R script for 3D geometric morphometrics of egg shape
This dataset contains the R script developed by Dr Emma Sherratt in Attard et al. (In review) to characterise egg shape using three-dimensional semilandmark-based geometric morphometrics.
The R script is divided into three files: Digitize egg source.R, Digitize egg script.R and Analysing Eggs.R. The first two scripts takes 3D surface files (.ply files from [refer to other dataset]) and digitises semilandmarks on the egg surfaces. The third script then takes the generated coordinate data (.nts files) and performs the analyses presented in the paper. Coordinate data (.nts files) of all egg surface meshes from the paper, consisting of eggs from four Australian bird species (four clutches per species), are provided as an example to run the Analysing Eggs.R script alone.
Overview of data: on the 3D surface models we placed 206 landmarks to cover the contours of the egg using a digitising routine written in R v.3.2.2 modified from those in the geomorph library. The landmark data was aligned using a generalised Procrustes superimposition and the resulting Procrustes shape coordinates were ordinated using a Principal Components Analysis (PCA), allowing visualisation of the variation in shape across all eggs. Full details on the digitising routines are provided in the method section of Attard et al. (In review).