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hilldiv
View on CRAN: Click
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Download and install hilldiv package within the R console
Install from CRAN:
install.packages("hilldiv")
Install from Github:
library("remotes")
install_github("cran/hilldiv")
Install by package version:
library("remotes")
install_version("hilldiv", "1.5.1")
Attach the package and use:
library("hilldiv")
Maintained by
Antton Alberdi
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-10-01
Latest Update: 2019-10-01
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
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. 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) ,
Chao et al. (2010) and Chiu et al. (2014)
; and reviewed in the framework of molecularly characterised
biological systems in Alberdi & Gilbert (2019) .
How to cite:
Antton Alberdi (2019). hilldiv: Integral Analysis of Diversity Based on Hill Numbers. R package version 1.5.1, https://cran.r-project.org/web/packages/hilldiv. Accessed 21 Nov. 2024.
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imports, suggests or enhances
Complete documentation for hilldiv
Functions, R codes and Examples using
the hilldiv R package
Some associated functions: CqN . SqN . UqN . VqN . alpha_div . bat.diet.hierarchy . bat.diet.otutable . bat.diet.tree . beta_dis . copy_filt . depth_cov . depth_filt . div_part . div_profile . div_profile_plot . div_test . div_test_plot . gamma_div . hill_div . index_div . is.nested . match_data . pair_dis . pair_dis_plot . to.incidence . tree_depth . tss .
Some associated R codes: CqN.R . SqN.R . UqN.R . VqN.R . alpha_div.R . beta_dis.R . copy_filt.R . data.R . depth_cov.R . depth_filt.R . div_part.R . div_profile.R . div_profile_plot.R . div_test.R . div_test_plot.R . gamma_div.R . hill_div.R . index_div.R . is.nested.R . match_data.R . pair_dis.R . pair_dis_plot.R . to.incidence.R . tree_depth.R . tss.R . Full hilldiv package functions and examples
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