Package: hilldiv 1.5.3
hilldiv: Integral Analysis of Diversity Based on Hill Numbers
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) <doi:10.1890/06-1736.1>, Chao et al. (2010) <doi:10.1098/rstb.2010.0272> and Chiu et al. (2014) <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>.
Authors:
hilldiv_1.5.3.tar.gz
hilldiv_1.5.3.tar.gz(r-4.4-noble)
hilldiv_1.5.3.tgz(r-4.4-emscripten)hilldiv_1.5.3.tgz(r-4.3-emscripten)
hilldiv.pdf |hilldiv.html✨
hilldiv/json (API)
# Install 'hilldiv' in R: |
install.packages('hilldiv', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/anttonalberdi/hilldiv/issues
- bat.diet.hierarchy - Bat diet hierarchy
- bat.diet.otutable - Bat diet OTU table
- bat.diet.tree - Bat diet OTU tree
Last updated 4 years agofrom:551c284eaa. Checks:OK: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 18 2024 |
Exports:alpha_divbeta_discopy_filtCqNdepth_covdepth_filtdis_nmdsdiv_partdiv_profilediv_profile_plotdiv_testdiv_test_plotgamma_divhill_divindex_divis.nestedmatch_datamerge_samplespair_dispair_dis_plotSqNto.incidenceto.occurrencestree_depthtssUqNVqN
Dependencies:abindapebackportsbase64encbootbroombslibcachemcarcarDatacheckmatecliclusterclusterGenerationcodacodetoolscolorspacecombinatcorpcorcorrplotcowplotcpp11data.tableDEoptimDerivdeSolvedigestdoBydoParalleldplyrdunn.testevaluateexpmfansifarverfastmapfastmatchfdrtoolfontawesomeforeachforeignFormulafsFSAgeigergenericsggplot2ggpubrggrepelggsciggseqlogoggsignifglassoglueGPArotationgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelavaanlifecyclelme4lmtestmagrittrmapsMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamnormtmodelrmunsellmvtnormncbitnlmenloptrnnetnumDerivoptimParallelpbapplypbivnormpbkrtestpermutephangornphytoolspillarpkgconfigplotrixplyrpngpolynompsychpurrrqgraphquadprogquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrpartrstatixrstudioapisassscalesscatterplot3dSparseMstringistringrsubplexsurvivaltibbletidyrtidyselecttinytexutf8vctrsveganviridisviridisLitewithrxfunyamlzoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Alpha diversity | alpha_div |
Bat diet hierarchy | bat.diet.hierarchy |
Bat diet OTU table | bat.diet.otutable |
Bat diet OTU tree | bat.diet.tree |
Beta dissimilarity | beta_dis |
OTU/ASV copy number filtering | copy_filt |
Sørensen-type overlap | CqN |
Depth coverage assessment | depth_cov |
Sequencing depth filtering | depth_filt |
Dissimilarity NMDS plot | dis_nmds |
Multi-level diversity partitioning | div_part |
Diversity profile | div_profile |
Diversity profile plot | div_profile_plot |
Diversity test | div_test |
Diversity test plotting | div_test_plot |
Gamma diversity | gamma_div |
Hill numbers computation | hill_div |
Diversity index computation | index_div |
Check if hierachy is nested | is.nested |
Match data | match_data |
Merge samples | merge_samples |
Pairwise dissimilarity | pair_dis |
Pairwise dissimilarity plot | pair_dis_plot |
Jaccard-type turnover-complement | SqN |
Transform to incidence | to.incidence |
Transform abundance vector or matrix into occurrences | to.occurrences |
Tree depth | tree_depth |
Total Sum Scaling normalisation | tss |
Jaccard-type overlap | UqN |
Sørensen-type turnover-complement | VqN |