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ms609/README.md

Martin R. Smith

I am an Associate Professor in Durham University's Department of Earth Sciences. I use the fossil record to illuminate the origins of life's complexity. To this end, I have developed and implemented a number of methods to improve the inference of phylogenetic history ("evolutionary family trees"), mainly in R/C++.

See https://smithlabdurham.github.io/ for more about my group's research interests.

Repo highlights

R packages

  • Ternary: create ternary plots and Holdridge diagrams.

  • Packages for calculating and evaluating distances between phylogenetic trees: TreeDist, TBRDist, Quartet.

  • MapTrees: an interactive user interface for the creation, visualization and evaluation of tree landscapes.

  • TreeTools: utilities for the creation, modification and analysis of phylogenetic trees.

  • TreeSearch: phylogenetic tree search in R, with an appropriate treatment of ‘inapplicable’ characters.

  • Rogue: Identify rogue taxa to improve consensus trees.

Student resources

  • Concentration: Strategies to improve concentration and maximize productivity.

  • Ancient Life and its Environment: Teaching resources for a palaeontological half-module.

  • preferences: Default configurations for scientific research software.

  • dictionary: Personal wordlist of scientific terms to supplement spell-checkers.

  • module-map: JavaScript interface to navigate Earth Science degree pathways.

Reproducible research

  • phylo-workflow: Workflow for semi-automatic phylogenetic analysis of morphological data.

  • hyoliths: Supplementary dataset for Sun et al. (2018): a useful template for morphological phylogenetic analysis.

Pinned Loading

  1. Ternary Ternary Public

    Create ternary plots in R

    R 32 3

  2. Rogue Rogue Public

    Identify rogue taxa in phylogenetic trees within R

    Bluespec 3

  3. TreeDist TreeDist Public

    Calculate distances between phylogenetic trees in R

    R 30 6

  4. TreeSearch TreeSearch Public

    R package for phylogenetic tree search under custom optimality criteria

    R 7 4

  5. Quartet Quartet Public

    R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)

    C++ 12 5

  6. Concentration Concentration Public

    Strategies to improve concentration

    2