READ ME File For 'Dataset for tree congruence: quantifying similarity between dendrogram topologies'
Dataset DOI:10.5258/SOTON/D1069
ReadMe Author: Steven U. Vidovic, University of Southampton [ORCiD:0000-0002-4726-8018]
This dataset supports the publication:
AUTHORS: Steven U. Vidovic
TITLE: Tree congruence: quantifying similarity between dendrogram topologies
JOURNAL: bioRxiv
PAPER DOI IF KNOWN: https://doi.org/10.1101/766840
This dataset contains:
R scripts for calculating the topological congruence metrics CRI, MASTxCF, CF, R-F, presenting them in Pac-man pie chart matrices and analysing ranked results using Kendall's tau b and Spearman's rho. The file is organised into tabs in a html markdown document and its associated MathJax.js. The tabs contain results of the analyses of dendrograms with 11 terminal nodes, 21 terminal nodes, 31 terminal nodes, 41 terminal nodes, and the results of comparing those anlyses using Kendall's tau b, Spearman's rho and plots. Each of the dendrogram size tabs contains drawings of the 10 fundamental trees, a table of the fundamental trees and their consensus trees in newick format, and Pac-man piechart matrices and plain text matrices for the results of each of the analyses.
The figures are as follows (listed top to bottom, left to right):
tab: Sample size = 11
-Fundamental dendrograms sampling 11 specimens - 10 fundamental dendrograms for which the results are presented in the tables and graphs in the same tab.
-CRI - A Pac-man pie chart matrix drawn from the results of CRI analyses on the 10 fundamental dendrograms.
-MASTxCF - A Pac-man pie chart matrix drawn from the results of MASTxCF analyses on the 10 fundamental dendrograms.
-CF - A Pac-man pie chart matrix drawn from the results of CF analyses on the 10 fundamental dendrograms.
-Distortion Coefficient (RI on MRP) - A Pac-man pie chart matrix drawn from the results of Distortion Coefficient analyses on the 10 fundamental dendrograms.
-R-F (1-(RF/((N-1)2))) - A Pac-man pie chart matrix drawn from the results of R-F analyses in R on the 10 fundamental dendrograms.
-R-F TNT - A Pac-man pie chart matrix drawn from the results of R-F analyses done in TNT on the 10 fundamental dendrograms.
-Mickevich’s CI~M - A Pac-man pie chart matrix drawn from the results of CI~M analyses done in PAUP* on the 10 fundamental dendrograms.
-Rohlf's CI~1 - A Pac-man pie chart matrix drawn from the results of CI~1 analyses done in PAUP* on the 10 fundamental dendrograms.
-Weighted CF - A Pac-man pie chart matrix drawn from the results of weighte CF analyses done in PAUP* on the 10 fundamental dendrograms.
-SPR distances - A Pac-man pie chart matrix drawn from the results of SPR distances analyses done in TNT on the 10 fundamental dendrograms.
tab: Sample size = 21
-Fundamental dendrograms sampling 21 specimens - 10 fundamental dendrograms for which the results are presented in the tables and graphs in the same tab.
-CRI - A Pac-man pie chart matrix drawn from the results of CRI analyses on the 10 fundamental dendrograms.
-MASTxCF - A Pac-man pie chart matrix drawn from the results of MASTxCF analyses on the 10 fundamental dendrograms.
-CF - A Pac-man pie chart matrix drawn from the results of CF analyses on the 10 fundamental dendrograms.
-Distortion Coefficient (RI on MRP) - A Pac-man pie chart matrix drawn from the results of Distortion Coefficient analyses on the 10 fundamental dendrograms.
-R-F (1-(RF/((N-1)2))) - A Pac-man pie chart matrix drawn from the results of R-F analyses in R on the 10 fundamental dendrograms.
-R-F TNT - A Pac-man pie chart matrix drawn from the results of R-F analyses done in TNT on the 10 fundamental dendrograms.
