Taxon Sampling and Inferred Community Phylogenies: Replication Code and Data

Harvard University Press provides R code and data for simulating community phylogenies and calculating phylogenetic diversity metrics. The resources support statistical analyses comparing simulated and empirical data, likely using linear mixed-effects models. This work appears in the fields of ecology and evolutionary biology, focusing on the impact of taxon sampling on phylogenetic inference.

Use Cases

• Simulating community phylogenies under different sampling scenarios using provided Perl and R scripts.
• Calculating and comparing phylogenetic diversity metrics for simulated and empirical communities.
• Conducting statistical analyses, such as linear mixed-effects modeling, on interval and summary data from phylogenetic simulations.
• Replicating published findings on taxon sampling effects in community phylogenetics.

Strengths

• Includes both simulation code and empirical data for comparative analysis.
• Provides replication materials associated with a publication from Harvard University Press.
• Contains structured data files (CSV) ready for statistical analysis in R.

Limitations

• Key metadata such as row counts, dataset size, and specific column names are unknown.
• The last update date is not provided, making freshness uncertain.
• Descriptions are technical but sparse on the specific empirical data's origin and scope.

Provenance

Source

Daniel Park, Harvard University Press

Collection Method

Likely generated through computational simulation and empirical data collection for research publication.