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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

Reproducible research

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

Pinned

  1. Ternary Public

    Create ternary plots in R

    R 21 1

  2. Rogue Public

    Identify rogue taxa in phylogenetic trees within R

    BrighterScript 2

  3. TreeDist Public

    Calculate distances between phylogenetic trees in R

    R 15 4

  4. TreeSearch Public

    R package for phylogenetic tree search under custom optimality criteria

    R 4 4

  5. Quartet Public

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

    C++ 5 5

  6. Strategies to improve concentration

2,589 contributions in the last year

Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Mon Wed Fri

Contribution activity

December 2022

Created 17 commits in 1 repository
Created 1 repository
Opened 1 issue in 1 repository
ms609/TreeSearch 1 open
87 contributions in private repositories Dec 1 – Dec 6

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