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

2014-12-15 Thread Emma Sherratt
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

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

2014-12-15 Thread Emma Sherratt
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: [MORPHMET] Default orientation of 3D plots in geomorph

2014-12-15 Thread Emma Sherratt
'); . -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L118 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5038 email: emma.sherr...@une.edu.au Caecilians are legless amphibians

Re: [MORPHMET] arrayspecs in geomorph giving error message

2014-12-30 Thread Emma Sherratt
://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org javascript:_e(%7B%7D,'cvml','morphmet%2bunsubscr...@morphometrics.org'); . -- ~~~ Emma Sherratt, PhD. Lecturer

Re: [MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Emma Sherratt
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 email

Re: [MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Emma Sherratt
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

Re: [MORPHMET] surface semilandmarks

2015-01-10 Thread Emma Sherratt
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 Tel: +61 2 6773

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

2015-02-10 Thread Emma Sherratt
the 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

2015-02-10 Thread Emma Sherratt
for inspecting the 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

Re: [MORPHMET] physignal in geomorph

2015-06-11 Thread Emma Sherratt
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 6773 5041 email: emma.sherr...@une.edu.au Twitter

Re: [MORPHMET] physignal in geomorph

2015-06-11 Thread Emma Sherratt
~~~ 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

2015-06-15 Thread Emma Sherratt
, we use the 3D array format to specify that the data are coordinate data, and the 2D matrix for multivariate data, not necessarily shape data. This allows several of the functions to be used with non-shape, multivariate datasets. Emma ~~~ Emma

Re: [MORPHMET] Landmark Editor -- MorphoJ problem

2015-06-15 Thread Emma Sherratt
'); . -- ~~~ 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: @DrEmSherratt

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

2015-06-15 Thread Emma Sherratt
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:

Re: [MORPHMET] Centroid size and isometric scaling

2015-05-31 Thread Emma Sherratt
~~~ 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: emma.sherr...@une.edu.au Twitter: @DrEmSherratt

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

2015-08-23 Thread Emma Sherratt
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 textures, which our read.ply function currently does not support. Resaving the file without the texture information made the file readable. FYI Stefan

Re: [MORPHMET] Estimating Ontogenetic Trajectories

2015-08-23 Thread Emma Sherratt
...@morphometrics.org javascript:_e(%7B%7D,'cvml','morphmet%2bunsubscr...@morphometrics.org'); . -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L112 Bldg C02, University of New

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

2015-11-09 Thread Emma Sherratt
gt; > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org <javascript:;>. > -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Envir

Re: [MORPHMET] Stuck on creating new dataset

2015-07-11 Thread Emma Sherratt
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 morphmet+unsubscr...@morphometrics.org javascript:;. -- ~~~ Emma

Re: [MORPHMET] writing .nts files from geomorph

2016-01-19 Thread Emma Sherratt
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=TRUE) } Emma ~~~

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

2016-06-27 Thread Emma Sherratt
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 School of B

Re: [MORPHMET] Read .landmarkAscii file into R

2016-01-19 Thread Emma Sherratt
of 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] PC scores of ancestral nodes/MorphoJ/Square change Parsimony

2016-05-19 Thread Emma Sherratt
alent 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 Nationa

Re: [MORPHMET] Using Semilandmarks

2016-05-11 Thread Emma Sherratt
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

[MORPHMET] geomorph R package users forum

2016-07-27 Thread Emma Sherratt
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] Cannot load STL file into Landmark Editor software

2016-07-17 Thread Emma Sherratt
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

Re: [MORPHMET] morphospace occupation

2016-08-05 Thread Emma Sherratt
om 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 <http://biology-assets.anu.edu.au/hosted_sites/Scott/> Division

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

2017-02-20 Thread Emma Sherratt
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

[MORPHMET] Terminology: Morphometry or Morphometrics?

2016-09-07 Thread Emma Sherratt
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

[MORPHMET] Re: Horizontally inverted aligned landmark clouds

2016-09-11 Thread Emma Sherratt
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] Terminology: Morphometry or Morphometrics?

2016-09-08 Thread Emma Sherratt
gt; translate from another language (French "morphom├ętrie", 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

Re: [MORPHMET] fitting lines to allometric plots?

2016-12-20 Thread Emma Sherratt
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 Researcher in the K

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

2016-12-23 Thread Emma Sherratt
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

Re: [MORPHMET] Curve sliding semilandmarks

2016-12-06 Thread Emma Sherratt
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://biol

Re: [MORPHMET] Question on combine datasets in MorphoJ

2017-08-14 Thread Emma Sherratt
/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 AUSTRALIA *