[MORPHMET] Re: physignal in geomorph
Dear all Thank you very much to those who have replied to my question. It turned out that my data was a 2D matrix instead of a 3D array and that that was causing the problem. Best wishes, Anneke On Thursday, June 11, 2015 at 1:41:55 PM UTC+2, Anneke van Heteren wrote: Dear friends and colleagues I am trying to run physignal in geomorph (R), but I am running into a problem I do not understand. Here is the code I am using and the error message: physignal(ursid_phyl, Regr_res_av, iter=99) Error in match.names(clabs, names(xi)) : names do not match previous names However: name.check(ursid_phyl,Regr_res_av) [1] OK But: match(ursid_phyl,Regr_res_av) [1] NA NA NA NA match(Regr_res_av,ursid_phyl) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA This suggested to me that physignal might need the columns to carry the same names rather than the rows (as my phylogeny is list of 4 and I have 15 landmarks=45 variables), but when I transposed my data, I get a different error message: trans_regr_res_av -t(Regr_res_av) physignal(ursid_phyl, trans_regr_res_av, iter=99) Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) : Number of taxa in data matrix and tree are not not equal. I do not know what I could try next to calculate physignal. Any help would be appreciated. This is the phylogeny that I am using: (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3); Thanks in advance. Best wishes, Anneke van Heteren -- 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.
[MORPHMET] Landmark Editor -- MorphoJ problem
Hello All, I need to ask a rather silly question for which I imagine there is a simple solution ... but I just can't figure it out. I've created a landmark file in IDAV Landmark Editor and exported an NTSYSpc (.dta) file for it. I then tried to upload that into MorphoJ, but to no avail. I keep getting the message There appear to be too many row labels in the file. I then tried to create the same dataset using text files exported from Landmark Editor but got roughly the same message. I have opened the files and looked at them and as far as I can tell there is nothing wrong. Has anyone else encountered and overcome this issue? 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.
Re: [MORPHMET] Re: physignal in geomorph
Anneke, I'm gad you've managed to solve your issue but I need to say that making your data a 3D array shouldn't be the fix. library(geomorph) Loading required package: rgl data(plethspecies) Y.gpa-gpagen(plethspecies$land)#GPA-alignment #Test for phylogenetic signal in shape using data in a 3D array physignal(plethspecies$phy, Y.gpa$coords, method=Kmult,iter=99) $phy.signal [,1] [1,] 0.9572538 $pvalue [,1] [1,] 0.04 #Test for phylogenetic signal in shape using data in a 2D matrix physignal(plethspecies$phy, two.d.array(Y.gpa$coords), method=Kmult,iter=99) $phy.signal [,1] [1,] 0.9572538 $pvalue [,1] [1,] 0.02 So there must have been something wrong with your 2D matrix to not work previously. Check that it is numeric, check that the rownames were assigned properly, and that it contained only the data you wanted to input. FYI, in geomorph, 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 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 Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians On 15 June 2015 at 20:24, Anneke van Heteren a.h.vanhete...@gmail.com wrote: Dear all Thank you very much to those who have replied to my question. It turned out that my data was a 2D matrix instead of a 3D array and that that was causing the problem. Best wishes, Anneke On Thursday, June 11, 2015 at 1:41:55 PM UTC+2, Anneke van Heteren wrote: Dear friends and colleagues I am trying to run physignal in geomorph (R), but I am running into a problem I do not understand. Here is the code I am using and the error message: physignal(ursid_phyl, Regr_res_av, iter=99) Error in match.names(clabs, names(xi)) : names do not match previous names However: name.check(ursid_phyl,Regr_res_av) [1] OK But: match(ursid_phyl,Regr_res_av) [1] NA NA NA NA match(Regr_res_av,ursid_phyl) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA This suggested to me that physignal might need the columns to carry the same names rather than the rows (as my phylogeny is list of 4 and I have 15 landmarks=45 variables), but when I transposed my data, I get a different error message: trans_regr_res_av -t(Regr_res_av) physignal(ursid_phyl, trans_regr_res_av, iter=99) Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) : Number of taxa in data matrix and tree are not not equal. I do not know what I could try next to calculate physignal. Any help would be appreciated. This is the phylogeny that I am using: (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3); Thanks in advance. Best wishes, Anneke van Heteren -- 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. -- 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.
