Publications by Emma Sherratt
Tips & Tricks 7: Plotting PCA with TPS grids
Geomorph users,Our function plotTangentSpace() performs a Principal Components Analysis (PCA) of shape variation and plots two dimensions of tangent space for a set of Procrustes-aligned specimens and also returns the shape changes associated with the two plotted principal axes. We purposefully restricted the options for this function be...
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News So Far for Geomorph v2.1.4beta
Dear geomorph users,we have so far recognised and fixed the following bugs known to be in geomorph v.2.1.3 on CRAN, and these are available in the GitHub repository of v.2.1.4beta: BUG FIXES Corrected error readland.tps() “Error in pts[i, 1] : subscript out of bounds” Corrected errors trajectory.analysis() Correc...
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Geomorph and Multivariate Datasets
Did you know that geomorph is not just for landmark-based geometric morphometric (shape) data?We are committed to providing statistical tools for multivariate AND multidimensional morphometric data.As laid out in the recent series of papers on Phylogenetic Comparative Methods for high-dimensional data (Adams 2014a, Adams 2014b, Adams ...
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Tips & Tricks 8: Examining Replicate Error
Geomorph users,When starting out in a geometric morphometrics study, the common questions are ones of repeatability and measurement error.How much of the variation in the Procrustes residuals is due to human (digitizing) error? How much is due to paralax (2D photographs)? How much is due to the threshold choice (3D surface meshes)?Today we use ...
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Geomorph update 2.1.4 Now Available!
Geomorph users,We have uploaded version 2.1.4 of geomorph to CRAN. The windows and mac binaries have been compiled and the tarball is available*.Small Changes:warpRefMesh() generalised – now takes a mesh3d object (i.e. made from read.ply()) rather than calling read.ply()directlyread.morphologika() now reads [groups] option and adds these data ...
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Geomorph beta in development (2.1.5)
Dear geomorph users,We’ve been busy adding some new functions to the forthcoming v.2.1.5, currently in beta stage and available on gitHub (installed using: devtools::install_github(“EmSherratt/geomorph”,ref = “Develop”)). Users be aware that we strongly discourage you from publishing results with this version, unless you c...
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Geomorph update 2.1.5 Now Available!
Geomorph users,We have uploaded version 2.1.5 of geomorph* to CRAN. The windows and mac binaries have been compiled and the tarball is available.New Features:New Auto Mode allows users to include pre-digitized landmarks added to build.template() and digitsurface() New gridPar() is a new function to customize plots of plotRefToTarget() New dig...
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Tips & Tricks 9: Shape Changes and Hypothetical Shapes
Geomorph users,This month’s tips and tricks was prompted by a user email from Tim Astrop, thanks Tim!How can I create a hypothetical shape representing a point in shape space?Today we will use some relatively simple R code to create a shape based on position in a Principal Component (PC) shape space and visualise this shape as a change from...
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Geomorph update 2.1.6 Now Available!
Geomorph users,We have uploaded version 2.1.6 of geomorph* to CRAN. The windows and mac binaries have been compiled and the tarball is available.New Features:New globalIntegration() function for evaluating integration vs. self-similarity of shape variation. This function implements the new method of Bookstein 2015 Integration, Disintegration, ...
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Geomorph update 2.1.7 Now Available!
Geomorph users,We have uploaded version 2.1.7 of geomorph to CRAN. The windows binaries have been compiled and the tarball is available. However, subsequent to this, we found that under certain input scenarios, some of the changes we made to underlying support code had undesirable outcomes. We have corrected these issues in version 2.1.7-1. T...
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