[MORPHMET] geomorph problem with morphologika file
Dear all, I'm trying to read a morphologika formatted file into geomorph, but getting the following error message: read.morphologika(combodatatest.txt) Error in dimnames(coords)[[3]] - names : length of 'dimnames' [3] not equal to array extent I'm not sure how I've formatted the .txt file incorrectly as it looks in keeping with the geomorph manual example (my file is attached). Any suggestions would be gratefully received! Many thanks Jo -- Joanna Gooding MSc Student Palaeobiology and Biodiversity Research Group School of Earth Sciences, University of Bristol -- 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. [individuals] 5 [landmarks] 44 [Dimensions] 3 [names] BRI_JBL_34 BRI_JBL_69 BRI_JBL_77 BRI_JBL_113 BRI_JBL_49 [rawpoints] ‘BRI_JBL_34 -287.9 -99.1 155.1 -291.4 -19398.8 -290.3 -191.2 86.5 -290.9 -203.5 33.5 -290.4 -207.6 21.9 -300.2 -187.3 81.3 -303.9 -18378.8 -321.5 -185.4 59.1 -335.9 -172.3 78.2 -322.7 -182.8 88.5 -345.9 -154.6 55.1 -282.4 -187.6 80.8 -278.6 -185.2 78.7 -263.4 -190.1 58.2 -244.4 -179.8 78.9 -256.5 -188.5 88 -233.4 -162.6 51.5 -234.4 -153.5 84.6 -227.2 -138.4 80.5 -225.7 -49.8 109 -349.4 -49.6 114 -230.5 -49.7 32.4 -281.8 2 77.5 -336-48.9 36.5 -346.1 -131.1 80.5 -342.7 -142.9 86.5 -291.8 -195.4 20.8 -290.9 -161.7 25.5 -289.6 -157.1 24.2 -328.7 -159.9 55.4 -335.6 -171.3 32.3 -349.1 -147.3 44.4 -331.8 -102.6 33.7 -315.7 -103.2 28.5 -340.6 -99.6 19.4 -286.3 -30 15.1 -293.3 -68.6 8.2 -289.9 -101.8 23.8 -242.1 -100.5 11.4 -266.8 -103.8 29.8 -254.1 -102.7 23.7 -232.5 -146.2 35.7 -246.9 -172.7 28.4 -253.7 -160.7 51.9 ‘BRI_JBL_69 -278.9 -110.4 173.9 -279.8 -212.6 116 -280.2 -212.8 101.6 -280.2 -222.1 46 -280.1 -22532.7 -287.2 -210.1 96.7 -294.5 -203.5 89 -310.2 -205.7 71 -328.8 -19189 -313.7 -201.6 102.4 -340.8 -172.5 64.8 -272.5 -209.7 96.6 -266.2 -204.5 86.9 -254.7 -207.9 72.1 -229.6 -193.6 90 -242.7 -203.3 102.5 -222.6 -175.8 68.2 -222.7 -161107.7 -215.8 -142.2 101 -209.5 -67.2 120.2 -352.3 -69.5 122.3 -220.9 -69.3 41.8 -278.1 -10 92.4 -332.5 -73.8 42.1 -342-139.5 102.9 NA NA NA -284.6 -210.9 36 -284.1 -185.8 36.7 -283.2 -176.8 33.4 -319-177.4 64.7 -327.6 -190.5 40.5 -342.2 -163.4 50.3 -317.8 -127.2 28.1 -303.5 -130.9 43 -334.9 -124.6 14.8 -280.6 -54.2 15 -283.3 -101.4 17.4 -282.6 -125.4 24.2 -232.9 -120.1 17 -260.1 -129.8 38.1 -248.5 -126.8 34.2 -218-161.2 53.9 -234.9 -189.4 42.9 -244.5 -173.8 66.7 ‘BRI_JBL_77 -279.4 -72.3 161.5 -284-175.2 109.4 -286-177.3 94.1 -288.8 -190.8 41.7 -289.9 -194.9 30.8 -292.3 -175.7 87.6 -296.9 -17084.6 -313.9 -170.7 64.8 -332.9 -154.6 85.1 -318.2 -164.3 100.2 -340.6 -139.3 58.3 -280.3 -177.5 86.8 -275.6 -171.4 82 -265.3 -174.5 64 -240.1 -162.9 81.1 -250.8 -169.1 96.9 -232.6 -140.8 50.6 -227-133.1 87.5 -222.5 -121.1 85.7 -213.6 -39.6 101.8 -342-31.4 110.8 -229.2 -48.8 30.6 -269.5 10.274.5 -329.8 -46.9 36.1 -344.5 -105.8 89.5 -341.6 -119.2 95.3 -291.8 -179.6 31.1 -288.6 -150.5 36.8 -288.4 -146.7 35.3 -317.9 -144.4 58.6 -328.1 -158.3 39.1 -339.3 -127.6 44.6 -322-90.9 30.2 -306-92.7 36.7 -331.1 -85.7 21.1 -276.9 -33.2 9.5 -282.5 -74.6 11.9 -283.5 -100.3 30.3 -238.7 -94.1 14.1 -268.7 -99 36.6 -251.7 -99.7 28.2 -235.1 -135.1 35 -250.5 -164.2 31 -256-15153.7 ‘BRI_JBL_113 -278.2 -83.1 165.6 -282.5 -173.7 115.4 -281.1 -174.7 99.5 -286.5 -198.1 43.8 -286.8 -20434.1 -290.9 -172.4 95.1 -295.9 -166.4 87.9 -314-17173.4 -333.2 -155.7 91 -318.5 -165.4 102.6 -348-139.4 67.2 -276.3 -173.3 93.9 -270.9 -168.6 86.1 -259.2 -174.1 73.6 -232.8 -163.5 88.1 -244.3 -170.4 99.5 -224.2 -146.5 64.1 -224.3 -132.8 96.6 -221-119.6 93 -218.7 -31.9 107.6 -339.9 -35.2 123.7 -223.8 -39 40.4 -274.1 14.487.4 -337.2 -31.6 44 -342-111.5 95.3 -340-118.7 99.8 -288.6 -185.3 34.7 -286-153.5 36.4 -285.3 -145.8 34.5 -319.9 -142.8 70.3 -335.1 -160.5 46.8 -349.4 -131.3 53.8 -324.9 -85.1 42.3 -311.3 -88.7 46.4 -341-77.4 22 -283.5 -15 20.4 -283.6 -49.5 17.4 -283.5 -87.8 27 -231.4 -84.5 15.2 -261.8 -92.6 39.4 -245.3 -91.3 33.2 -222.5 -13945.5 -239.4 -169.3 43.5 -248.3 -147.6 62.5 ‘BRI_JBL_49 -288.4 -92.8 155.3 -295.3 -184.5 110.6 -297-188.2 94.3 -300.3 -203.3 43.4 -301.7 -207.4 30 -304-185.1 89.3 -308.4 -179.6 85.4 -325.5 -181.4
