Skip to content
Diversity analysis based on Hill numbers
R
Branch: master
Clone or download
Latest commit ff4555e Aug 23, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github/ISSUE_TEMPLATE Update issue templates Aug 14, 2019
R Documentation updates Aug 23, 2019
data Add files via upload Dec 17, 2018
documentation Documentation updates Aug 23, 2019
figures 1.4 update Aug 15, 2019
man
.DS_Store XqN man updates May 10, 2019
CHANGELOG.md Update CHANGELOG.md Aug 23, 2019
DESCRIPTION
LICENSE Create LICENSE Aug 14, 2019
NAMESPACE div.profile() and div.profile.plot() update Aug 22, 2019
README.md Update README.md Aug 23, 2019

README.md

hilldiv 1.4 (Last update: August 2019)

hilldiv is an R package that provides a set of functions to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers.

The statistical framework developed around Hill numbers encompasses many of the most broadly employed diversity (e.g. richness, Shannon index, Simpson index), phylogenetic diversity (e.g. Faith’s PD, Allen’s H, Rao’s quadratic entropy) and dissimilarity (e.g. Sørensen index, Unifrac distances) metrics. This enables the most common analyses of diversity to be performed while grounded in a single statistical framework. For details about the use of Hill numbers in molecularly characterised biological systems, read the following article.

Alberdi A, Gilbert MTP. (2019). A guide to the application of Hill numbers to DNA‐based diversity analyses. Molecular Ecology Resources. 19(4): 804-817. https://doi.org/10.1111/1755-0998.13014

If you want/need to cite hilldiv: Alberdi A, Gilbert MTP. 2019. hilldiv: an R package for the integral analysis of diversity based on Hill numbers. bioRxiv 545665. https://www.biorxiv.org/content/10.1101/545665v1

Some recent papers that used hilldiv:

  • Alberdi et al. (2019) Diet diversification shapes broad-scale distribution patterns in European bats. bioRxiv. https://doi.org/10.1101/704759

  • Siren et al. (2019) Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.00697

  • Chang et al. (2019) The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish‐eating bat Myotis pilosus. Molecular Ecology. https://doi.org/10.1111/mec.15127

List of functions

Function Short explanation Documentation
hill.div() Neutral or phylogenetic Hill number computation LINK
index.div() Neutral or phylogenetic diversity index computation LINK
div.profile() (Phylo)Diversity profiles of individual samples or groups of samples LINK
div.test() Diversity comparison between two or multiple groups of samples LINK
div.test.plot() Visual representation of div.test() LINK
depth.cov() Assessment of the sequencing depth per sample LINK
div.part() Hierarchical diversity partitioning LINK
alpha.div() Alpha diversity computation LINK
gamma.div() Gamma diversity computation LINK
beta.dis() (Dis)similarity computation based on beta diversities LINK
pair.dis() Pairwise (dis)similarity computation based on beta diversities LINK
pair.dis.plot() Visual representation of pair.dis() LINK
UqN() Jaccard-type overlap computation from beta diversities LINK
CqN() Sørensen-type overlap from beta diversities LINK
SqN() Jaccard-type turnover-complement from beta diversities LINK
VqN() Sørensen-type turnover-complement from beta diversities LINK
to.incidence() Convert an abundance-based count (OTU/ASV) table into an incidence-based object LINK
match.data() Filter OTU tables and trees to match OTUs in both data files LINK
depth.filt() Filter samples according to a minimum sequencing depth threshold LINK
copy.filt() Filter OTUs according to a minimum copy number threshold LINK
tss() Total sum scaling per sample LINK
tree.depth() Tree depth computation LINK

Installation

To install hilldiv in your R environment, you need to 1) install devtools, 2) load devtools library, 3) install hilldiv using devtools and 4) finally load hilldiv library to your environment.

install.packages("devtools")
library(devtools)
install_github("anttonalberdi/hilldiv")
library(hilldiv,quietly=TRUE)

If not installed, it will automatically install the following dependencies: ggplot2, ggpubr, RColorBrewer, data.table, ape, ade4, iNEXT, iNextPD.

If the console returns the following error:

"tar: Failed to set default locale"

Type the following in the console and restart R

system('defaults write org.R-project.R force.LANG en_US.UTF-8')

Workflow

Documentation

I am creating extensive documentation about Hill numbers and implementation of hilldiv in the Hilldiv WIKI.

0 - Introduction to Hill numbers: an introduction to Hill numbers. If you don't know the basics about Hill numbers, you should first read this page.

1 - Data files: basic information about the data types implemented in the package hilldiv.

2 - Data preprocessing: count table, phylogenetic tree and metadata processing for the optimal using the functions copy.filt(), depth.cov(), match.data() and to.incidence()

3.1 - Diversity computation of a single system: diversity computation of a single system using the functions hill.div() and index.div().

3.2 - Diversity computation and comparison of multiple systems: diversity computation and comparison of multiple systems or contrasting groups using the functions hill.div(), div.test() and div.test.plot().

3.3 - Diversity profiles: generation of diversity profile tables and plots using functions div.profile() and div.profile.plot().

4 - Diversity partitioning: hierarchical diversity partitioning using the function div.part().

References

  • Alberdi A., Gilbert M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources, 19(4), 804-817.
  • Chao, A. & Jost, L. (2015) Estimating diversity and entropy profiles via discovery rates of new species. Methods in Ecology and Evolution, 6, 873-882.
  • Chao, A., Chiu, C.-H., & Hsieh, T. C. (2012). Proposing a resolution to debates on diversity partitioning. Ecology, 93(9), 2037–2051.
  • Chao, A., Chiu, C.-H., & Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365(1558), 3599–3609.
  • Hill, M. O. (1973). Diversity and Evenness: A Unifying Notation and Its Consequences. Ecology, 54(2), 427–432.
  • Hsieh, T. C., & Chao, A. (2017). Rarefaction and Extrapolation: Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple Assemblages. Systematic Biology, 66(1), 100–111.
  • Hsieh, T. C., Ma, K. H., & Chao, A. (2016). iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution / British Ecological Society, 7(12), 1451–1456.
  • Jost, L. (2006). Entropy and diversity. Oikos , 113, 363–375.
  • Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88(10), 2427–2439.
  • Marcon, E., & Hérault, B. (2015). entropart: An R Package to Measure and Partition Diversity. Journal of Statistical Software, Articles, 67(8), 1–26.
  • Tuomisto, H. (2010). A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity. Ecography, 33(1), 2–22.
You can’t perform that action at this time.