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

Hi David, Turns out my answer went to only you and not this group. I believe that your ply file has duplicated vertices and so it is not able to match up the vertex coordinates to the triangles. Please send me the file so that I can examine it. Emma On Monday, 15 December 2014 11:53:17 UTC+11

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

Dear David and Stefan, The issue was that the PLY file of David has textures, which our read.ply function currently does not support. Resaving the file without the texture information made the file readable. FYI Stefan, the original file read fine with your vsgImport function, but only when re

Re: [MORPHMET] Default orientation of 3D plots in geomorph

ty > South Parks Road > Oxford OX1 3AN > United Kingdom > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org &g

Re: [MORPHMET] arrayspecs in geomorph giving error message

808 0.03663254 > 34 -0.2894727 0.00027348 -0.4324036 0.03879201 > 35 -0.2900338 -0.00101017 -0.4352513 0.02773395 > 36 -0.2911340 0.00317057 -0.4371728 0.03853357 > 37 -0.2887806 -0.00350296 -0.4380146 0.04047513 > 38 -0.2940667 -0.00058660 -0.4469157 0.03693919 > 39 -0.295832

Re: [MORPHMET] surface semilandmarks

regime and we can discuss how to work with these files. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351

Re: [MORPHMET] CVA and Discriminant Analysis in Morpho J

data for the aspects of shape that delimit and discriminate between two or more groups. Not as reduced axes for use in correlation tests. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science

Re: [MORPHMET] CVA and Discriminant Analysis in Morpho J

g to use for comparison to other variables...What would you suggest > would be a more appropriate index to use in order to compare the shape > ordination results to say, environmental variables, such as sediment size > (I am studying clam morphology differences)? > > On Tuesday, Febru

Re: [MORPHMET] Warped Grids in MorphoJ

hen right click and disply graphs. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 em

Re: [MORPHMET] Warped Grids in MorphoJ

Oh sorry, I think the latter way just shows the group mean from the overall mean - so you may need to do some cutting and pasting... Contact Chris Klingenberg, he might have an easier way up his sleeve. Emma ~~~ Emma Sherratt, PhD. Lecturer in

[MORPHMET] Update to geomorph R package now available

Dear Morphometricians, We have uploaded version 2.1.3 of geomorph to CRAN . The windows and mac binaries have been compiled and the tarball is available. In order to make this package the most accessible to the morphometrics community, and giv

Re: [MORPHMET] Centroid size and isometric scaling

(1993, Evolution). Best, Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: e

Re: [MORPHMET] physignal in geomorph

. It's likely to be a trailing space or _. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L112 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2

Re: [MORPHMET] physignal in geomorph

~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L112 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Twitter

Re: [MORPHMET] Re: physignal in geomorph

ctions to be used with non-shape, multivariate datasets. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L112 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.ed

Re: [MORPHMET] Landmark Editor --> MorphoJ problem

ssue? For the time being I > am stumped. > > Best, > Ari > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org > > . &g

[MORPHMET] Re: Using ImageJ for digitizing on Mac OS X

Dear Edouard, You can find a comprehensive guide by David Polly here: http://www.indiana.edu/~g562/Handouts/Collecting%20Landmarks.pdf And a few tips on digitizing 2D data can be found here: http://www.emmasherratt.com/morphometrics/-goal-gathering-two-dimensional-landmark-coordinates-to-descr

Re: [MORPHMET] Suggestions for geomorph

e talking about. Please can you send me a copy of this error? Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L112 Bldg C02, University of New England, Armidale, NSW, Australia,

Re: [MORPHMET] Suggestions for geomorph

Thank you for those pieces of information, Mauro. I shall update the version for 2.1.6 so that a single specimen can be digitized and there is a check for the length of scale and length of filelist. Em ~~~ Emma Sherratt, PhD. Lecturer in Zoology

Re: [MORPHMET] Stuck on "creating new dataset"

ggestions or other tips, I would be very glad to hear > them. > > With kind regards, > Abel > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to mo

Re: [MORPHMET] Estimating Ontogenetic Trajectories

ban > > PhD Candidate, University of Iowa > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org > > . >

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

Lab: (479) 575-5296 > > Email: cterh...@uark.edu > > > Web page: terhunelab.uark.edu > > > > On Monday, December 15, 2014 at 10:02:39 PM UTC-6, Emma Sherratt wrote: >> >> Dear David and Stefan, >> >> The issue was that the PLY file of David has tex

Re: [MORPHMET] Important update for geomorph

An oversight on our part not to emphasise this in the first post, our apologies. Full insulation instructions can be found here:  http://www.geomorph.net/p/installing-geomorph.html ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division

Re: [MORPHMET] Geomorph R package: digit.curves (several curves with different starting points at once)

rg > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org . > -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L112 B

