Journal of Mammalian Evolution

, Volume 23, Issue 4, pp 397–412 | Cite as

Introducing molaR: a New R Package for Quantitative Topographic Analysis of Teeth (and Other Topographic Surfaces)

  • James D. PampushEmail author
  • Julia M. Winchester
  • Paul E. Morse
  • Alexander Q. Vining
  • Doug M. Boyer
  • Richard F. Kay
Original Paper


Researchers studying mammalian dentitions from functional and adaptive perspectives increasingly have moved towards using dental topography measures that can be estimated from 3D surface scans, which do not require identification of specific homologous landmarks. Here we present molaR, a new R package designed to assist researchers in calculating four commonly used topographic measures: Dirichlet Normal Energy (DNE), Relief Index (RFI), Orientation Patch Count (OPC), and Orientation Patch Count Rotated (OPCR) from surface scans of teeth, enabling a unified application of these informative new metrics. In addition to providing topographic measuring tools, molaR has complimentary plotting functions enabling highly customizable visualization of results. This article gives a detailed description of the DNE measure, walks researchers through installing, operating, and troubleshooting molaR and its functions, and gives an example of a simple comparison that measured teeth of the primates Alouatta and Pithecia in molaR and other available software packages. molaR is a free and open source software extension, which can be found at the doi: 10.13140/RG.2.1.3563.4961 (molaR v. 2.0) as well as on the Internet repository CRAN, which stores R packages.


Dirichlet Normal Energy Relief Index Orientation Patch Count Plotting functions 



The authors thank redditor /u/Kiss_My_Wookiee for help in naming the package, and Roxanne Larsen for assistance with deciphering MATLAB code. The authors declare no known conflicts of interest.

Supplementary material

10914_2016_9326_MOESM1_ESM.xls (72 kb)
ESM 1 (XLS 72 kb)


