Distance Metrics for Trees Generated by Congreve and Lamsdell

Includes the 100 datasets simulated by Congreve and Lamsdell (2016) , and analyses of the partition and quartet distance of reconstructed trees from the generative tree, as analysed by Smith (2019) .


Project Status: Inactive. Build Status CRAN Status Badge CRAN Downloads DOI

This R package provides data and analyses that accompany the paper

  • Smith, M. R. (2019), Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets, Biological Letters, 15:20180632, doi:10.1098/rsbl.2018.0632.

It incorporates data from:

  • Congreve, C. R., and J. C. Lamsdell. 2016. Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices. Palaeontology, 59:447–462. doi:10.1111/pala.12236.

  • Congreve, C. R., and J. C. Lamsdell. 2016. Data from: Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices. Dryad Digital Repository, doi:10.5061/dryad.7dq0j.

Some of these data are used in the Quartet package.

Equivalent data and analyses from data simulated by O'Reilly et al. (2016) are available at ms609.github.io/OReillyEtAl2016.

Installation

Install and load the library from CRAN as follows:

install.packages('CongreveLamsdell2016')
library('CongreveLamsdell2016')

Documentation

The package includes documentation and visualizations of its results:

  • R Package manual: PDF

  • How to conduct the analyses: HTML | PDF

  • Node support comparisons: HTML | PDF

  • Comparisons of phylogenetic methods: HTML | PDF

News

CongreveLamsdell2016 v1.0.1

  • Update description to meet CRAN formatting requirements.

CongreveLamsdell2016 v1.0.0

  • Stand-alone package created.

Reference manual

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install.packages("CongreveLamsdell2016")

1.0.1 by Martin R. Smith, 10 months ago


https://github.com/ms609/CongreveLamsdell2016


Report a bug at https://github.com/ms609/Quartet/issues


Browse source code at https://github.com/cran/CongreveLamsdell2016


Authors: Martin R. Smith [aut, cre, cph] , Curtis R. Congreve [cph, dtc] , James C. Lamsdell [cph, dtc]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports Ternary

Suggests ape, bookdown, knitr, phangorn, Quartet, rmarkdown, TreeSearch, usethis


See at CRAN