Colleagues,
Version 3.1.2 of geomorph is now available on CRAN as source-file, and over the
next few days the CRAN folks will generate the binaries also.
This version is a patch, fixing some issues created when the RGL library
recently made changes to their package - regarding how colors/materi
To add briefly to Dennis' comment. If landmark estimation is the route taken,
both TPS-based and regression-based imputation are implemented in geomorph.
Dean
Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa Sta
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
Charles,
There are several ways to do what you wish within geomorph. First, the
plotTangentSpace function does allow one to specify which axes are plotted.
This can be useful for obtaining shape deformations along the extremes of axes
other than PC1 and PC2.
A more flexible option is to use
Folks,
I think it is important to recognize that the example in Andrea’s earlier post
does not really address the validity of sliding semilandmark methods, because
all of the data were simulated using isotropic error. Thus, the points called
semilandmarks in that example were actually independ
Igor,
The components, $means contain the least squares means from the linear model
implemented in trajectory analysis. These can be visualized relative to some
reference (e.g., the overall mean shape), using ‘plotRefToTarget’. Note that
the $means must first be converted to a 2D array using ‘a
Lawrence,
Though you mentioned that you checked them, what you described frequently
occurs when names are not the same in the data matrix and phylogeny. Since you
did not specify how they were checked, I would use the ‘match’ function. If any
NAs appear, you have a name mismatch.
If that is no
Morphometrics colleagues,
Version 3.0.6 of geomorph has now been released and is up on the CRAN
repository for download and installation. As with all version updates, changes
have been documented in the News file.
Of particular note is the incorporation of a refined residual randomization
perm
Sarah,
As far as I am aware, MorphoJ estimates a set of PICs one dimension at a time.
Thus, for a multivariate dataset of N species and p-trait dimensions, this will
return a matrix of N-1 by p. Here, each of the N-1 rows (nodes of the
bifurcating tree) contains a vector of PICs, one per trait
katz.w...@gmail.com] On Behalf Of David Katz
Sent: Wednesday, January 24, 2018 11:48 AM
To: Adams, Dean [EEOBS]
Cc: Christy Anna Hipsley ; MORPHMET
Subject: Re: [MORPHMET] relative positions of landmark partitions in
integration tests - how important?
I read Christy's question a little diffe
Christy,
That data example contained variation in relative jaw position among specimens,
which could affect shape estimates, as well as down-stream shape analyses.
Several approaches have been proposed for dealing with such rotational
variation (see Adams 1999; also Bookstein’s Orange book). O
Anderson,
I don’t think you appreciated the importance of the Murat’s comments on your
earlier post on this same topic.
In theory, there is no problem combining objects digitized at different
magnifications, or even digitized by different researchers. However, before
doing so one must carefull
Skip,
It is difficult to troubleshoot this without seeing your full code and data
file. If you send me those off-line I can try to take a look in the near future
to identify what is going on.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Depar
Andrey,
To repeat: there is no reason to expect the numbers to match identically across
software packages, particularly column by column (if that is what you are
examining). Even if two packages perform things identically in terms of the
algebra (e.g,. GPA using TpsRelw and geomorph), the numbe
Andrey,
It is unreasonable to expect the numbers will match perfectly between these two
software packages, as the way in which they perform the operations differs.
First, MorphoJ uses Full Procrustes fit, whereas the TPS series, geomorph, and
others use Partial Procrustes fitting. That will ma
Colleagues,
We have made two small updates to geomorph which we wish to bring to your
attention. Both are rather specialized and may affect only a small subset of
users, however we wanted to alert everyone just in case.
First, a recent change to the underlying code in procD.fit inadvertently
pre
Gonzalo,
You received that error message because you have no primary landmark points
(LM=0 in your example). All of your points are in the form of curve points
representing semilandmarks.