RE: [MORPHMET] Suggestions for geomorph
Thank you Mauro for the suggestions. Indeed, as you surmise, digitizing within R is not at all straightforward, but we will do our best to improve the experience for users of geomorph. Best, Dean Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University www.public.iastate.edu/~dcadams/http://www.public.iastate.edu/~dcadams/ phone: 515-294-3834 From: Mauro Cavalcanti [mailto:mauro...@gmail.com] Sent: Monday, June 8, 2015 3:59 PM To: MORPHMET Subject: [MORPHMET] Suggestions for geomorph Dear members of the geomorph Development Team, I have been using the digitize2d() function of the geomorph R package to obtain landmark coordinates from my fish specimens.It works fine, but I respectfully have two suggestions for its improvement. First one is quite simple: when end of file is reached and the last specimen has been digitized, the function stops with one of those ugly and arcane error messages (well, all programming languages generate ugly and arcane error messages! ;-)). This should not happen; instead, the function should issue a user-friendly warning, like End of file, Last specimen (or perhaps something less friendly, like Can't you see you have reached the end of file, you moron? ;-)) Second suggestion may be more difficult to implement, but if it can be done, it would provide a great improvement: the ability to edit a previoulsly created file. Currently, the function detects the specimens without landmark coordinates and starts digitizing from this specimen on; if all specimens have already landmark coordinates, then the function stops with the same ugly error messages referred to above. It would be really great if one could see each specimen with the superimposed digitized landmarks, one by one, so that landmarks could be checked, added, or deleted. Hope this helps! With warmest regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.commailto: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.orgmailto: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: [R-sig-phylo] [MORPHMET] Re: Stability of p-values (physignal and testing for morphological integration)
Yes that is more precise. In my post to the query I only noted that the variance in significance levels across multiple permutation tests decreases as the number of iterations increases. Joe's post provides the equation for the expected value of that variance; mine provided reference to an empirical example (Adams and Anthony, 1996). Dean Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University www.public.iastate.edu/~dcadams/ phone: 515-294-3834 -Original Message- From: R-sig-phylo [mailto:r-sig-phylo-boun...@r-project.org] On Behalf Of Joe Felsenstein Sent: Monday, June 8, 2015 1:29 AM To: Dennis E. Slice; r-sig-phylo mailman Subject: Re: [R-sig-phylo] [MORPHMET] Re: Stability of p-values (physignal and testing for morphological integration) A number of people have suggested that P values should stabilize after a number of samples (in a permutation test) that depends on the data set. I suspect that these were unintended misstatements. As Dennis Slice has mentioned, one can regard each permutation in the permutation test as a random sample from a distribution. Comparing a test statistic X to its value in the data (say, Y), each permutation draws from a distribution in which there is a probability P that X exceeds Y. So each permutation is (to good approximation) a coin toss with probability P of Heads. There obviously no number of tosses beyond which the fraction of Heads stabilizes. The fraction of heads after N tosses will depart from the true value P by an amount which has expectation 0, and variance P(1-P)/N. This is a fairly slow approach of the fraction of Heads to the true value. So to get twice as close to the true P value, one needs 4 times as many permutations. And this need for more and more samples continues indefinitely. There is no sudden change as one reaches a threshold number of permutations. But that's what you really meant, right? Joe --- Joe Felsenstein j...