Re: [MORPHMET] writing .nts files from geomorph

0,"dim=2"),file= ntsfile,sep="\n",append=TRUE) } else if (dims[2] == 3){ cat(paste(1,dims[1],3,0, "dim=3"),file= ntsfile,sep="\n",append=TRUE) } write.table(A ,file= ntsfile,col.names = FALSE, row.names = FALSE,sep=" ",append=TRU

Re: [MORPHMET] Read .landmarkAscii file into R

people using AVIZO for digitising, we can include a function in geomorph. Regarding a read function writing? Nope, never heard of that. Em ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science

Re: [MORPHMET] Using Semilandmarks

d analyses. Emma ~~~~~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab <http://biology-assets.anu.edu.au/hosted_sites/Scott/> Division of Evolution, Ecology & Genetics Research School of Biology 116 Daley Road The Australian Natio

Re: [MORPHMET] PC scores of ancestral nodes/MorphoJ/Square change Parsimony

equivalent assuming BM model of evolution ~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab <http://biology-assets.anu.edu.au/hosted_sites/Scott/> Division of Evolution, Ecology & Genetics Research School of Biology 116 Daley Road The Australian Na

Re: [MORPHMET] Newly added samples as outliers in TPS file

one of the previous specimens to see where that falls. Emma ~~~~~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab <http://biology-assets.anu.edu.au/hosted_sites/Scott/> Division of Evolution, Ecology & Genetics Research S

Re: [MORPHMET] Cannot load STL file into Landmark Editor software

Patrick, The icon against your "sample" file indicates that the .stl is not being read as a 3D model but as a coordinate file. You might need to resave it as a .ply file using meshlab, or something similar. Emma ~~~~~~~ Emma She

[MORPHMET] geomorph R package users forum

Dear Colleagues, We have followed in the footsteps of this extremely useful MORPHMET discussion forum and have started our own, specifically for geomorph R package questions, discussions and troubleshooting. This replaces the archaic system we had on the blog site

Re: [MORPHMET] morphospace occupation

s group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > > -- ~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab <http://biology-assets.anu.edu.au/hosted_sites/Scott/> Division of Evolution, Ecology &

[MORPHMET] Terminology: Morphometry or Morphometrics?

Dear Morphmet-hive mind, I've been curious for some time about the terms "morphometry" and "morphometrics" and whether they are in fact interchangeable or quite distinct. Also, is it related to the difference between phylogeny and phylogenetics? Regards, Emma -- MORPHMET may be accessed v

Re: [MORPHMET] Terminology: Morphometry or Morphometrics?

te from another language (French "morphométrie", German > "Morphometrie" etc.). > > There would be room for linguistic research here > > Best wishes, > Chris > > > On 08/09/2016 06:01, Emma Sherratt wrote: > >> Dear Morphmet-hi

[MORPHMET] Re: Horizontally inverted aligned landmark clouds

Dear Christopher, What comes to mind is the option in geomorph's gpagen() function "PrinAxes". When this option is TRUE, the shape coordinates are aligned by their principal axes rather than how the configuration was digitized- this is for visualisation and isn't changing the shape infomration

Re: [MORPHMET] Semilandmarks in geomorph

ps > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org . > -- ~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab &l

Re: [MORPHMET] Curve sliding semilandmarks

rk as linked and places equally distant semis on each curve separately). Details of geomorph below in my signature, including the extensive help guide. Emma ~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab <http:/

Re: [MORPHMET] fitting lines to allometric plots?

ariate summary, and the "line" is just an approximation of the trajectory in a multidimensional space. I think that putting such a line would mislead people and wouldn't be accurate. Em ~~~~~~~ Emma Sherratt, PhD. Postdoctoral Researche

Re: [MORPHMET] Re: plotting landmarks on Morpheus?

For 3D surface models, I suggest IDAV Landmark Editor ( http://graphics.idav.ucdavis.edu/research/EvoMorph) or the commercial version Checkpoint that Dennis mentioned below. Meshlab's pick points function works. Also digit.fixed() function in geomorph R package depending on the specimens. If you h

Re: [MORPHMET] Help needed - Extract classifiers form ID String in Geomoprh or export complete datasets from MorphoJ

Dear Marcos, 1- The functions you need are in base R, not in the geomorph package. use the function strsplit() to split a character string by any character. See related functions for alternatives for manipulating character strings. 2- yes. In MorphoJ, choose the dataset in the file tree then go t

Re: [MORPHMET] Question on combine datasets in MorphoJ

ttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146166 Emma ~~~ Emma Sherratt, PhD. *University Research Fellow* Department of Genetics and Evolution School of Biological Sciences The University of Adelaide Adelaide, SA 5005 AUSTRAL