-Mickevich’s CI~M - A Pac-man pie chart matrix drawn from the results of CI~M analyses done in PAUP* on the 10 fundamental dendrograms.
-Rohlf's CI~1 - A Pac-man pie chart matrix drawn from the results of CI~1 analyses done in PAUP* on the 10 fundamental dendrograms.
-Weighted CF - A Pac-man pie chart matrix drawn from the results of weighte CF analyses done in PAUP* on the 10 fundamental dendrograms.
-SPR distances - A Pac-man pie chart matrix drawn from the results of SPR distances analyses done in TNT on the 10 fundamental dendrograms.
tab: Sample size = 31
-Fundamental dendrograms sampling 31 specimens - 10 fundamental dendrograms for which the results are presented in the tables and graphs in the same tab.
-CRI - A Pac-man pie chart matrix drawn from the results of CRI analyses on the 10 fundamental dendrograms.
-MASTxCF - A Pac-man pie chart matrix drawn from the results of MASTxCF analyses on the 10 fundamental dendrograms.
-CF - A Pac-man pie chart matrix drawn from the results of CF analyses on the 10 fundamental dendrograms.
-Distortion Coefficient (RI on MRP) - A Pac-man pie chart matrix drawn from the results of Distortion Coefficient analyses on the 10 fundamental dendrograms.
-R-F (1-(RF/((N-1)2))) - A Pac-man pie chart matrix drawn from the results of R-F analyses in R on the 10 fundamental dendrograms.
-R-F TNT - A Pac-man pie chart matrix drawn from the results of R-F analyses done in TNT on the 10 fundamental dendrograms.
-Mickevich’s CI~M - A Pac-man pie chart matrix drawn from the results of CI~M analyses done in PAUP* on the 10 fundamental dendrograms.
-Rohlf's CI~1 - A Pac-man pie chart matrix drawn from the results of CI~1 analyses done in PAUP* on the 10 fundamental dendrograms.
-Weighted CF - A Pac-man pie chart matrix drawn from the results of weighte CF analyses done in PAUP* on the 10 fundamental dendrograms.
-SPR distances - A Pac-man pie chart matrix drawn from the results of SPR distances analyses done in TNT on the 10 fundamental dendrograms.
tab: Sample size = 41
-Fundamental dendrograms sampling 41 specimens - 10 fundamental dendrograms for which the results are presented in the tables and graphs in the same tab.
-CRI - A Pac-man pie chart matrix drawn from the results of CRI analyses on the 10 fundamental dendrograms.
-MASTxCF - A Pac-man pie chart matrix drawn from the results of MASTxCF analyses on the 10 fundamental dendrograms.
-CF - A Pac-man pie chart matrix drawn from the results of CF analyses on the 10 fundamental dendrograms.
-Distortion Coefficient (RI on MRP) - A Pac-man pie chart matrix drawn from the results of Distortion Coefficient analyses on the 10 fundamental dendrograms.
-R-F (1-(RF/((N-1)2))) - A Pac-man pie chart matrix drawn from the results of R-F analyses in R on the 10 fundamental dendrograms.
-R-F TNT - A Pac-man pie chart matrix drawn from the results of R-F analyses done in TNT on the 10 fundamental dendrograms.
-Mickevich’s CI~M - A Pac-man pie chart matrix drawn from the results of CI~M analyses done in PAUP* on the 10 fundamental dendrograms.
-Rohlf's CI~1 - A Pac-man pie chart matrix drawn from the results of CI~1 analyses done in PAUP* on the 10 fundamental dendrograms.
-Weighted CF - A Pac-man pie chart matrix drawn from the results of weighte CF analyses done in PAUP* on the 10 fundamental dendrograms.
-SPR distances - A Pac-man pie chart matrix drawn from the results of SPR distances analyses done in TNT on the 10 fundamental dendrograms.
Licence: CC BY
Related projects:
Vidovic 2016
Vidovic & Martill 2017
Date that the file was created: September, 2019