Colleagues,
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:
install.packages('geomorph')
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:
browseVignettes(package="geomorph")
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
geomorph.
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
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://www.eeob.iastate.edu/faculty/adams/
phone: 515-294-3834
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