Re: [MORPHMET] pairwise matrix of vector angles in R

2017-11-06 Thread Mike Collyer
Hi David, What you touched on is the art of statistical computing. You used a logical function to only calculate angles between non-identical vectors and avoid NaN values; our geomorph function turns off warnings and waits until the end and replaces what should be computational 0 values with a

[MORPHMET] Geometric Morphometric variables used as traits

2017-11-06 Thread Jonathan Miller
Dear all, I´d like to ask you if any of you could suggest me some geometric morfometric variables that could be used as traits for a phylogenetic signal test. Up to now I have taken only the PC1 and PC2 from a PCA after doing the nomal treatment to the landmarks sets... After that I also used

[MORPHMET] Landmarks coming up funny in MorphoJ

2017-11-06 Thread Candice Neves
Hi All, I'm trying to analyze measurement error in MorphoJ but I'm running into a problem. When I digitized my landmarks I used tpsDIG2, however I had to organize those coordinates into a CSV. file because I digitized them in two separate .tps files and tpsUtil wouldn't allow me to open the one

[MORPHMET] New publication on measurement error and scan sharing

2017-11-06 Thread ltallman
Hello all, Today our manuscript evaluating potential causes of inter- and intra-observer error in 3DGM data was published in PLoS One. In it, we evaluate how scan type, experience with morphology and morphemetrics and in-person training impact rates of error in datasets. Might be of interest

Re: [MORPHMET] Procrustes fit

2017-11-06 Thread Philipp Mitteröcker
Not, e.g., if all specimens are rotated 90 degrees. Then x coordinates in one set would correspond to the y coordinates in the other. Multivariate R^2 should be close to 1, though. Philipp Mitteroecker Von meinem iPhone gesendet > Am 31.10.2017 um 16:20 schrieb Andrey Lissovsky : > > Thank y

Re: [MORPHMET] Geometric Morphometric variables used as traits

2017-11-06 Thread Antigoni Kaliontzopoulou
Hi Jonathan, there is a multivariate estimate for phylogenetic signal, with the corresponding significance testing, were you can test for phylogenetic signal in shape as a multidimensional trait. The method is described in Adams, D.C. 2014. A generalized K statistic for estimating phylogenetic sig

Re: [MORPHMET] Landmarks coming up funny in MorphoJ

2017-11-06 Thread Candice Neves
Hi Guido Thanks so much for the suggestion, I'll definitely do that. Is there a particular way to save a wordpad/notepad file as a .tps format file? I've tried to do this before but it kept saving as a .txt file, or would this still work? Thanks for the help Candice Neves On 6 November 2017 at 1

Re: [MORPHMET] Landmarks coming up funny in MorphoJ

2017-11-06 Thread f.james.rohlf
Let it save it as a txt file then just rename the file. -F. James RohlfDepts. of Ecology & Evolution and of Anthropology Stony Brook University  Original message From: Candice Neves <536...@students.wits.ac.za> Date: 11/6/17 12:59 PM (GMT-05:00) To: Guid

Re: [MORPHMET] Landmarks coming up funny in MorphoJ

2017-11-06 Thread K. James Soda
Dear Ms. Neves, Quick addition to Dr. Rohlf's solution. To change a file extension on a Windows machine, you will need to do the following: 1) Open a Windows Explorer window. 2) On the ribbon at the top of the window, click "View" 3) Click the box for "File Name Extensions" (in the "Show/Hide" s