[MORPHMET] geomorph 3.1.2 available

2019-05-21 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe

2019-05-07 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 3.1.1 released on CRAN

2019-04-03 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Visualizing shape differences in PCA

2019-03-27 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Re: semilandmarks in biology

2018-11-07 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Re: Conceptual clarification of plotting shape deformation grids in geomorph

2018-11-07 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 3.0.6 released

2018-05-17 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Multivariate PICs?

2018-03-27 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] relative positions of landmark partitions in integration tests - how important?

2018-01-24 Thread Adams, Dean [EEOBS]
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).

RE: [MORPHMET] Doubt about scalling photos

2018-01-08 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Issues with subsetting nts array with classifiers and plotTangentSpace visualization

2018-01-05 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Procrustes fit

2017-10-31 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] reading shapes with only semilandmarks, Error in readland.tps: No landmark data for some specimens.

2017-09-20 Thread Adams, Dean [EEOBS]
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.

[MORPHMET] geomorph 3.0.5

2017-08-14 Thread Adams, Dean [EEOBS]
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

[MORPHMET] FW: geomorph 3.0.4 now available

2017-06-20 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 3.0.4 now available

2017-06-12 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Re: number of landmarks and sample size

2017-06-02 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Error in estimate.missing (package geomorph)

2017-01-31 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] question about raw tps files in R

2017-01-25 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] allometry adjustment in R

2016-12-14 Thread Adams, Dean [EEOBS]
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] <dcad...@iastate.edu> Cc: MORPHMET <morphmet@morphometrics.org> Subject: Re: [MORPHMET] allometry adjustment in R

RE: [MORPHMET] allometry adjustment in R

2016-12-13 Thread Adams, Dean [EEOBS]
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

RE: brief comment on non-significance Re: [MORPHMET] procD.allometry with group inclusion

2016-12-12 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Re: the problem with CVA... or is it?

2016-11-29 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Measurements to Landmarks

2016-11-09 Thread Adams, Dean [EEOBS]
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

[MORPHMET] RE: [geomorph-r-package] Re: geomorph updates

2016-10-28 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Question about size adjusted residuals in Geomorph

2016-10-10 Thread Adams, Dean [EEOBS]
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

[MORPHMET] New integration method and geomorph

2016-09-12 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Re: allometry and phylogeny

2016-09-06 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 3.0.2 on CRAN

2016-07-21 Thread Adams, Dean [EEOBS]
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,

[MORPHMET] RE: allometry and phylogeny

2016-06-30 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Split tps file in R using a factor

2016-06-20 Thread Adams, Dean [EEOBS]
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)

RE: [MORPHMET] Form Space?

2016-04-04 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 3.0.1 on CRAN

2016-03-26 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] using regression residuals for other analyses

2016-03-24 Thread Adams, Dean [EEOBS]
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.

[MORPHMET] small update to geomorph

2016-02-15 Thread Adams, Dean [EEOBS]
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

[MORPHMET] small update to geomorph

2016-02-03 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Questions regarding correction for allometry & evolutionary allometry

2016-02-02 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 3.0 released

2016-01-26 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph blog

2016-01-11 Thread Adams, Dean [EEOBS]
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

[MORPHMET] RE: R code for CR modularity test

2015-12-02 Thread Adams, Dean [EEOBS]
e: 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 accom

[MORPHMET] R code for CR modularity test

2015-12-02 Thread Adams, Dean [EEOBS]
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

[MORPHMET] new modularity method

2015-11-27 Thread Adams, Dean [EEOBS]
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:

[MORPHMET] small update to geomorph on CRAN

2015-10-30 Thread Adams, Dean [EEOBS]
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.

[MORPHMET] RE: Important update for geomorph

2015-09-28 Thread Adams, Dean [EEOBS]
Randau, Marcela [mailto:m.ran...@ucl.ac.uk] Sent: Monday, September 28, 2015 1:30 PM To: Adams, Dean [EEOBS] <dcad...@iastate.edu>; 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 b

[MORPHMET] Important update for geomorph

2015-09-28 Thread Adams, Dean [EEOBS]
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

[MORPHMET] new phylogenetic comparative method for shape data

2015-09-16 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Suggestions for geomorph

2015-06-08 Thread Adams, Dean [EEOBS]
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

RE: [R-sig-phylo] [MORPHMET] Re: Stability of p-values (physignal and testing for morphological integration)

2015-06-08 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] geomorph problem with morphologika file

2015-06-08 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Analysis of semilandmark data

2015-05-06 Thread Adams, Dean [EEOBS]
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 would

[MORPHMET] RE: Testing for sexual dimorphism

2015-04-29 Thread Adams, Dean [EEOBS]
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

[MORPHMET] geomorph 2.1.4 released

2015-04-06 Thread Adams, Dean [EEOBS]
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

[MORPHMET] New paper: phylogenetic comparative analysis of shape; different permutation methods provide contrasting results

2015-01-13 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Error with read.ply in geomorph

2014-12-15 Thread Adams, Dean [EEOBS]
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

RE: [MORPHMET] Re: gpagen in geomorph flipping axes?

2014-12-14 Thread Adams, Dean [EEOBS]
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