One solution is as you suggested: simply remove the curve lines so the points
are read in as landmarks. S
Fellow morphometricians,
I have two announcements regarding geomorph. First, a new version of geomorph
(version 3.0.5) is available on CRAN, as well as on the geomorph github
repository (https://github.com/geomorphR/geomorph). As always the list of major
changes is found in the NEWS file that
Hello all,
Just a quick announcement to let you know that geomorph version 3.0.4 is now
available on CRAN. The list of new features is below, and includes:
o An option to use types I, II, or III sums of squares and cross-products for
ANOVA analyses (e.g., procD.lm, procD.pgls)
o PGLS option
Hello all,
Just a quick announcement to let you know that geomorph version 3.0.4 is now
available on CRAN. The list of new features is below, and includes:
o An option to use types I, II, or III sums of squares and cross-products for
ANOVA analyses (e.g., procD.lm, procD.pgls)
o PGLS option
Will,
I’m not quite sure what over-parameterizing means in the case of PCA, as it is
simply a rigid-rotation of the dataspace and does not provide parameters for
statistical inference.
As for the distribution of eigenvalues, this of course is based on the
underlying covariance matrix for the t
Pere,
I agree that there is likely some issue in the data array and how it is
configured, but it is difficult to troubleshoot without knowing more and seeing
the input data.
If you communicate with me off-line I am willing to take a look for you.
Best,
Dean
Dr. Dean C. Adams
Professor
Depart
Marcelo,
If your TPS file contains a scale for each specimen, this information is used
when reading the landmarks. In other words the specimens are scaled by the
scale values you have specified in your file, placing them in the units you
have specified rather than pixel units.
Dean
Dr. Dean C
ttp://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834
From: Wong Jin Yung [mailto:wongjiny...@gmail.com]
Sent: Tuesday, December 13, 2016 9:54 PM
To: Adams, Dean [EEOBS]
Cc: MORPHMET
Subject: Re: [MORPHMET] allometry adjustment in R
Dear Dean,
Thank you for pointing out my conceptual mista
Jin Yung,
Before sorting out an R-code equivalent for what MorphoJ does, I recommend that
you revisit and re-read the last few posts on Morphmet concerning statistical
and biological significance of comparisons of slopes. The important thing to
determine first and foremost is whether or not th
Andrea,
I agree that one must consider both statistical significance and biological
meaningfulness in evaluating patterns. Considering one of these without the
other can often get one into trouble.
Your post concerned the inability to statistically detect differences due to
sample size limita
Christy,
If your model is: shape~eco.group, then the LS means for each ecological group
can be extracted. These can then be examined visually by using TPS from the
overall reference to each LS mean.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Christy,
I would strongly advocate using visualizations of group means for describing
shape differences among groups as compared to CVA.
A Procrustes MANOVA provides the statistical inferences related to any
differences that might be present among groups, and the corresponding
thin-plate splin
Edgar,
That would depend on how the measurements intersect with one another. For a
series of truss-like measurements, it is possible. See the paper by Carpenter
et al. 1996 in the white book.
If I recall correctly, this, and a related approach was implemented in
Morpheus, though I have not inv
Milena,
Installing from Github requires installing from the stable branch, not Master.
Try this:
devtools::install_github("geomorphR/geomorph", ref = "Stable")
Note the ‘Stable’ option at the end.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Edgar,
If you perform a multivariate regression of shape on size (shape~size), the
residuals from this regression represent that shape component not explained by
size variation and the relationship between the two. In the literature, this is
commonly referred to as size-adjusted residuals or al
Colleagues,
We wish to alert you to a new statistical method for comparing the strength of
integration across morphological datasets. The method is based on PLS, and may
be used to evaluate whether the degree of integration among partitions is
greater in one dataset relative to another. An earl
Christy,
Yes, the ‘slopes’ component of the output contains the regression parameters
for each species. These can then be used as input for ancestral state
estimation and other down-stream analyses that you have planned.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Or
Colleagues,
I wish to announce that geomorph 3.0.2 is now up on CRAN. This upgrade
includes a number of enhancements and features, and a few minor bug fixes, as
outlined in the News file of the program. As always, the most up to date
version of geomorph may also be found on Github.
