Embedded Files
Inverse Modeling with Compatibility: Programs to Simulate Anatomical Evolution based on empirical data sets and determine frequencies of change needed to generate observed compatibility.
Abundance and Occurrence Distribution Tests: Programs to determine best fit models given either abundance or occurrence data. Includes tests to assess significance of one model over another as well as range of viable alternative hypotheses for each model.
Curation: Programs for downloading and curating data in the Paleobiology Database.
RevBayes_Setup: Programs for generating RevBayes scripts and data files (including appropriate Nexus files) given an original Nexus file and the Paleobiology Database.
1) Stratigraphic Database: Database of formations, members & groups, including reported zonal correlations, associations with isotopic events, radiometric dates, regional chronostratigraphic age assignments, superposition information and general correaltion information. This is nearly complete for pre-Ediacaran, Ediacaran, Paleozoic, Triassic and rock units in the Paleobiology Database, and fairly complete for Jurassic and Cretaceous. The Cenozoic is a bit dodgy, but I've never heard that anything important happened then 😎. The database includes extensive synonymizations for very old rock units as well as the various Western European spellings for Chinese and Russian rock-units.
2) Time Scales: Gradstein et al. 2020 time scale, with extensive regional chronostratigraphic and outdated chronostratigraphic units dated based on reported zonal correlations. A separate zone database includes most of the biostratigraphic zones from Gradstein et al. plus many regional zonation schemes, plus reported correlations of those local schemes with the global / widespread ones reported in Gradstein et al. Also includes many isotopic excursions and bentonites.
3) The Paleobiology Database; This condenses the PBDB, and uses the Stratigraphic and Time Scale databases to produce a separate PBDB_Sites_Refined table that often greatly refines dates returned by the PBDB and sometimes even corrects dates when the age assignments of rock-units has changed (or when correlations between regional and global stages have changed). This also includes occurrence data (PBDB_Finds), taxonomic, ecological & taphonomic information) with some "fixes" that bugs in the PBDB scripts do not handle (PBDB_Taxonomy), and taxonomic opinions (PBDB_Opinions). I update this fairly frequently, so if you've entered data into the PBDB that are not yet included in this, then check back in a couple of days.
4) PBDB Addenda; This includes mass edits that would require too much time for me to enter by hand and also edits to localities that I did not have permission to edit under the former permissions scheme.
5) PBDB references: In addition to all of the references, this also includes alternate spellings of Russian author names and for 19th century workers with 27 names that get used differently in different citations.
6) PBDB Extended Paleogeography: This provides different paleocoordinate reconstructions for PBDB localities given the different reconstruction algorithms used by Geoplates.
7) The Sepkoski Compendium: this contains a cleaned version Jack's great work (long story, but the "unclean" parts came from the fact that his last RA used a Mac whereas Jack used Etruscan, and waaaay back in the 1990s, you had to use programs to convert text from Mac to DOS, and right now the post-GenXers are wondering what the hell kind of world was this...) Also contains ranges for genera summarized from the PBDB.
8) Published Character Data: These are a series of arrays containing the Nexus file information from many (many!) published phylogenetic and morphospace studies.
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