RE: [MORPHMET2] Procrustes Motion Analysis

Sandra, Yes it can. Please see the help file of ‘trajectory.analysis’. One data input option for the function allows for full trajectory inputs, and then mirrors the analysis of Adams and Cerney 2007 for Procrustes Motion Analysis. The ‘motionpaths’ dataset in geomorph provides an example,

[MORPHMET2] Postdoctoral Associate: morphometrics and phylogenetic comparative methods

Postdoctoral Associate: morphometrics and phylogenetic comparative methods The Adams laboratory, Department of Ecology, Evolution and Organismal Biology (EEOB) at Iowa State University, is seeking applicants for a fulltime postdoctoral position in geometric morphometrics and phylogenetic

RE: [MORPHMET2] Higlhy fragmented collection - missing bilateral symetry

Diane, As I answered on the geomorph.google group, the package geomorph does not have a 'bilateral missing' function. The 'estimate.missing' function allows either TPS-based or regression-based landmark estimation. For bilateral options, one could see functions in the package LOST or Morpho

RE: [MORPHMET2] allometric correction

Damien, To your first point (inter-species allometry), you are correct that it does not make sense when there is a significant species:size interaction. In that case, the data have changed one’s question: away from pairwise differences of least squares species means, and towards a question of

[MORPHMET2] geomorph patch: 3.3.1

Folks, We found that an old piece of support code for PLS was inadvertently re-introduced in our recent release. The corrected version (3.3.1) is up on CRAN as a tarball: the binary executables will be generated soon by CRAN. This version is also on Git-develop branch. Our apologies for

[MORPHMET2] new version of RRPP and geomorph on CRAN

Colleagues, I want to inform you that new versions of RRPP (0.6.0) and of geomorph (3.3.0) are now on CRAN. These include some new functions, as well as some minor bug fixes; all of which are described in the News and help files. There are also new vignettes, which we hope are informative.

RE: [MORPHMET2] ID to the various individuals

Luca, The array you are creating using abind will have 3 dimensions. After you have read the data into that array, simply assign the 3rd dimension of the array the list of file names for the specimens. dimnames(mydata)[[3]] <- myspec.names where ‘myspec.names’ is a list of specimen names from

[MORPHMET2] RRPP 0.6.2 and geomorph 3.3.2 available on CRAN

Colleagues, We would like to announce that updates to both RRPP and geomorph are now available on CRAN. With these versions, one may notice slight differences in the point estimates of effect sizes (Z-scores) returned from certain tests, due to the inclusion of Box-Cox transformations when

[MORPHMET2] RESEND: CALL FOR NOMINATIONS: 2021 Rohlf Medal

The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the

[MORPHMET2] CALL FOR NOMINATIONS: 2021 Rohlf Medal

The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the

RE: [MORPHMET2] Doubt regarding compare.evol.rates function of Geomorph r package

Mariana, The phylogeny and data do not be combined into a single file, but do need to be called separately by the function. If you see the help file, the example has: compare.evol.rates(A=Y.gpa$coords, phy=plethspecies$phy, method="simulation",gp=gp.end,iter=999) The ‘A=Y.gpa$coords’ portion

RE: [MORPHMET2] Doubt regarding compare.evol.rates function of Geomorph r package

To: Adams, Dean [EEOB] Cc: morphmet2@googlegroups.com Subject: Re: [MORPHMET2] Doubt regarding compare.evol.rates function of Geomorph r package Thank you for your answers, it was helpful to know that I do not have to merge the files to run the analysis. I runned compare.evol.rates

RE: [MORPHMET2] Questions about Kendall’s shape space and tangent space projection

Karolin, A reading of Rohlf 1999 may help. Dean Rohlf, F.J. 1999. Shape statistics: Procrustes superimpositions and tangent spaces. Journal of Classification. 16:197-223. Dr. Dean C. Adams Distinguished Professor of Evolutionary Biology Director of Graduate Education, EEB Program Department

[MORPHMET2] geomorph 4.0.1 released on Github and CRAN

Colleagues, We wish to announce that an updated version of geomorph (4.0.1) is now available on Github (geomorphR/geomorph) and on CRAN. This is a minor release with some small bug fixes, that largely updates support code to be compliant with base-R 4.1 updates. Similar changes were made to

[MORPHMET2] PhD position available

Folks, A PhD position is now available in my lab. Current research in the lab centers on the interface between morphometrics and phylogenetic comparative biology, morphological evolution in vertebrates, and permutation theory. Prospective graduate students interested in geometric

RE: [MORPHMET2] 3D Warping/morphing methods using PCs

Pablo, Yes this can be done in geomorph. The step you are missing is to first predict the shapes at say, the min/max of your data for PC1. For instance: PC <- pca$x[,1] preds <- shape.predictor(shape, x= PC, Intercept = FALSE, pred1 = min(PC), pred2 = max(PC)) The

