Anurag,
I assume you are doing one GPA for the combined data and not combining the data
after GPA has been performed separately on both subsets. The latter surely
could lead to the problem you describe.
I recommend, if you have not done so already, using the plotOutliers function.
It will
F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University
From: Collyer, Michael [mailto:michael.coll...@wku.edu]
Sent: Tuesday, April 5, 2016 5:29 AM
To: Brenna Hays <bkhays...@gmail.com<m
Brenna,
The PCA you performed produces a list of objects, one of which is a matrix of
PC scores.
Change AIS.PC to AISPC$x, and it should work. In this case, $x is the matrix
of scores.
The help files for the functions you use tell you the objects that are
returned. You can also use
Dear Brenna,
There is a lot to digest here, so apologies up front if I miss something.
Also, I’ll keep my response general for the benefit of our colleagues. We can
work out specific issues with your data and your analyses via direct email
communication.
First, you have two sets of shape
Colleagues,
We have made a small update to the procD.allometry function to fix a bug with
centering shape data to calculate CAC scores. Thanks to Borja Figueirido for
discovering the problem!
As always, updates to geomorph are made available via our GitHub repository,
and the latest version
d to be negligible with 'standard'
landmarks. Is this different with semilandmarks? Are there sensitivity analyses
that explore the issue (if it's an issue)?
Thanks in advance.
Cheers
Andrea
At 17:06 18/02/2016, Collyer, Michael wrote:
Contrary to your logic, subsetting your sample could have an
Ari,
If you are using geomorph, you might want to update it via GitHub. Just a few
days ago we updated the software with some bug fixes for surface points (one
bug fix was for assuring non-arbitrary directions in PC planes for tangents of
surface points). If you are unsure how to do that,
Dear Brenna,
It appears the problem is that you are attempting to use prcomp on your
points(p) x dimensions(k) x n Procrustes coordinates without converting these
data into a n x pk matrix, required by prcomp. Unfortunately, prcomp will use
the first p x k part of the array of coordinates,
This is correct. The function, trajectory.analysis, compares multi-point
trajectories; therefore, age would need to be modeled as a categorical variable
(factor). If one wishes to have age (or similar variable) in the model as a
continuous variable, then advanced.procD.lm would be more
editions of Biometry and Statistical Tables are now
available:
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
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P Please consider the environment before printing this email
From: Collyer, Michael
Folks, we apologize for the delayed announcement but wanted the morphometrics
community to be aware of a new paper we have recently published. We compared
two methods for performing phylogenetic regression using shape data (PIC vs
D-PGLS). In it we demonstrate that while test statistics from
Thanks for the alert Alejo! This was the result of one missing word in the
code. It has been fixed (I hope) and you can update geomorph via Github, if
you like.
e.g.,
devtools::install_github(“EmSherratt/geomorph”)
Note that this requires having devtools installed.
Cheers!
Mike
Michael
Mauro, plus others,
As a follow up, we are also working on a new function in geomorph to allow
users to modify transformation (deformation) grids. Much like the R par
function, this function will allow users to vary the colors, width, and style
of grid lines and link links, the density of
Here is a direct link for the article Dean mentioned.
http://onlinelibrary.wiley.com/doi/10./evo.12596/pdf
Michael Collyer
Assistant Professor
Department of Biology
Western Kentucky University
1906 College Heights Blvd. #11080
Bowling Green, KY 42101-1080
Phone: 270-745-8765; Fax:
Hi Michelle,
One problem might be misinterpreting what R displays when you use a function
rather than what R might save as an object if you create an object based on the
function.
For example, you could input the following
gpagen(mylandmarks, curves = mycurves, PrinAxes = T)
and R would
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