[MORPHMET] Using ImageJ for digitizing on Mac OS X
Hello, Is there a guide for the complete beginner on how to use ImageJ instead of tpsdig, especially on how to set the scale before digitizing? Many thanks Edouard - Edouard Masson-MacLean PhD Candidate Room 119 Department of Archaeology School of Geosciences University of Aberdeen St. Mary's, Elphinstone Road Aberdeen, AB24 3UF Scotland, UK -- 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] Landmark Editor -- MorphoJ problem
Ari, This issue is probably due to having spaces in the names of your specimens. Find and replace with _ then try again Emma On Monday, June 15, 2015, a.l.schulz ariadne.sch...@gmail.com wrote: Hello All, I need to ask a rather silly question for which I imagine there is a simple solution ... but I just can't figure it out. I've created a landmark file in IDAV Landmark Editor and exported an NTSYSpc (.dta) file for it. I then tried to upload that into MorphoJ, but to no avail. I keep getting the message There appear to be too many row labels in the file. I then tried to create the same dataset using text files exported from Landmark Editor but got roughly the same message. I have opened the files and looked at them and as far as I can tell there is nothing wrong. Has anyone else encountered and overcome this issue? 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 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 England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Twitter: @DrEmSherratt Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians -- 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] Using ImageJ for digitizing on Mac OS X
hi there, Analyze Set Scale... + http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html hth best, v 2015-06-15 14:59 GMT+02:00 Edouard Masson-MacLean e.massonmacl...@gmail.com : Hello, Is there a guide for the complete beginner on how to use ImageJ instead of tpsdig, especially on how to set the scale before digitizing? Many thanks Edouard - Edouard Masson-MacLean PhD Candidate Room 119 Department of Archaeology School of Geosciences University of Aberdeen St. Mary's, Elphinstone Road Aberdeen, AB24 3UF Scotland, UK -- 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. -- vincentbonhomme.fr http://www.vincentbonhomme.fr -- 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.
[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-describe-the-shape-of-my-favourite-structure Best, Emma On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote: Hello, Is there a guide for the complete beginner on how to use ImageJ instead of tpsdig, especially on how to set the scale before digitizing? Many thanks Edouard - Edouard Masson-MacLean PhD Candidate Room 119 Department of Archaeology School of Geosciences University of Aberdeen St. Mary's, Elphinstone Road Aberdeen, AB24 3UF Scotland, UK -- 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] Re: Using ImageJ for digitizing on Mac OS X
Dear Emma Many thanks for your help that’s very useful Best Edouard Le 15 juin 2015 à 22:56, Emma Sherratt emma.sherr...@gmail.com a écrit : 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-describe-the-shape-of-my-favourite-structure Best, Emma On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote: Hello, Is there a guide for the complete beginner on how to use ImageJ instead of tpsdig, especially on how to set the scale before digitizing? Many thanks Edouard - Edouard Masson-MacLean PhD Candidate Room 119 Department of Archaeology School of Geosciences University of Aberdeen St. Mary's, Elphinstone Road Aberdeen, AB24 3UF Scotland, UK -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org http://www.morphometrics.org/ To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org mailto:morphmet+unsubscr...@morphometrics.org. -- 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] Using ImageJ for digitizing on Mac OS X
Great thanks Vincent! Edouard Le 15 juin 2015 à 21:41, Vincent Bonhomme bonhomme.vinc...@gmail.com a écrit : hi there, Analyze Set Scale... + http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html hth best, v 2015-06-15 14:59 GMT+02:00 Edouard Masson-MacLean e.massonmacl...@gmail.com mailto:e.massonmacl...@gmail.com: Hello, Is there a guide for the complete beginner on how to use ImageJ instead of tpsdig, especially on how to set the scale before digitizing? Many thanks Edouard - Edouard Masson-MacLean PhD Candidate Room 119 Department of Archaeology School of Geosciences University of Aberdeen St. Mary's, Elphinstone Road Aberdeen, AB24 3UF Scotland, UK -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org http://www.morphometrics.org/ To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org mailto:morphmet+unsubscr...@morphometrics.org. -- vincentbonhomme.fr http://www.vincentbonhomme.fr/ -- 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] Re: Using ImageJ for digitizing on Mac OS X
Dear Emma, Thanks, very helpful indeed. Best regards, 2015-06-15 18:56 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com: 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-describe-the-shape-of-my-favourite-structure Best, Emma On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote: Hello, Is there a guide for the complete beginner on how to use ImageJ instead of tpsdig, especially on how to set the scale before digitizing? Many thanks Edouard - Edouard Masson-MacLean PhD Candidate Room 119 Department of Archaeology School of Geosciences University of Aberdeen St. Mary's, Elphinstone Road Aberdeen, AB24 3UF Scotland, UK -- 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. -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- 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.
