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>).

Last updated 9 months ago

bayesianglmminlaphylogenyspecies-distribution-modeling

8.57 score 30 stars 2 packages 106 scripts 3.3k 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>.

Last updated 7 months ago

biodiversityhill-numbers

8.19 score 31 stars 3 packages 159 scripts 664 downloads

rtrees - Deriving Phylogenies from Synthesis Trees

To facilitate generating phylogenies from synthesis trees.

Last updated 5 months ago

phylogenetic-trees

5.64 score 31 stars 70 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, fish, herptiles, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized using R package `ecocomDP` (<https://github.com/EDIorg/ecocomDP>).

Last updated 6 months ago

4.33 score 14 stars 17 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 phylogeneies to conduct analyses. This data package serves this purpose by providing a small number (100) 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 5 months ago

2.78 score 4 stars 1 packages 2 scripts

lirrr - Functions collected/wrote by Daijiang Li

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

Last updated 10 months ago

1.70 score 1 stars 3 scripts