To add briefly to Dennis' comment. If landmark estimation is the route taken, both TPS-based and regression-based imputation are implemented in geomorph.
Dean Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University https://www.eeob.iastate.edu/faculty/adams/ phone: 515-294-3834 -----Original Message----- From: morphmet <dsl...@morphometrics.org> Sent: Tuesday, May 7, 2019 8:18 AM To: morphmet@morphometrics.org Subject: Re: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe It depends on what is wrong with the data (I haven't checked it). Morpheus et al. can be used to correct data after visual inspection or mark bad data points as missing or delete whole sets of coordinates for particular points. The easiest way to do this is to get the data into a form importable by Morpheus - NTSYSpc is the easiest, and import the data. You can then set up links between points (there is a menu option). Then, you can just page through the objects looking for one whose links are obviously wrong. You can then swap points (another menu option) until they are in the correct order. For this, it is useful to use the plot Opts button to set the point plotting symbol as "number", which locates the points with their number, e.g., "1", "2", etc. You can also mark any offending points (with genuinely bad data) as "missing" or delete points/landmarks. If there are too few or too many, you can insert missing points (which will be marked as missing data) or delete specific points from specific objects. Another suggestion to find objects with bad points is to do a PCA plot (I use R) to check for any outliers. If there are a few scattered points with missing data at the end of all of this, the data can be filled in using missing data imputation - mean substitution is the only method currently implemented. Mean substitution generally does not affect parameter estimates, but does result in error estimates that are undervalued - there is more variance than apparent in the data since mean values were substituted for missing data. -ds PS: NTSYSpc format for import. On the first line, 1 is NTSYS for rectangular data matrix, n is for the number of objects in the file (you have to provide a number, not 'n'); a number representing the number of landmarks, p, times the number of dimensions, 3 in your case; and a '0' indicating there are no missing data in the data set. If there are missing data, then the '0' is replace by something like "1 -999", where the '1' indicates the presence of missing data and the next item, e.g., -999, is the code used to indicate missing data... 1 n nDimxp 0 x1 y1 z1 x2 y2 z2 ... xp yp zp ...repeated (except for the first line) for more objects On 5/7/19 8:09 AM, Azadeh Mohaseb wrote: > Dear all > I am a post-doc researcher on GMM and I work on equids bones. Recently, I > digitized some modern equid bones by a microscribe and then I realized that > the 3d coordinates of some of these individuals are not correcte. > As I don't have access to these bones to digitize them again, I wondered if > you could help me to fix this problem. > I send you the correct coordinates of one individual and the incorrect > coordinates of another one. These two individuals have been digitized at the > same time, with same microscribe and the same settings on machine and > software. > > Individual 1: correct > > 228.6438 203.1991 156.5325 > 220.2511 204.6701 143.3459 > 223.9106 202.3835 121.6829 > 242.5923 225.1355 121.4050 > 240.4551 225.8690 136.0673 > 238.9128 226.4731 141.2689 > 240.9662 226.0292 146.4538 > 243.8571 223.4773 158.7283 > 248.3989 203.3913 162.7939 > 247.9284 204.2474 147.2226 > 249.7594 202.0327 140.3145 > 247.2640 205.0845 134.1143 > 246.3540 204.5467 115.9491 > 88.1469 334.5199 162.2996 > 79.0490 330.4259 152.7271 > 74.0790 325.4809 142.4243 > 79.8139 324.6076 119.4693 > 86.4637 331.0746 115.0139 > 88.8453 333.9695 120.4097 > 87.0741 333.9286 128.0646 > 85.8100 336.1603 144.5840 > 83.5972 335.3779 150.5125 > 90.8324 337.0566 156.8697 > 92.3339 337.9303 154.1111 > 87.5753 339.9321 145.9987 > 93.6211 346.3407 145.2005 > 98.7993 344.1494 152.6361 > 89.2627 341.3373 127.1407 > 91.0691 339.7504 123.6672 > 94.9706 342.5350 123.9575 > 93.9787 344.1297 127.5435 > > Individual 2: incorrect > > 117.1907 72.8549 331.5414 > 63.8556 106.7571 324.6544 > 64.2134 108.2755 327.6326 > 125.5818 22.1134 446.8474 > 117.3735 26.4359 458.0952 > 110.4884 27.9800 458.7083 > 111.1632 21.4185 461.2170 > 106.1536 18.8334 468.0809 > 71.8894 25.9454 248.6469 > 49.2014 61.3649 250.9960 > 50.9447 62.2230 251.7744 > 31.1992 99.5425 270.7333 > 38.6410 96.3750 268.3234 > 104.8402 76.1165 472.1013 > 104.0343 79.0076 464.1394 > 81.7345 108.8425 464.0654 > 85.9537 128.9866 461.4308 > 88.6260 142.0624 468.9539 > 96.1857 130.2672 474.6507 > 85.1190 135.9783 473.3503 > 79.3694 122.8234 477.4590 > 78.4327 115.8613 477.4715 > 84.2949 108.1328 485.4598 > 97.2760 93.4345 481.8105 > 89.2901 111.8870 483.4924 > 90.0784 117.8522 490.4405 > 91.4313 106.3994 494.9362 > 79.4173 144.0817 472.9395 > 88.3825 141.0176 474.3985 > 90.9274 140.2106 477.6371 > 85.2512 140.7932 478.2403 > > I would apreciate if somebody could help me. > Please don't hesitate to ask me for more details. > > King regards > Azadeh > > -- 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. 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