Momocs: Outline Analysis Using R

We introduce here Momocs, a package intended to ease and popularize modern morphometrics with R, and particularly outline analysis, which aims to extract quantitative variables from shapes. It mostly hinges on the functions published in the book entitled Modern Morphometrics Using R by Claude (2008). From outline extraction from raw data to multivariate analysis, Momocs provides an integrated and convenient toolkit to students and researchers who are, or may become, interested in describing the shape and its variation. The methods implemented so far in Momocs are introduced through a simplistic case study that aims to test if two sets of bottles have different shapes.

[1]  Anne-Béatrice Dufour,et al.  The ade4 Package: Implementing the Duality Diagram for Ecologists , 2007 .

[2]  Elizabeth A. Wentz,et al.  A Shape Definition for Geographic Applications Based on Edge, Elongation, and Perforation , 2010 .

[3]  Charles R. Giardina,et al.  Elliptic Fourier features of a closed contour , 1982, Comput. Graph. Image Process..

[4]  Barbara R. Holland,et al.  Analysis of Phylogenetics and Evolution with R , 2007 .

[5]  Ralph Roskies,et al.  Fourier Descriptors for Plane Closed Curves , 1972, IEEE Transactions on Computers.

[6]  S. Lele,et al.  The promise of geometric morphometrics. , 2002, American journal of physical anthropology.

[7]  F. Bookstein,et al.  Morphometric Tools for Landmark Data: Geometry and Biology , 1999 .

[8]  Seishi Ninomiya,et al.  Analysis of petal shape variation of Primula sieboldii by elliptic fourier descriptors and principal component analysis. , 2004, Annals of botany.

[9]  James S. Crampton,et al.  Elliptic Fourier shape analysis of fossil bivalves: some practical considerations , 1995 .

[10]  D'arcy W. Thompson,et al.  On Growth and Form , 1917, Nature.

[11]  Michel Baylac,et al.  Exploring artificial cranial deformation using elliptic Fourier analysis of Procrustes aligned outlines. , 2003, American journal of physical anthropology.

[12]  F. Rohlf,et al.  A revolution morphometrics. , 1993, Trends in ecology & evolution.

[13]  Erik Otárola-Castillo,et al.  geomorph: an r package for the collection and analysis of geometric morphometric shape data , 2013 .

[14]  Michel Raymond,et al.  Height and body mass influence on human body outlines: a quantitative approach using an elliptic Fourier analysis. , 2009, American journal of physical anthropology.

[15]  D. Kendall A Survey of the Statistical Theory of Shape , 1989 .

[16]  C. Giardina,et al.  Accuracy of curve approximation by harmonically related vectors with elliptical loci , 1977 .

[17]  Johan Michaux,et al.  Adaptive latitudinal trends in the mandible shape of Apodemus wood mice , 2003 .

[18]  J. Claude,et al.  Log-Shape Ratios, Procrustes Superimposition, Elliptic Fourier Analysis: Three Worked Examples in R , 2013 .

[19]  Julien Claude,et al.  Morphometrics with R , 2009 .

[20]  Cédric Gaucherel,et al.  Intraspecific variability of pollen morphology as revealed by elliptic Fourier analysis , 2013, Plant Systematics and Evolution.

[21]  F. Rohlf,et al.  Geometric morphometrics: Ten years of progress following the ‘revolution’ , 2004 .

[22]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[23]  Cédric Gaucherel,et al.  Application of elliptical Fourier analysis to watershed boundaries: a case study in Haiti , 2013 .

[24]  Douglas M. Bates,et al.  Programming With Data: A Guide to the S Language , 1999, Technometrics.

[25]  S. Ninomiya,et al.  Diallel Analysis of Leaf Shape Variations of Citrus Varieties Based on Elliptic Fourier Descriptors. , 2002 .

[26]  F. Rohlf,et al.  Extensions of the Procrustes Method for the Optimal Superimposition of Landmarks , 1990 .

[27]  Seiji Matsuura,et al.  Evaluation of variation of root shape of Japanese radish (Raphanus sativus L.) based on image analysis using elliptic Fourier descriptors , 1998, Euphytica.

[28]  Rikard Berthilsson,et al.  A Statistical Theory of Shape , 1998, SSPR/SPR.

[29]  Joan T. Richtsmeier,et al.  Advances in Anthropological Morphometrics , 1992 .

[30]  F. Rohlf,et al.  A COMPARISON OF FOURIER METHODS FOR THE DESCRIPTION OF WING SHAPE IN MOSQUITOES (DIPTERA: CULICIDAE) , 1984 .

[31]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[32]  C. Klingenberg MorphoJ: an integrated software package for geometric morphometrics , 2011, Molecular ecology resources.

[33]  Norman MacLeod,et al.  Generalizing and extending the eigenshape method of shape space visualization and analysis , 1999, Paleobiology.

[34]  S. Ferson,et al.  Measuring shape variation of two-dimensional outlines , 1985 .

[35]  H. Miller,et al.  Representation and Spatial Analysis in Geographic Information Systems , 2003 .

[36]  Harold Moellering,et al.  The Harmonic Analysis of Spatial Shapes Using Dual Axis Fourier Shape Analysis (DAFSA) , 1981 .