DOI: 10.5061/dryad.xsj3tx9sn
title: Using machine learning to investigate premolar ecomorphology in anthropoid primates

description: This dataset includes raw linear and topographic measurements taken on the
 mandibular dentitions of 313 extant anthropoid primates. Measurements
 include cusp reliefs of mandibular second molars (M2), mandibular fourth
 premolars (P4), and mandibular honing premolars (P2/P3), positive ariaDNE
 of M2, P4, and P2/P3, the heights, widths, and breadths of mandibular
 first incisors (I1), and lengths of mandibular first molars (M1).
 Demographic data (genus, species, dietary ecology, specimen ID, sex, and
 institution) is also included for each specimen. This dataset also
 includes the R scripts for performing phylogenetic ANOVAs and Random
 Forest permutation feature importance, and the Python script for
 calculating positive ariaDNE.
description: # Using machine learning to investigate premolar ecomorphology in
 anthropoid primates Dataset DOI:
 [10.5061/dryad.xsj3tx9sn](10.5061/dryad.xsj3tx9sn) ## Description of the
 data and file structure The rawdata_premolar csv file includes linear and
 topographic measurements for the mandibular incisors, molars, and
 premolars of 313 specimens of crown anthropoid. Linear measurements were
 taken in GeoMagic Wrap 2024 software on 3D scans of mandibular dentitions
 and, in the case of incisor linear dimensions, using digital calipers on
 epoxy casts of mandibular dentitions. Topographic measurements were
 calculated for ply files of cropped premolars and molars in PyCharm using
 the Python batch_ariaDNE.py script.  Phylogenetic ANOVAs were performed
 for species' averages of scaled premolar data using the R script
 phylANOVAs.R.  Random Forest permutation feature importance was calculated
 for the unworn dataset of molar, premolar, and incisor data (i.e., for a
 subset of specimens for which no averaged dental variable is
 "NA" or "worn") using the R script
 RF_feature_importance.R ### Files and variables #### File:
 rawdata_premolar_manuscript.csv **Description:**  ##### Variables * Genus:
 Taxonomic genus of specimen * Species: Taxonomic species of specimen *
 Subspecies: Taxonomic subspecies of specimen * Binomial: Genus and species
 name of specimen * SpecimenID: Museum catalogue number of specimen *
 Institution: Museum code indicating institution from which the specimen
 was sourced * Sex: Biological sex (male [M] or female [F]) of specimen *
 Side: Signifies whether left tooth or right tooth was measured, or the
 average (Avg) of left and right dental measurements. When a single tooth
 was measured, the value listed for "Avg" is simply the value for
 that tooth, for purposes of streamlining our workflow. * Diet: Dietary
 category based on literature review (see paper for more information). * P4
 protoconid relief: Vertical height of the protoconid on the distal
 mandibular premolar (p4) in millimeters (mm) * P4 metaconid relief:
 Vertical height of metaconid on the distal mandibular premolar (p4) in
 millimeters (mm) * P4 positive ariaDNE: Positive aria Dirichlet Normal
 Energy of the distal mandibular premolar (p4). This is a dimensionless
 variable with no units. * P3 protoconid relief: Vertical height of
 protoconid on the anterior-most mandibular premolar (p2/p3). This is a
 dimensionless variable with no units. * P3 positive ariaDNE: Positive aria
 Dirichlet Normal Energy of the anterior-most mandibular premolar (p2/p3).
 This is a dimensionless variable with no units. * M2 protoconid
 relief: Vertical height of protoconid on the second mandibular molar (m2)
 in millimeters (mm) * M2 positive ariaDNE: Positive aria Dirichlet Normal
 Energy of the second mandibular molar. This is a dimensionless variable
 with no units. * M1 length: Mesiodistal length of the first mandibular
 molar (m1) in millimeters (mm) * I1 labiolingual breadth: Labiolingual
 breadth of the first mandibular incisor (i1) in millimeters (mm) * I1
 height: Crown height of the first mandibular incisor (i1) in millimeters
 (mm) * I1 mesiodistal width: Mesiodistal width of the first mandibular
 incisor (i1) in millimeters (mm) #### File: phylANOVAs.R
 **Description:** R script to perform phylogenetic ANOVAs for datasets of
 species averages. #### File: permutation_feature_importance.R
 **Description:** R script to train a Random Forest classification model
 and check permutation feature importance. #### File: batch_ariaDNE.py
 **Description:** Python script to batch calculate positive ariaDNE,
 negative ariaDNE, and ariaDNE for ply files of 3D mesh objects. ##
 Code/software RStudio or R is needed, with the caret package, geiger
 package, and phytools package installed.  A platform for coding in Python
 such as PyCharm is needed with the signDNE package installed. ## Access
 information Data was derived from the following sources: * All dental
 measurements were taken by the authors; see linked manuscript for
 comprehensive citations list of dietary literature.