  1. Abramoff MD, Magelhaes PJ, Ram SJ (2004) Image processing with ImageJ. Biophoton Internatl 11:36–42Google Scholar
  2. Adams DC, Otárola-Castillo E (2013) geomorph: an R package for the collection and analysis of geometric morphometric shape data. Method Ecol Evol 4:393–399CrossRefGoogle Scholar
  3. Adler D, Murdoch D, Nenadic O, Urbanek S, Chen M, Gebhardt A, Bolker B, Csardi G, Strzelecki A, Senger A (2015) rgl: 3D visualization using OpenGL. R package version 0.95.1247Google Scholar
  4. Allen KL, Cooke SB, Gonzales LA, Kay RF (2015) Dietary inference from upper and lower molar morphology in platyrrhine primates. PLoS ONE 10:e0118732. doi:0118710.0111371/journal.pone.0118732 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bargo MS, Vizcaíno SF, Kay RF (2009) Predominance of orthal masticatory movements in the early Miocene Eucholaeops (Mammalia, Xenarthra, Tardigrada, Megalonychidae) and other megatherioid sloths. J Vertebr Paleontol 29:870–880CrossRefGoogle Scholar
  6. Boyer DM (2008) Relief index of second mandibular molars is a correlate of diet among prosimian primates and other euarchontan mammals. J Hum Evol 55:1118–1137CrossRefPubMedGoogle Scholar
  7. Boyer DM, Evans AR, Jernvall J (2010) Evidence of dietary differentiation among late Paleocene-early Eocene plesiadapids (Mammalia, Primates). Am J Phys Anthropol 142:194–210PubMedGoogle Scholar
  8. Boyer DM, Puente J, Gladman JT, Glynn C, Mukherjee S, Yapuncich GS, Daubechies I (2015b) A new fully automated approach for aligning and comparing shapes. Anat Rec 298:249–276CrossRefGoogle Scholar
  9. Boyer DM, Winchester J, Kay RF (2015a) Technical Note: The effects of differences in methodology among some recent applications of shearing quotients. Am J Phys Anthropol 156:166–178CrossRefPubMedGoogle Scholar
  10. Bunn JM, Boyer DM, Lipman Y, St. Clair EM, Jernvall J, Daubechies I (2011) Comparing Dirichlet normal surface energy of tooth crowns, a new technique of molar shape quantification for dietary inference, with previous methods in isolation and in combination. Am J Phys Anthropol 145:247–261CrossRefPubMedGoogle Scholar
  11. Copes LE, Lucas LM, Boyer DM (2016) A collection of non-human primate CT scans house in MorphoSource, a repository for 3D data. Sci DataGoogle Scholar
  12. Evans AR, Janis CM (2014) The evolution of high dental complexity in the horse lineage. Ann Zool Fenn 51:73–79CrossRefGoogle Scholar
  13. Evans AR, Wilson GP, Fortelius M, Jernvall J (2007) High-level of similarity of dentitions in carnivorans and rodents. Nature 445:78–81CrossRefPubMedGoogle Scholar
  14. M’Kirera F, Ungar PS (2003) Occlusal relief changes with molar wear in Pan troglodytes troglodytes and Gorilla gorilla gorilla. Am J Primatol 60:31–41CrossRefPubMedGoogle Scholar
  15. Pateiro-Lopez B, Rodriguez-Casal A (2015) alphahull: generalization of the convex hull of a sample of points in the plane. R package version 2.0Google Scholar
  16. Plyusnin I, Evans AR, Karme A, Glonis A, Jernvall J (2008) Automated 3D phenotype analysis using data mining. PLoS ONE 3:e1742. doi:1710.1137/journal.pone.0001742 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Prufrock KA, Boyer DM, Silcox MT (2016) The first major primate extinction: an evaluation of paleoecological dynamics of North American stem primates using a homology free measure of tooth shape. Am J Phys AnthropolGoogle Scholar
  18. R Core Team (2015) R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical ComputingGoogle Scholar
  19. Revelle W (2015) psych: Procedures for Personality and Psychological Research, Northwestern Univeristy, Evanston, IL Version=1.5.8
  20. Schlager S (2015a) Package ‘Rvcg’ Manipulations of Triangular Meshes Based on the ‘VCGLIB’ API Version=
  21. Schlager S (2015b) Morpho: Calculations and Visualisations Related to Geometric Morphometrics Version=
  22. Ungar PS, M’Kirera F (2003) A solution to the worn tooth conundrum in primate functional anatomy. Proc Natl Acad Sci USA 100:3874–3877CrossRefPubMedPubMedCentralGoogle Scholar
  23. Wilson GP, Evans AR, Corfe IJ, Smits PD, Fortelius M, Jernvall J (2012) Adaptive radiation of multituberculate mammals before the extinction of the dinosaurs. Nature 483:457–460CrossRefPubMedGoogle Scholar
  24. Winchester JM (2016) MorphoTester: an open source application for morphological topographic analysis. PLoS ONE 11:e0147649. doi: 10.1371/journal.pone.0147649 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Winchester JM, Boyer DM, St. Clair EM, Gosselin-Ildari AD, Cooke SB, Ledogar JA (2014) Dental topography of platyrrhines and prosimians: convergence and contrasts. Am J Phys Anthropol 153:29–44CrossRefPubMedGoogle Scholar
  26. Zuccotti LF, Williamson MD, Limp WF, Ungar PS (1998) Technical Note: Modeling primate occlusal topography using geographic information systems technology. Am J Phys Anthropol 107:137–142CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • James D. Pampush
    • 1
    Email author
  • Julia M. Winchester
    • 2
  • Paul E. Morse
    • 3
  • Alexander Q. Vining
    • 1
  • Doug M. Boyer
    • 1
  • Richard F. Kay
    • 1
  1. 1.Department of Evolutionary AnthropologyDuke UniversityDurhamUSA
  2. 2.Interdepartmental Doctoral Program in Anthropological SciencesStony Brook UniversityStony BrookUSA
  3. 3.Department of AnthropologyUniversity of FloridaGainesvilleUSA

Personalised recommendations