Thanks everyone for the helpful insight!

Turns out that by including "PrinAxes=False" in the gpagen command the 
original orientation of the specimen is maintained (thanks to the ever 
helpful Emma Sherratt for pointing this out!) 

On Wednesday, December 10, 2014 7:35:59 PM UTC, timastrop wrote:
>
> Hello all,
>
> Does anyone have any experience with 2D landmarks in the geomorph package? 
> When using the gpagen function my specimens are projected at different 
> rotations depending on some unknown factor. Can anyone help?
>
> Tim
>
> *Tim Astrop PhD <http://timastrop.wordpress.com/>*
> Ammonoid Palaeobiology Lab <http://aplbath.wordpress.com/>
> Department of Biology & Biochemistry
> University of Bath
>  

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