Dear Joanna, this is something you can easily check: compare a PCA, shape distances and also centroid size from TPSRelw with those from MorphoJ after redoing the GPA: are they different? If they are, I'd worry. But, unless there's a mistake, I'd say they will be virtually identical.
Cheers Andrea On 22 June 2017 at 12:18, Joanna Lenarczyk <j.kowal...@botany.pl> wrote: > Hello All, > I was thinking about using TpsRelw to slide semilandmarks before analysing > the aligned specimens data in MorphoJ, but does it really make sense to > double the alignment? > Even if I have the file after TpsRelw, where landmarks and semilandmarks > are treated differently, im MorphoJ I make the alignment - Procrustes fit > again, in which the semilandmarks are treated as landmarks, they are > computed as landmarks. So, do I lose the information on the placement of > semilandmarks or not in MorphoJ? > Best, > Joanna > > 2017-06-22 11:18 GMT+02:00 Paolo Piras <paolopir...@gmail.com>: > >> Hi folks/Andrea, >> >> just to underline this: >> >> Andrea,when you say >> >> "an 'apparent size variable' which is a series of numbers virtually >> equal to 1 (differences will be approximation errors)." >> I think that MorphoJ "reads" the actual CS values from the aligned >> coordinates saved by TPSrelw that, as you say, have lost their original >> size. However, small deviations from 1 are not due to approximation error >> as I *suspect* that the "aligned coordinates" saved by TPSrelw are those >> projected on the tangent plane (by an orthogonal [more commonly used] or >> stereographic projection) and for this reason they have necesarily a CS >> larger than 1 that is the radius of the hyperspherical Kendall's Shape >> Space. In order to reach the tangent plane from the sphere one necessarily >> must go beyond its radius (that geometrically *IS* the size of a >> configuration lying on that space) and the CS will be inevitably larger >> than 1. >> An indirect proof for this would be to verify that what you call >> "approximation error" gives CS values always slightly larger than 1 and >> never smaller. >> So I think there is no error in having, for those data, CS >> slightly different (=larger) from 1 as they MUST have CS larger than 1 by >> construction. >> However,I'm not sure at 100% if TPSrelw works as I hypothesized here.. >> Playing a bit with TPSrelw could unveil this. >> All the best >> Paolo >> >> >> 2017-06-22 11:00 GMT+02:00 andrea cardini <alcard...@gmail.com>: >> >>> Hi Pere, >>> there's plenty of work arounds this. I agree with Carmelo that the nts >>> format may be easier to edit manually, so that you can put back the >>> necessary labels. >>> >>> HOWEVER, PLEASE BE CAREFUL because SIZE WILL BE MISSING from those data. >>> As most of the time you may want to analyse both size and shape, instead of >>> importing in MorphoJ the aligned specimens from the TPSRelw slid >>> configurations, I'd suggest to save the SCALED ALIGNED SPECIMENS in >>> TPSRelw. Jim added this option for this purpose: this way you get the >>> aligned specimens rescaled to the original centroid size. Therefore, when >>> you import them in MorphoJ and redo the Procrustes fit, you will get both >>> the aligned specimens as well as their size. >>> In contrast, if you import the aligned data (not rescaled), size won't >>> be there but you may be easily tricked and think it is there, because >>> MorphoJ requires that you redo the Procrustes fit and then you'll get an >>> 'apparent size variable' which is a series of numbers virtually equal to 1 >>> (differences will be approximation errors). >>> Use the scaled aligned and you won't have this issue. >>> >>> Cheers >>> >>> Andrea >>> >>> On 22/06/17 10:07, Pere Ibáñez wrote: >>> >>>> Hello All, >>>> >>>> I am using TPSRelW to slide semilandmarks. Once I have the consensus, I >>>> use Save aligned to export the aligned coordinates (including slid >>>> semilandmarks) as a tps file, that I want to import into MorphoJ. >>>> >>>> The problem is that the file that is exported has the IDs of the >>>> specimens empty, with no information. And MorphoJ doesn't import it without >>>> that information, so I have to type it one by one on the tps file. Does >>>> anyone know how to export that tps file from TPSRelW without losing the ID? >>>> >>>> Thanks! >>>> >>>> -- >>>> MORPHMET may be accessed via its webpage at >>>> http://www.morphometrics.org >>>> --- >>>> You received this message because you are subscribed to the Google >>>> Groups "MORPHMET" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to morphmet+unsubscr...@morphometrics.org <mailto: >>>> morphmet+unsubscr...@morphometrics.org>. >>>> >>> >>> -- >>> >>> Dr. Andrea Cardini >>> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di >>> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy >>> tel. 0039 059 2058472 <059%20205%208472> >>> >>> Adjunct Associate Professor, School of Anatomy, Physiology and Human >>> Biology, The University of Western Australia, 35 Stirling Highway, Crawley >>> WA 6009, Australia >>> >>> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it >>> WEBPAGE: https://sites.google.com/site/alcardini/home/main >>> >>> FREE Yellow BOOK on Geometric Morphometrics: >>> http://www.italian-journal-of-mammalogy.it/public/journals/3 >>> /issue_241_complete_100.pdf >>> >>> ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.or >>> g/en/index.php/GFN/page/calculators/ >>> >>> -- >>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >>> --- You received this message because you are subscribed to the Google >>> Groups "MORPHMET" group. >>> 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 >> --- >> You received this message because you are subscribed to the Google Groups >> "MORPHMET" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to morphmet+unsubscr...@morphometrics.org. >> > > > > -- > Joanna Lenarczyk > > Zakład Fykologii > Instytut Botaniki im. W. Szafera Polskiej Akademii Nauk > ul. Lubicz 46, 31-512 Kraków > tel. 12 42 41 876 > > Department of Phycology > W. Szafer Institute of Botany, Polish Academy of Sciences > Lubicz 46, PL-31-512 Cracow > phone +48 12 42 41 876 > > e-mail: j.lenarc...@botany.pl > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- Dr. Andrea Cardini Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy tel. 0039 059 2058472 Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: alcard...@gmail.com, andrea.card...@unimore.it WEBPAGE: https://sites.google.com/site/alcardini/home/main FREE Yellow BOOK on Geometric Morphometrics: http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
