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protoRomance

This directory contains all data and scripts used and produced for Section 3 of the TL target article Computational Historical Linguistics.

The subdirectory reply/ contains the code used for the computations described in my reply Model evaluation in computational historical linguistics in the same volume.

Table of contents

original data:

dataset.tab (ASJP v. 17, accessed from asjp.clld.org on 8/2/16)

Script files

Python

  • alignment.py
  • estimatePMI.py
  • cognateClustering.py
  • combinePartitions.py
  • mbPostprocessing.py
  • asrCC.py
  • asrSounds.py
  • evaluation.py

####R (for conversion between Newick and Nexus format for phylogenies)

  • convert_mccTree.r
  • convertTrees.r

MrBayes

  • albanoRomance.mb.nex

BayesTraits

  • asrCC.bt
  • btAlignments.txt

Paup*

  • convertRomancePosterior.paup

Intermediate results

  • pmi-albanoRomance.csv (PMI scores)
  • albanoRomanceASJP.csv (word lists used)
  • albanoRomanceSC.nex (character matrix)
  • albanoRomance.wordpairs.zip (word pairs with PMI similarities, used for cognate clustering; zipped csv file)
  • albanoRomanceCC.nex (character matrix)
  • albanoRomanceCCbin.csv (character matrix)
  • albanoRomanceCC.csv (word lists with inferred class labels)
  • albanoRomance_sc_cc.nex (combined character matrix)
  • albanoRomance.run1.p (MrBayes output)
  • albanoRomance.run1.t (MrBayes output)
  • albanoRomance.run2.p (MrBayes output)
  • albanoRomance.run2.t (MrBayes output)
  • albanoRomance.ckp (MrBayes output)
  • albanoRomance.con.tre (MrBayes output)
  • albanoRomance.parts (MrBayes output)
  • albanoRomance.mcmc (MrBayes output)
  • albanoRomance.trprobs (MrBayes output)
  • albanoRomance.tstat (MrBayes output)
  • albanoRomance.vstat (MrBayes output)
  • albanoRomance.run1.tre (MrBayes output, converted to Newick)
  • albanoRomance.run2.tre (MrBayes output, converted to Newick)
  • albanoRomance.posterior.tree (posterior sample)
  • romance.posterior.tree (posterior sample, rooted and pruned to Romance)
  • romance.posterior.nex.tree (posterior sample, rooted and pruned to Romance, Nexus format)
  • albanoRomance.mcc.tre (maximum clade credibility tree, Nexus format)
  • albanoRomance.mcc.nwk (maximum clade credibility tree, Newick format)
  • romanceCC.tsv (character matrix for BayesTraits)
  • romanceCC.tsv.log.txt (BayesTraits log file)
  • asrCC.csv (ASR for cognate classes)
  • romanceAlignments.nex (character matrix)
  • romanceAlignments.tsv (character matrix for BayesTraits)
  • romanceAlignments.tsv.log.txt (BayesTraits log file)

Final results

  • reconstruction.csv (reconstructed word list)
  • romanceEvaluation.csv (evaluation results)

Documentation

  • workflow.txt
  • README.md