with type =.

tree <- ape::read.tree(text = "((t1:1,t2:1):1,t3:2);")
hilldiv(counts, tree = tree)                   # neutral + phylogenetic
#> Computing "neutral" and "phylogenetic" Hill numbers of "q0", "q1", and "q2".
#> ℹ 3 taxa across 4 samples.
#> <hilldiv3 result: neutral, phylogenetic>
#> 24 rows x 4 cols
#> 
#>    q sample         type    value
#> 1  0     s1      neutral 2.000000
#> 2  1     s1      neutral 1.889882
#> 3  2     s1      neutral 1.800000
#> 4  0     s2      neutral 3.000000
#> 5  1     s2      neutral 2.137309
#> 6  2     s2      neutral 1.753623
#> 7  0     s3      neutral 2.000000
#> 8  1     s3      neutral 1.979626
#> 9  2     s3      neutral 1.960000
#> 10 0     s4      neutral 3.000000
#> 11 1     s4      neutral 2.693484
#> 12 2     s4      neutral 2.528090
#> 13 0     s1 phylogenetic 2.000000
#> 14 1     s1 phylogenetic 1.889882
#> 15 2     s1 phylogenetic 1.800000
#> 16 0     s2 phylogenetic 2.500000
#> 17 1     s2 phylogenetic 1.702490
#> 18 2     s2 phylogenetic 1.423529
#> 19 0     s3 phylogenetic 1.500000
#> 20 1     s3 phylogenetic 1.406992
#> 21 2     s3 phylogenetic 1.324324
#> 22 0     s4 phylogenetic 2.500000
#> 23 1     s4 phylogenetic 2.318405
#> 24 2     s4 phylogenetic 2.227723
hilldiv(counts, tree = tree, type = "phylogenetic")   # phylogenetic only
#> Computing "phylogenetic" Hill numbers of "q0", "q1", and "q2".
#> ℹ 3 taxa across 4 samples.
#> <hilldiv3 result: phylogenetic>
#> 12 rows x 3 cols
#> 
#>    q sample    value
#> 1  0     s1 2.000000
#> 2  1     s1 1.889882
#> 3  2     s1 1.800000
#> 4  0     s2 2.500000
#> 5  1     s2 1.702490
#> 6  2     s2 1.423529
#> 7  0     s3 1.500000
#> 8  1     s3 1.406992
#> 9  2     s3 1.324324
#> 10 0     s4 2.500000
#> 11 1     s4 2.318405
#> 12 2     s4 2.227723

Which taxa carry the Hill power sum?

hillshare() assigns each taxon a share of the Hill power sum at each order q. Give it named sets to add the shares of several taxa. With a tree or functional distances, it applies the corresponding phylogenetic or functional calculation. The default allocation is "qpower"; these shares are not percentages of the effective Hill number returned by hilldiv().

sets <- list(t1 = "t1", t1_and_t2 = c("t1", "t2"))
fdist <- as.matrix(stats::dist(c(t1 = 0, t2 = 0.5, t3 = 1)))
hillshare(counts[, "s2"], q = c(0, 1, 2),
          tree = tree, dist = fdist, sets = sets)
#>    q  sample         type       set      share allocation
#> 1  0 sample1      neutral        t1 0.33333333     qpower
#> 2  0 sample1      neutral t1_and_t2 0.66666667     qpower
#> 3  1 sample1      neutral        t1 0.18181818     qpower
#> 4  1 sample1      neutral t1_and_t2 0.90909091     qpower
#> 5  2 sample1      neutral        t1 0.05797101     qpower
#> 6  2 sample1      neutral t1_and_t2 0.98550725     qpower
#> 7  0 sample1 phylogenetic        t1 0.30000000     qpower
#> 8  0 sample1 phylogenetic t1_and_t2 0.60000000     qpower
#> 9  1 sample1 phylogenetic        t1 0.18181818     qpower
#> 10 1 sample1 phylogenetic t1_and_t2 0.90909091     qpower
#> 11 2 sample1 phylogenetic        t1 0.05813149     qpower
#> 12 2 sample1 phylogenetic t1_and_t2 0.98823529     qpower
#> 13 0 sample1   functional        t1 0.24234694     qpower
#> 14 0 sample1   functional t1_and_t2 0.85459184     qpower
#> 15 1 sample1   functional        t1 0.18181818     qpower
#> 16 1 sample1   functional t1_and_t2 0.90909091     qpower
#> 17 2 sample1   functional        t1 0.12903226     qpower
#> 18 2 sample1   functional t1_and_t2 0.94623656     qpower

Each row gives a share between zero and one for one sample, diversity type, order and set. With sets = NULL, every taxon gets its own row and their shares sum to one within each combination. Named sets may overlap. At q = 1, functional shares equal relative abundances, even though functional Hill diversity still depends on the distances.

Partitioning and dissimilarity

hillpart() splits diversity across samples into alpha (within-sample), gamma (pooled) and beta (gamma / alpha, the number of effectively distinct communities):

hillpart(counts)
#> Partitioning neutral Hill numbers of "q0", "q1", and
#> "q2".
#> <hilldiv3 result: neutral>
#> 9 rows x 3 cols
#> 
#>   q component    value
#> 1 0     alpha 2.500000
#> 2 1     alpha 2.154269
#> 3 2     alpha 1.968927
#> 4 0     gamma 3.000000
#> 5 1     gamma 2.905735
#> 6 2     gamma 2.828374
#> 7 0      beta 1.200000
#> 8 1      beta 1.348827
#> 9 2      beta 1.436505

hilldiss() and hillsim() turn beta into bounded dissimilarity / similarity metrics (Sorensen-, Jaccard-, and UniFrac-type), and hillpair() returns a dist object of pairwise dissimilarities ready for ordination:

hilldiss(counts, q = 1)
#> dissimilarity from neutral Hill numbers of "q1".
#> <hilldiv3 result: neutral>
#> 4 rows x 3 cols
#> 
#>   q metric     value
#> 1 1      S 0.3448199
#> 2 1      C 0.2158525
#> 3 1      U 0.2158525
#> 4 1      V 0.1162756

Where to next

The website carries in-depth articles:

• Diversity types — neutral, phylogenetic and functional measurement.
• Taxon and set shares — how hillshare() allocates each Hill power sum to taxa and groups of taxa.
• Partitioning and (dis)similarity — alpha/beta/gamma, the S/C/U/V metrics, and pairwise dissimilarity for ordination.
• Profiles, evenness and redundancy — hillprof(), hilleven(), hillred().
• Preparing your data — input formats, phyloseq/TreeSummarizedExperiment, tss(), traits2dist() and match_data().

References

• Hill, M.O. (1973). Diversity and evenness. Ecology, 54, 427–432.
• Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88, 2427–2439.
• Alberdi, A. & Gilbert, M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Mol. Ecol. Resour., 19, 804–817.