RE: [MORPHMET2] Phylegenetic Signal in Graphs

Peter, Both Kmult and its associated significance level are not effect sizes, so comparisons of these can be dicey. I would suggest examining their associated Z-score as obtained from the RRPP distribution and the observed value (see geomorph’s help file). As to your second question, if one

RE: [MORPHMET2] Help with Geomorph function gm.prcomp

Mariana, In R, objects of the class ‘phylo’ have a particular structure to the manner in which nodes are labeled. The easiest way to see these is to do this: library(ape) plot(phylo) nodelabels() Dean Dr. Dean C. Adams (he/him) Distinguished Professor of Evolutionary Biology Director of

Re: [MORPHMET2] How to transform Procrustes distances to mlilimeters

There is also a function in geomorph fir this. Dean Get Outlook for Android From: morphmet2@googlegroups.com on behalf of alcardini Sent: Friday, October 7, 2022 9:17:43 AM Cc: Morphmet Subject: Re: [MORPHMET2] How to transform

Re: [MORPHMET2] measuring morphological diversity

Fabio, A quantification and comparison of morphological disparity among groups may be accomplished in geomorph or RRPP on R. Dean Get Outlook for Android From: morphmet2@googlegroups.com on behalf of Fabio Pinheiro Sent: Friday,

RE: [MORPHMET2] Measurement error in geometric morphometrics

Jim, I agree that the term ‘bias’ without any clarification can be confusing. Your classic 2003 was clear to state bias ‘in what’ up-front (bias in estimating the mean shape) as well as provide clear definitions in terms of how you were using the word. That was then connected to the

[MORPHMET2] geomorph 4.0.5 upate now on CRAN

Colleagues, I wanted to let you know that geomorph 4.0.5 has been uploaded to CRAN, and is ready for use. This small update contains several new functions for comparing the strength of phylogenetic signal across datasets (following Collyer, Baken, and Adams, 2022: MEE), and several internal

RE: [MORPHMET2] Measurement error in geometric morphometrics

Andrea, I disagree with: " As I said, I really like this idea but would like to see a variety of examples in publications and I am not sure how easy it is to do this objectively (not purely based on judgement) and exhaustively. I must be able to detect the effect of a potential bias on all

[MORPHMET2] 2023 Rohlf Medal: Call for Nominations

The Rohlf Medal for Excellence in Morphometric Methods and Applications was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department

Re: [MORPHMET2] 3D WARP analysis

One can estimate the positions of missing landmarks using 'estimate.missing' in geomorph. The help file points you to the correct literature to cite for the method, describes the two approaches we implement, and provides examples. Dean Get Outlook for Android

[MORPHMET2] FINAL CALL: 2023 Rohlf Medal: Call for Nominations

The Rohlf Medal for Excellence in Morphometric Methods and Applications was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department

RE: [MORPHMET2] Error message from geomorph.data.frame

Hi Dan, The error message is straightforward: it is an issue with your data. The error message and tells you that there are differing numbers of observations somewhere: in your gpagen output, your sex, your locality, or some combination. Check the upstream code in your data preparation

[MORPHMET2] Philipp Mitteroecker is the 2023 recipient of the Rohlf Medal for Excellence in Morphometric Methods and Applications

Philipp Mitteroecker is the 2023 recipient of the Rohlf Medal for Excellence in Morphometric Methods and Applications [Rohlf Medal.gif] On October 24, 2023 at Stony Brook University, the seventh Rohlf Medal for Excellence in Morphometric Methods and Applications will be awarded to Philipp

RE: [MORPHMET2] related question on comparative methods using fossils

Andrea, It is the case that one risks getting into a bit of a circularity issue when using traits to estimate phylogenetic relationships and then evaluating the evolution of those traits on that same tree. The problem is most acute when the traits for both objectives are the same, are entirely

RE: [MORPHMET2] ontogenetic trajectories and phylogenetic hierarchy

This paper looks at ontogenetic trajectories and their convergence. Some discussion of phylogenetic shifts are discussed at the end: Adams, D.C. and A. Nistri. 2010. Ontogenetic convergence and evolution of foot morphology in European cave salamanders (Family: Plethodontidae). BMC

[MORPHMET2] new measurement error paper and methods

Colleagues, We would like to alert you to our new paper on measurement error: "Interrogating Random and Systematic Measurement Error in Morphometric Data", currently In Press at Evolutionary Biology (https://link.springer.com/article/10.1007/s11692-024-09627-6: also available upon request).

RE: [MORPHMET2] Error attempting running 'plotAllSpecimens()' function in geomorph R package

For reasons due to CRAN becoming more stringent with S3-type function calls, we needed to change the plot.param to: plot_param … (the previous no looks for an object or function called ‘param’). Dean Dr. Dean C. Adams Distinguished Professor of Evolutionary Biology Department of Ecology,