I'm pleased to announce that geomorph 3.1.1 is now available on CRAN. As 
always, all changes are noted in the NEWS file and in the appropriate help 
pages. To install geomorph 3.1.1 from within R, simply type:


We wish to emphasize that this was a rather substantial update; thus, users are 
highly encouraged to consult all help files for additional information. Though 
some functions have been deprecated, all analyses previously available in 
geomorph are still available (though some more advanced options are now 
accessed in slightly modified form).  Also, to ease users through this 
transition, we have developed a vignette that describes the differences in the 
current version, and how to implement various analyses using the newer 
notation. The vignette is distributed with the installation of geomorph, and 
may be accessed by typing:


In particular, users will notice a change in usage of the 'procD' family of 
functions for assessing linear models. Beginning with geomorph 3.1.1, only 
'procD.lm' and 'procD.pgls' remain, and these have greatly enhanced 
functionality. For instance, one may now utilize type I, type II, or type III 
sums of squares, may specify the error term against which various factors are 
evaluated (to incorporate random effects in simple mixed model designs), and 
may incorporate object-covariance matrices describing non-independence.  
Additionally, pairwise comparisons of means, of slopes, and of within-group 
variation may be accomplished using the 'pairwise' function based off of fitted 
models from 'procD.lm' or 'procD.pgls'. The functions: procD.allometry, 
advanced.procD.lm, and nested.update, have all been deprecated, as their 
analyses are now accomplished (and enhanced) via these other functions. These 
enhancements were made possible by use of the RRPP package (Collyer and Adams, 
2018: Methods Ecol. Evol) which is now more tightly interconnected with 

Finally, for graphical visualization of shapes, we encourage users to explore 
the new picknplot.shapes function, which allows one to select locations from 
just about any kind of plot obtained in geomorph, and generate estimates of 
shapes that correspond to those locations (much like in the TPS series). Also, 
the new plotAllometry function provides several graphical plots commonly used 
in allometric studies. We hope these new graphical options provide additional 
flexibility and usability of geomorph.

Best to all,

Dean, Mike, and Antigoni (the geomorph team)

Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
phone: 515-294-3834

MORPHMET may be accessed via its webpage at
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