@gs.washington.edu [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - r-sig-ph...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.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] geomorph problem with morphologika file
Jo, There were two issues with the file. First, you had single curly quotes in front of the specimen names. These should be simple ascii character quotes instead. Second, you had missing data in one of the specimens. For downstream analyses in geomorph that is fine, but at present the read.morphologika function does not handle these. The immediate solution is to replace these with -, then read the file, and then replace them back to ‘NA’ within R. You can then estimate the missing landmark locations using the ‘estimate.missing’ function in geomorph, and continue with your other analyses. Note that in the next version of geomorph we will add the ability to read missing data directly from morphologika files, as is possible when reading TPS files. Thank you for bringing this oversight to our attention! Best, Dean Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University www.public.iastate.edu/~dcadams/http://www.public.iastate.edu/~dcadams/ phone: 515-294-3834 From: Jo Gooding [mailto:jg1753.2...@my.bristol.ac.uk] Sent: Monday, June 8, 2015 1:39 PM To: morphmet@morphometrics.org Subject: [MORPHMET] geomorph problem with morphologika file Dear all, I'm trying to read a morphologika formatted file into geomorph, but getting the following error message: read.morphologika(combodatatest.txt) Error in dimnames(coords)[[3]] - names : length of 'dimnames' [3] not equal to array extent I'm not sure how I've formatted the .txt file incorrectly as it looks in keeping with the geomorph manual example (my file is attached). Any suggestions would be gratefully received! Many thanks Jo -- Joanna Gooding MSc Student Palaeobiology and Biodiversity Research Group School of Earth Sciences, University of Bristol -- 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.orgmailto: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: [R-sig-phylo] [MORPHMET] Re: Stability of p-values (physignal and testing for morphological integration)
If the expectation of the empirical estimator for mean p-value is a function of the number iterations that becomes asymptotically unbiased, then this would explain the simulation results (attachment in the original posting), since for small number of iterations, some bias would remain, and only disappear (hence the stabilization feeling) when number of iterations is large. Thanks again for all for clarifying the issue. On Tuesday, June 9, 2015 at 7:04:52 AM UTC+8, dcadams wrote: Yes that is more precise. In my post to the query I only noted that the variance in significance levels across multiple permutation tests decreases as the number of iterations increases. Joe's post provides the equation for the expected value of that variance; mine provided reference to an empirical example (Adams and Anthony, 1996). Dean Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University www.public.iastate.edu/~dcadams/ phone: 515-294-3834 -Original Message- From: R-sig-phylo [mailto:r-sig-phy...