Teiphy

The main change introduced in this release is support for tagging of potential transcriptional explanations with notBefore and notAfter attributes. If these attributes are present in a variation unit's transcriptional relations list, teiphy will now map the transcriptional relations to an EpochSubstitutionModel with a different substitution model for different slices of time. This feature is only supported for BEAST 2.7 XML outputs. This means that BEAST users can now model time-dependent transcriptional changes (like assimilation to later popular texts, paleographic confusions possible only for earlier or later scripts, etc.) more accurately.

A related change is the addition of more comprehensive rules for updating witness date ranges based on the date range of the work's composition (and vice-versa). This change affects age/date calibrations for NEXUS and BEAST 2.7 XML formats (including the MrBayes NEXUS input format).

This release also fixes an error that prevented the --verbose flag from working correctly.

Starting from this release, teiphy now correctly uses AncestralSequenceLogger elements (from the BEAST_CLASSIC package) instead of AncestralStateLogger elements (from the BEASTLabs package) in BEAST XML outputs.

Previously, works with known dates of origin (specified as a `date` element with a `when` attribute) generated BEAST XML outputs with unnecessary prior distributions on the origin of the birth-death-skyline model. This release fixes the handling of such cases.

In this release, teiphy's options for tabular outputs (in CSV, TSV, and Excel format) have been expanded and better organized. The type of tabular output desired can now be specified on the command line with the `--table` flag. Valid options are `matrix` (the default option, with rows for variant readings, columns for witnesses, and frequency values in cells), `distance` (a pairwise distance/dissimilarity matrix with rows and columns for witnesses and counts or proportions of disagreements at extant variation units in cells), `nexus` (with rows for witnesses, columns for variation units, and reading IDs in cells), and `long` (a series of rows with witness, variation unit ID, reading index, and reading text entries). Notably, `--table long` replaces the old `--long-table` command-line flag. A fix has been added to ensure that Unicode CSV and TSV files are loaded correctly in Excel. Finally, teiphy will now create directories in the output filepath if they do not already exist.

In this release, STEMMA outputs generated by teiphy are written with the corresponding chron file specified with a relative rather than absolute path for better portability, and BEAST 2.7 XML outputs now initialize transcriptional rate parameters with bounds between 0.0 and Infinity and gamma distribution priors. Rates that are not fixed in the TEI XML file will be assigned random values (according to a gamma distribution) in the BEAST 2.7 XML output to avoid singular matrix errors in BEAST's initial computation of site/variation unit likelihoods. A --seed command-line parameter has been added to teiphy to make these assignments replicable.

With this release, `teiphy` can now convert TEI XML collation files to BEAST 2.7 XML input files directly. The conversion process for this format can accommodate judgments of intrinsic probabilities (odds ratios describing how much more likely one variant reading is than another to be authorial, which correspond to root frequencies in BEAST) and transcriptional change classes (describing one or more potential causes for specific transitions between readings, which correspond to rate parameters that can be fixed or estimated in substitution models).

In addition, `teiphy` now includes tree priors and clock models (with multiple options for clock models on the command-line interface) in BEAST 2.7 XML and MrBayes NEXUS outputs. For BEAST, a birth-death skyline prior is used, which can incorporate a date range for the start of the manuscript tradition if one is specified, and strict, uncorrelated relaxed, and local relaxed clock models are supported.