Title: Coordinate Indexing on Hilbert Curves
Description: Provides utilities for encoding and decoding coordinates to/from Hilbert curves
based on the iterative encoding implementation described in Chen et al. (2006) <doi:10.1002/spe.793>.
Suggests: bit64 (>= 4.0.0), testthat (>= 3.0.0), covr, knitr, rmarkdown

Title: Hilbert Similarity Index for High Dimensional Data
Description: Quantifying similarity between high-dimensional single cell samples is challenging, and usually requires
some simplifying hypothesis to be made. By transforming the high dimensional space into a high dimensional grid,
the number of cells in each sub-space of the grid is characteristic of a given sample. Using a Hilbert curve
each sample can be visualized as a simple density plot, and the distance between samples can be calculated from
the distribution of cells using the Jensen-Shannon distance. Bins that correspond to significant differences
between samples can identified using a simple bootstrap procedure.
Suggests: knitr, rmarkdown, ggplot2, dplyr, tidyr, reshape2,

person("Sebastian", "Kalucza", email = "sebastian.kalucza@gmail.com", role = c("aut", "cre")),
person("Sara", "Kalucza", email = "sara.kalucza@gmail.com", role = c("aut")))
Description: Makes it easy to extract and combine variables from the HILDA (Household, Income and Labour Dynamics in Australia) survey maintained by the Melbourne Institute <https://melbourneinstitute.unimelb.edu.au/hilda>.

Description: Calculate taxonomic, functional and phylogenetic diversity measures
through Hill Numbers proposed by Chao, Chiu and Jost (2014)

Imports: FD, plyr, ade4, ape, tibble, geiger
Suggests: testthat, vegetarian, covr, betapart

Title: Integral Analysis of Diversity Based on Hill Numbers
Description: Tools for analysing, comparing, visualising and partitioning diversity based on Hill numbers.
'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/ASV 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
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. Sorensen index, Unifrac distances) metrics. This enables the most
common analyses of diversity to be performed while grounded in a single statistical
framework. The methods are described in Jost et al. (2007) <DOI:10.1890/06-1736.1>,
<DOI:10.1890/12-0960.1>; and reviewed in the framework of molecularly characterised
biological systems in Alberdi & Gilbert (2019) <DOI:10.1111/1755-0998.13014>.
Imports: stats, ggplot2, scales, ggpubr, RColorBrewer, data.table, ape,
'beta_dis.R' 'pair_dis.R' 'pair_dis_plot.R' 'UqN.R' 'CqN.R'
'VqN.R' 'SqN.R' 'match_data.R' 'depth_filt.R' 'copy_filt.R'
'to.incidence.R' 'tss.R' 'is.nested.R' 'tree_depth.R' 'data.R'