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