@r-project.org javascript:] On Behalf Of Joe Felsenstein Sent: Monday, June 8, 2015 1:29 AM To: Dennis E. Slice; r-sig-phylo mailman Subject: Re: [R-sig-phylo] [MORPHMET] Re: Stability of p-values (physignal and testing for morphological integration) A number of people have suggested that P values should stabilize after a number of samples (in a permutation test) that depends on the data set. I suspect that these were unintended misstatements. As Dennis Slice has mentioned, one can regard each permutation in the permutation test as a random sample from a distribution. Comparing a test statistic X to its value in the data (say, Y), each permutation draws from a distribution in which there is a probability P that X exceeds Y. So each permutation is (to good approximation) a coin toss with probability P of Heads. There obviously no number of tosses beyond which the fraction of Heads stabilizes. The fraction of heads after N tosses will depart from the true value P by an amount which has expectation 0, and variance P(1-P)/N. This is a fairly slow approach of the fraction of Heads to the true value. So to get twice as close to the true P value, one needs 4 times as many permutations. And this need for more and more samples continues indefinitely. There is no sudden change as one reaches a threshold number of permutations. But that's what you really meant, right? Joe --- Joe Felsenstein j...@gs.washington.edu javascript: [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - r-sig...@r-project.org javascript: https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya (Mesej) adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. DISCLAIMER: This e-mail and any files transmitted with it (Message) is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of University of Malaya shall be understood as neither given nor endorsed by any of the forementioned. -- 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] 2D Capture Protocol for mostly 2D specimens
Zack Daugherty zackdaughe...@gmail.com ha scritto: Hello all, This is my first time wading into geometric mophometry as a PhD candidate. First off the project: I plan to track geometric morphometry data of Nassau grouper we have raised in the lab. There are some 130 juveniles that are now capable of being anesthetized and handled. I plan to gather data down to the individual level for this cohort monthly to establish data on individual ontogenetic trajectories. But I have some questions regarding 2D capture, because *once I start this there is no going back*. The welfare of these animals supercedes the morphometry work I have planned (these fish will be used for future broodstock at our aquaculture facility). [cut] Questions: Any other protocols that people are aware of I should look at for digital capture? Dear Zack, if I was you, I would also think about the advantages/disadvantages of anesthesia. I have used it in certain situations but, depending on what your downstream application and target speies are, sometimes one can get away with not anestesizing fish (certain species, especially when raised in captive conditions, even let you pin them to extend their fins). Considering that you stated that welfare of the fish is particularly important for you, that's the first thing that came to mind. Also, this is probably very obvious, pay attention to keeping the fish straight (i.e. limit dorso-ventral arching). This kind of artifact will still probably present in your data, but it's good to try limiting it at its source. Your fish species is not extremely elongated so it's probably not going to be a very strong problem. Should I surround my specimens in black material? In my opinion, probably not if they are mostly grey as the specimen in the picture... Should I purchase any white balance card sets? I guess it depends how important is color to you... Would a grid backdrop be neccessary for every photo behind the specimen or just to initially calibrate a field a view before photographing specimens? In my opinion, the most important part is having some sort of scale in the picture, possibly not too far from the specimen. Well, that's my two cents, I hope this helps... Best, Carmelo -- Carmelo Fruciano Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- 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.
