Dear Antonio, Thank you for sharing your nicely explained protocol and for the offer to help with the code. I was able to get the estimation in Morpho working with the help from another group member. Turns out the errors I was running into with fixLMmirror were because some specimens were missing both paired landmarks so there was nothing to mirror. I have experience with 3D reconstruction and dataset registration, but am new to geometric morphometrics and working with paleo specimens that have missing structures. Seems I have quite a bit to learn for what I thought would be a straightforward side project with some former collaborators ;)
Now that I've gotten all the functions I'm interested in using to work, I'm trying to confirm that I'm using them properly. Have you worked with landmark datasets that have two planes of bilateral symmetry? I'm wondering if I should do PCAs for each plane of symmetry separately, or if it makes more sense to compare both planes simultaneously. Best, Katie On Tuesday, September 22, 2020 at 2:26:37 PM UTC-4 [email protected] wrote: > Dear Katherine, > > Morpho and geomorph usually work fine in estimating missing data. If you > have the information about paired landmarks my suggestion is to use this > information in the estimation. Of course it depends on the specific case > study. For example, if I need to estimate missing landmarks in a deformed > fossil specimen I use this protocol: i) symmetrization of the specimen, ii) > estimation of missing landmarks on the retrodeformed specimen, and iii) > calculation of the estimated landmarks coordinates on the original model > (i.e., the deformed one). > > If you share with us an example data with missing landmarks I can send you > an R script with the code to estimate missing data by using Morpho and > geomorph. > > Best, > > Antonio > > On Mon, 21 Sep 2020 at 01:11, Katherine Wolcott <[email protected]> > wrote: > >> Hi everyone, I'm new here! >> >> I have a landmark dataset created in Amira for seeds with bilateral >> symmetry. Some specimens are fossils with missing landmarks. I converted >> the Amira datasets to text files formatted like TPS 3D landmarks and as a >> csv file (see screenshots below). >> ->sample TPS formatted 3D landmark file (1 specimen) >> >> [image: sample_landmark.jpg] >> -> sample landmark csv file (4 specimens, landmarks 1-2) >> [image: sample_landmarkcsv.jpg] >> >> I successfully imported them into R geomorph, used estimate.missing with >> TPS, gpagen for Procrustes fit, and bilat.symmetry to look at the effects >> of size. However, I'm not happy with the precision of the landmark >> estimation (see screenshots of estimated landmarks-above and without >> estimated landmarks-below). >> >> [image: landmarks_procrustes_Page_2.jpg] >> [image: landmarks_procrustes_Page_3.jpg] >> I'd like to try Morpho for estimating landmarks considering bilaterial >> symmetry with fixLMmirror, but I'm not able to load my data into Morpho. >> ->When loading my TPS-formatted landmark file using readallTPS, I get the >> error: Error in if (nLM[i] > 0) { : missing value where TRUE/FALSE needed. >> ->When loading landmark csv file using readLandmarks.csv, I get the >> error: Error in dimnames(arr) <- list(rown, c("X", "Y", "Z")) : length of >> 'dimnames' [2] not equal to array extent. >> -->I assumed the 2nd error means that XYZ coordinates for each landmark >> should be combined in the csv file, so I reformatted the data (screenshot >> below) and tried again. >> [image: sample_landmarkcsv2.jpg] >> -->New error: Error in h(simpleError(msg, call)) : error in evaluating >> the argument 'x' in selecting a method for function 'as.matrix': undefined >> columns selected >> >> *Summary* >> I am not sure why my TPS-formatted landmark file isn't working with >> Morpho, because it looks like all examples I've seen and works in geomorph. >> I also haven't been able to find a sample landmark csv dataset to compare >> with. >> *->Does anyone have small sample datasets of either they could share with >> me or show me screenshots of?* >> >> PS I also tried LOST, but am having some problems with dependencies and >> my R version so I'd prefer to use Morpho. >> >> Thanks in advance, >> >> Katie >> >> -- >> 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 [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/morphmet2/6fd8ba69-18fb-4103-a1df-de22b8642cbdn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/morphmet2/6fd8ba69-18fb-4103-a1df-de22b8642cbdn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > > > -- > Antonio Profico > PhD > Palaeohub – Department of Archaeology > University of York > > morphomap: https://twitter.com/morphomap > twitter: https://twitter.com/ProficoA > > > > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/772445e6-304a-473e-972b-e2bf2cb7df91n%40googlegroups.com.
