3 packages on CRAN
Three methods to calculate R2 for models with correlated errors, including Phylogenetic GLS, Phylogenetic Logistic Regression, Linear Mixed Models (LMMs), and Generalized Linear Mixed Models (GLMMs). See details in Ives 2018 <doi:10.1093/sysbio/syy060>.
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('pez.shape', 'pez.evenness', 'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').