{ "_id": "6a23e0c3530b9bc726be7b24", "Package": "hilldiv", "Title": "Integral Analysis of Diversity Based on Hill Numbers", "Version": "1.5.3", "Author": "Antton Alberdi [aut, cre]", "Maintainer": "Antton Alberdi ", "Description": "Tools for analysing, comparing, visualising and\npartitioning diversity based on Hill numbers. 'hilldiv' is an R\npackage that provides a set of functions to assist analysis of\ndiversity for diet reconstruction, microbial community\nprofiling or more general ecosystem characterisation analyses\nbased on Hill numbers, using OTU/ASV tables and associated\nphylogenetic trees as inputs. The package includes functions\nfor (phylo)diversity measurement, (phylo)diversity profile\nplotting, (phylo)diversity comparison between samples and\ngroups, (phylo)diversity partitioning and (dis)similarity\nmeasurement. All of these grounded in abundance-based and\nincidence-based Hill numbers. The statistical framework\ndeveloped around Hill numbers encompasses many of the most\nbroadly employed diversity (e.g. richness, Shannon index,\nSimpson index), phylogenetic diversity (e.g. Faith's PD,\nAllen's H, Rao's quadratic entropy) and dissimilarity (e.g.\nSorensen index, Unifrac distances) metrics. This enables the\nmost common analyses of diversity to be performed while\ngrounded in a single statistical framework. The methods are\ndescribed in Jost et al. (2007) , Chao\net al. (2010) and Chiu et al.\n(2014) ; and reviewed in the framework\nof molecularly characterised biological systems in Alberdi &\nGilbert (2019) .", "License": "GPL-3", "LazyData": "true", "URL": "https://github.com/anttonalberdi/hilldiv", "BugReports": "https://github.com/anttonalberdi/hilldiv/issues", "Encoding": "UTF-8", "RoxygenNote": "7.1.0", "Collate": "'index_div.R' 'hill_div.R' 'div_profile.R'\n'div_profile_plot.R' 'div_test.R' 'div_test_plot.R'\n'depth_cov.R' 'div_part.R' 'alpha_div.R' 'gamma_div.R'\n'beta_dis.R' 'pair_dis.R' 'pair_dis_plot.R' 'dis_nmds.R'\n'UqN.R' 'CqN.R' 'VqN.R' 'SqN.R' 'match_data.R'\n'merge_samples.R' 'depth_filt.R' 'copy_filt.R' 'to.incidence.R'\n'to.occurrences.R' 'tss.R' 'is.nested.R' 'tree_depth.R'\n'data.R'", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libjpeg-dev\nlibpng-dev libuv1-dev libxml2-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2021-02-08 08:35:16 UTC", "RemoteUrl": 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