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phyr - Model Based Phylogenetic Analysis

A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).

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bayesianglmminlaphylogenyspecies-distribution-modelingopenblascpp

9.98 score 36 stars 2 dependents 123 scripts 12k downloads

hillR - Diversity Through Hill Numbers

Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.

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biodiversityhill-numbers

8.08 score 36 stars 3 dependents 214 scripts 780 downloads

rtrees - Deriving Phylogenies from Synthesis Trees

Provides tools to derive species-level phylogenies from large synthesis mega-trees for a wide range of taxonomic groups, including plants, birds, mammals, amphibians, reptiles, fish, bees, butterflies, and sharks. When a queried species is absent from the mega-tree, it is grafted onto the tree using one of two placement strategies: attachment at the basal node of the most closely related genus or family ('at_basal_node'), or random attachment below that basal node with probability proportional to branch length ('random_below_basal'). See Li (2023) <doi:10.1111/ecog.06643> for details. Multiple species from a genus not represented in the mega-tree are placed as a polytomy to preserve clade coherence. The package interfaces with the 'megatrees' data package, which bundles or downloads on demand curated mega-trees. Users can also provide their own mega-trees.

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phylogenetic-treescpp

6.66 score 36 stars 91 scripts

neonDivData - Standardized NEON Organismal Data for Biodiversity Research

Cleaned, simplified, and standardized NEON organismal data for biodiversity research. The following taxonomic groups are included so far: algae, beetles, birds, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized.

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4.71 score 18 stars 19 scripts

megatrees - Subsets of Randomly Selected Phylogenies from Existing Mega-Phylogenies

There are an increasing number of mega-phylogenies available nowadays, with many of them being sets of thousands of posterior distribution phylogenies. For ecological studies, we may need to randomly select many such posterior phylogenies to conduct analyses. This data package serves this purpose by providing a small number (100 or 50) of randomly selected posterior phylogenies (if available) so that we can readily use them for our downstream analyses without repeating the downloading and selecting processes.

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3.35 score 5 stars 1 dependents 5 scripts

megatrees - Subsets of Randomly Selected Phylogenies from Existing Mega-Phylogenies

There are an increasing number of mega-phylogenies available nowadays, with many of them being sets of thousands of posterior distribution phylogenies. For ecological studies, we may need to randomly select many such posterior phylogenies to conduct analyses. This data package serves this purpose by providing a small number (100 or 50) of randomly selected posterior phylogenies (if available) so that we can readily use them for our downstream analyses without repeating the downloading and selecting processes.

Last updated

2.18 score 1 dependents 5 scripts

lirrr - Functions collected/wrote by Daijiang Li

To keep all my functions in one place, and to use them more easily.

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2.00 score 1 stars 3 scripts