Introducing molaR: a New R Package for Quantitative Topographic Analysis of Teeth (and Other Topographic Surfaces)
- 694 Downloads
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.
KeywordsDirichlet 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.
- Abramoff MD, Magelhaes PJ, Ram SJ (2004) Image processing with ImageJ. Biophoton Internatl 11:36–42Google Scholar
- 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
- 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
- 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
- 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
- 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
- R Core Team (2015) R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical ComputingGoogle Scholar
- Revelle W (2015) psych: Procedures for Personality and Psychological Research, Northwestern Univeristy, Evanston, IL http://cran.r-project.org/package=psych Version=1.5.8
- Schlager S (2015a) Package ‘Rvcg’ Manipulations of Triangular Meshes Based on the ‘VCGLIB’ API https://cran.r-project.org/web/packages/Rvcg/index.html Version=0.13.1.2
- Schlager S (2015b) Morpho: Calculations and Visualisations Related to Geometric Morphometrics https://cran.r.project.org/web/packages/Morpho/index.html Version=220.127.116.11