Best,
D
Damien,
Yes, one can take the regression parameters for each species and use these as
‘tips’ data to obtain ancestral estimates of the regression slope. In this
case, the species’ data is the multivariate set of slope coefficients for each
multivariate regression. Thus, the ancestral state of t
Anurag,
One can do this using geomorph and the base-R function 'which'. Below is an
example, using the plethodon dataset from geomorph, where one extracts a subset
of specimens that are designated Allo in another vector (in this case a vector
designating locality type):
library(geomorph)
dat
Ariadne,
The remaining components of the procedure in Mitteroecker et al. (2004) involve
calculating the common allometric and residual shape components (CAC & RSC
respectively), and then visualizing allometric trends using a series of plots:
CAC vs. size, RSC1 vs. CAC, etc. While the plot of
Colleagues,
We wish to announce that geomorph 3.0.1 is now uploaded to CRAN. This version
matches the version already found on github. This version contains the minor
enhancements and changes made since the release of 3.0.0. The News page details
all changes made.
As always, geomorph may be in
Hi Andrea,
It is generally preferable to perform the more complex analysis with size
included as a covariate. Using a sequential approach that first obtains the
shape residuals and then examines patterns using these as data is not
guaranteed to get to the same, or even the correct, place. And
Colleagues,
We have made a small change to geomorph that affects the sliding of surface
points during GPA. The latest version may be found on Github:
devtools:::install_github("geomorphR/geomorph", ref = "Stable")
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Orga
Friends,
A small update was made to geomorph, and may be found on our Github repository.
One change fixes an issue with outputting the scale in digitize2d, and another
change was made to allow 3+ partitions in phylo.integration. Thanks to Melanie
Hopkins and Bryan McLean for identifying these
Nicole,
There is no need to perform multiple residual-based analyses. If you wish to
obtain shape residuals where both the phylogeny and allometry (size) have been
taken into account, these are found as residuals from the PGLS analysis:
shape~size|phylogeny.
However, a question then is what wi
Colleagues,
I am very excited to announce the release of geomorph 3.0. This version
represents an entire rewrite of the analytical functions and their underlying
support code, which has resulted in improved speed, performance, and
flexibility of the package. We are especially grateful to those
Colleagues,
We wish to inform you of a location change to our geomorph web
page and blog. The blog and associated pages may now be viewed at:
http://geomorphpackage.blogspot.com. All prior posts are available at this
location.
Dean and the geomorph team
Dr. Dean C. Adams
Profe
lcanti [mailto:mauro...@gmail.com]
Sent: Wednesday, December 16, 2015 8:18 PM
To: Adams, Dean [EEOBS]
Cc: MORPHMET
Subject: Re: [MORPHMET] Yet another sequel to complaints about 'geomorph' R
package
Dean,
Thanks for you reply.
As I wrote in the first message that started this sequence, th
Mauro,
Please re-read the news file. There was a documented change in version 2.1.6
with respect to how the scale was handled (which remains documented in
subsequent updated versions). Please see the News file where this was
mentioned, and the help file for digitize2d which explained the change
/>
phone: 515-294-3834
From: Adams, Dean [EEOBS]
Sent: Wednesday, December 2, 2015 9:11 AM
To: morphmet@morphometrics.org
Subject: R code for CR modularity test
Colleagues,
I have received a number of requests for the R code for implementing the CR
coefficient for evaluating modularity. To
Colleagues,
I have received a number of requests for the R code for implementing the CR
coefficient for evaluating modularity. To accommodate this request I have
uploaded the basic-code on my software page:
http://www.public.iastate.edu/~dcadams/software.html . It is method #13, near
the top o
Colleagues,
I wish to alert you to a new paper, currently accepted at Methods in Ecology
and Evolution, in which I describe a new measure for modularity; called the
covariance ratio, or CR. The accepted version of the paper may be found at:
http://onlinelibrary.wiley.com/doi/10./2041-210X.
