Publications by Emma Sherratt
Update to read.ply() and associated digitizing functions
Dear morphometricians,Geomorph 1.1-4 has been recently uploaded to CRAN. Please update your R package list or go here to download the latest version. The news section highlights the following changes: CHANGES IN GEOMORPH VERSION 1.1-4 NEW FEATURES o Enhanced plotting of ply files in read.ply() o digitsurface(), buildtemplate(), plotspec(...
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Geomorph 1.1-5 Now available!
Geomorph users,We have uploaded version 1.1-5 to CRAN. The windows binary has been compiled and the tarball is available. The MAC OSX binary may take a few days (mac users can install the package from source using the tar.gz file). The PDF of helpfiles has not yet been updated – as of 10am CST Dec 13 2013.In this new version, there are some edi...
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Geomorph and MacOS X
Happy New Year to all Geomorph users,I have received a few emails from Mac users wanting to update to the new version of Geomorph. Unfortunately there is still a lag on the CRAN repository for a MacOS X binary of version 1.1-5. While this is a nuisance, there is a work around.The package source ‘tarball’ can be installed in R or ...
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Tips & Tricks 1: Averaging Data By Group
I thought it would be helpful to new users of Geomorph and R to discuss some tips and tricks for manipulating morphometric datasets in R. So I am starting a series called “Tips & Tricks”. These will be published as I think of them, and assume you have already inputted your data into R using geomorph functions, such as readland.nts...
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Tips & Tricks 2: Deleting Specimens and Landmarks
Today’s exercise is nice and simple, and allows you to get used to manipulating datasets in R.Exercise 2 – How to delete specimens or landmarks from a dataset of morphometric data (shape data).When you load your shape data into R with Geomorph (with the read… functions), it will typically be in a 3D array format (class array). R...
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Geomorph 1.1-6 Now Available!
Geomorph users,We have uploaded version 1.1-6 to CRAN. The windows and mac binaries have been compiled and the tarball is available.The issue of the Mac OS X installers has been resolved. The problem stemmed from a dependancy (to JPEG), which was lagging behind for Mac binaries. We thank the curators for helping us with this issue.Version 1.1-6 ...
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Geomorph Version 2.0 Now Available!
Geomorph users,We have uploaded version 2.0 to CRAN. The windows and mac binaries have been compiled and the tarball is available.Version 2.0 comes with substantial changes and new features: New function phylo.pls()for assessing the multivariate association between two blocks of variables in a phylogenetic context. This is based on a new paper ...
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Geomorph 3D Visualization
Dear geomorph users,version 2.0 of geomorph brings new developments in how shape deformations from 3D coordinate shape data can be viewed. We have implemented warping of 3D surface files (e.g., .ply files), which allows the user to visualize the shape deformations along Principal Component axes, Multivariate Regression slopes, Partial Least ...
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Physignal Input is 3D Array Only
Geomorph users,The function physignal() in version 2.0 has a mistake in the manual regarding the input matrix: only 3D array can be used at this time. The next version will have this generalized to 2D array and 3D array. In the meantime, if any users need a 2D array input (i.e., using the function on non-shape data) please contact me for the�...
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Tips & Tricks 3: Ordering Datasets Alphabetically
Today’s exercise is another nice and simple one, and allows you to get used to manipulating datasets in R.Exercise 3 – How to reorder the dataset alphabetically by specimen name.Say you have a 2D array dataset with specimen names (here species) as the row names of species data (I have jumbled up the species of geomorph’s data(plethspecie...
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