philr

philr applies a phylogenetically informed isometric log-ratio (ILR) transform to compositional microbiota survey data to enable standard statistical analyses while accounting for evolutionary relationships.

Key Features:

• Integration with Phylogenetic Models: Integrates microbial evolutionary models with the isometric log-ratio (ILR) transform to incorporate phylogenetic relationships into compositional analyses.
• Phylogenetically tailored ILR transform: Employs an ILR transformation derived from a phylogenetic tree using a weighted reference measure to convert relative abundance data into coordinates amenable to conventional statistics.
• Decomposition of distances and variance: Enables decomposition of distances and variance in the transformed space to reveal covariation patterns among bacterial clades.
• Avoidance of compositional artifacts: Transforms compositional relative-abundance data to permit application of standard statistical tools without common artifacts affecting relative abundance analyses.
• Benchmark performance: Has been demonstrated to perform on par with or surpass standard analytical tools in benchmark tests on microbiota survey data.

Scientific Applications:

• Microbial Community Analysis: Analysis of microbial community structure and dynamics in microbiota survey data using phylogenetically informed compositional coordinates.
• Identification of Evolutionary Adaptations: Decomposition of distances in the transformed space to identify neighboring clades that may be adapted to distinct human body sites.
• Variance Decomposition: Decomposition of variance to reveal patterns of covariation among bacterial clades and how covariation scales with phylogenetic relatedness across human body sites.

Methodology:

Apply an ILR transformation tailored from a phylogenetic tree using a weighted reference measure; integrate microbial evolutionary models with the ILR transform; decompose distances and variance in the transformed space for downstream statistical analysis.