Colleagues,
Just a quick note to inform you of a geomorph update on CRAN. This version
(2.1.7-1) contains the fixes previously found on the stable branch of our
Github repository. For those who have already updated using Github, there is
no need to update via CRAN.
Best,
Dean
Dr. Dean C. Ad
Randau, Marcela [mailto:m.ran...@ucl.ac.uk]
Sent: Monday, September 28, 2015 1:30 PM
To: Adams, Dean [EEOBS] ; morphmet@morphometrics.org
Subject: RE: Important update for geomorph
Dear Dr Dean Adams,
Many thanks for sending the information on the new version of geomorph with bug
fixes.
I have tried to i
Colleagues,
We recently uploaded version 2.1.7 of geomorph to CRAN. However, subsequent to
this, we found that under certain input scenarios, some of the changes we made
to underlying support code had undesirable outcomes. We have corrected these
issues in version 2.1.7-1. The corrected versio
Colleagues,
I wish to alert you to a new method John Denton and I just published in
Evolution. The approach enables one to compare rates of phenotypic evolution
between two or more multivariate traits in a phylogenetic context under
Brownian motion. The method is described in our paper "A new
Colleagues,
I am happy to announce that a new version of geomorph (2.1.6) has been uploaded
to CRAN. This version includes Bookstein's recent approach to evaluating
integration relative self-similarity of shape variation, and includes a more
general phylogenetic simulation procedure in compar
Yes that is more precise.
In my post to the query I only noted that the variance in significance levels
across multiple permutation tests decreases as the number of iterations
increases. Joe's post provides the equation for the expected value of that
variance; mine provided reference to an emp
Thank you Mauro for the suggestions. Indeed, as you surmise, digitizing within
R is not at all straightforward, but we will do our best to improve the
experience for users of geomorph.
Best,
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Depar
Jo,
There were two issues with the file. First, you had single curly quotes in
front of the specimen names. These should be simple ascii character quotes
instead.
Second, you had missing data in one of the specimens. For downstream analyses
in geomorph that is fine, but at present the read.mo
Tsung,
This property of permutation tests has been known for some time. Generally
speaking, as the number of permutations increases the variation in significance
levels obtained from repeated runs decreases. Earlier work in the statistics
literature from the 70s and 80s by Edgington and others
Colleagues,
Geomorph version 2.1.5 is now up on CRAN. This version has several enhancements
and new features, and fixes the verbose output in plotAllometry. Full details
are found in the NEWS file. Downloads at:
http://cran.r-project.org/web/packages/geomorph/index.html
Best,
Dean and the g
Nico,
>From the image you attached, things seem to be coded properly. In your case,
>the resulting slider file should be a 6 X 3 matrix:
1 2 3
2 3 4
3 4 5
4 5 6
5 6 7
6 7 8
As for analyses, one would first perform a generalized Procrustes analysis,
including the slider information. Inputs woul
Miranda,
The required inputs for gpagen do not change based on how you have organized
the data or how you collected it. From your description, it seems you have
incorrectly specified the input components.
First, the slide= option is for one to specify a ‘sliders’ matrix, in the style
used in TPS
Morphometrics colleagues,
Version 2.1.4 of geomorph has been released. This may be obtained via the CRAN
R repository, or by installing from our GitHub repository. This version has
underlying source code that is now compatible with changes in R 3.1.3 use of
base functions for linear models. As
Colleagues,
I want to alert your attention to a new article on-line at Evolution (Adams and
Collyer 2015: doi:10./evo.12596). In it we compare two approaches for
performing phylogenetic regression of high-dimensional shape data (one based on
PICs and another based on PGLS). We show that alt
David,
Geomorph only reads ASCII ply files (see man pages). You could use MeshLab or
some other reader to convert to ASCII ply first. Then it should be fine.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State Uni
Tim,
You might also make sure you have the very latest version of geomorph from CRAN
(version 2.1.2). In the previous version with PrinAxes the ‘flipping’ sometimes
occurred. That should be resolved in vsn 2.1.2.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal
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