Hi, Thank you both! I asked this question since I guess that deciding on how many semi-landmarks I can digitize isn't only a matter of how complex the specimen is, or my willing to estimate missing data (Gunz & Mitteroecker, 2013), but also the number of specimens I posses. So just to clarify Jim's answer: 2p-4 means that having for instance 300 specimens I can use a total of 154 landmarks in 2D? Thanks, Avi
On Wednesday, March 14, 2018 at 5:06:03 AM UTC+2, f.james.rohlf wrote: > > Actually the rule is that the number of specimens should be larger than > the number of variables 2p-4 not p landmarks in the case of 2D data. > > > > __________________ > F. James Rohlf, Distinguished Prof. Emeritus > Dept. Anthropology and Ecology & Evolution > Stonybrook University > > -------- Original message -------- > From: Carmelo Fruciano <c.fru...@unict.it <javascript:>> > Date: 3/12/18 9:51 PM (GMT-10:00) > To: MORPHMET <morp...@morphometrics.org <javascript:>> > Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae > > Dear Avi, > > I guess it's hard to formulate any rule of thumb. > > Some analyses might not be defined if the number of variables exceed the > number of observations. Some other analyses might be defined (there is many > distance-based analyses nowadays which circumvent that problem). > > However, whether a given analysis is defined doesn't mean that the > inference is necessarily accurate. I guess it depends on what you plan to > test/measure and the effect size you expect. > > > Andrea Cardini has some papers that can give you some hint on this, such > as: > > Cardini & Elton 2007 - Zoomorphology > > Cardini et al. 2015 - Zoomorphology > > Cardini & Elton 2017 - Hystrix > > They should be downloadable from his website > https://sites.google.com/site/alcardini/home/pubs > > > Obviously, having an idea of variation on your own data would be better. > I hope this helps. > Carmelo > > > > > On 3/12/2018 8:27 PM, Avi Koplovich wrote: > > Hi Carmelo, > Thank you for those answers. > One more question please: > I know that the number of specimens should exceed the number of the total > landmarks (fixed-landmarks + semi-landmarks). Is there a rule of thumb of > by how much or what ratio between specimens to semi-landmarks one should > keep? > > Thank you, > > Avi > > On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote: >> >> >> >> Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto: >> > Hi Carmelo, >> > Thank you for your answer. >> > My project tests for the influence of kairomones of a predator fish on >> > the morphology of Salamander larvae during its development. To do this, >> > I take pictures every other week of larvae spawned from six different >> > females and assigned to 3 treatments: No fish, 3 caged fish, 6 caged >> fish. >> >> Hi Avi, >> it sounds like an interesting experiment. I will try to answer to your >> questions but keeping in mind that I'm not very knowledgeable on >> salamander development. >> >> > 1. I intend to use landmark 1 (dorsal connection of the tail fin) as a >> > fixed factor. But I thought I may be able to use the tail tip >> > (landmark 20) and head tip (landmark 48) as fixed landmarks as >> well. >> > Do you think it's ok in an ontogeny experiment? >> >> I guess it will depend on how long into ontogeny you will track the >> larvae and whether or not that point will "disappear" over ontogeny >> and/or slide unreasonably (depends also on your question). You, being >> knowledgeable on their biology, are the best judge on that. >> >> > If not, do you think >> > it's ok to slide all semi-landmarks of the tail on landmark 1, and >> > all head semi-landmarks on an eye landmark? Since the eye isn't >> part >> > of the head contour, is it ok if I slide one semi-landmark to the >> > eye and all rest semi-landmarks of the head one to each other as a >> > closed shape? >> >> The point(s) slid relative to the eye won't be sliding along the >> direction tangent to the curve you want to approximate (i.e., the >> curvature of the head). A good starting point on the method could be >> Gunz & Mitteroecker 2013 - Hystrix >> >> > 2. Is it ok if landmarks 1 and 39 slid relative to each other as well >> > as 41 and 55, since both describe a closed shape? >> >> It's not particularly desirable (see answer above). >> >> > 3. Another worry I have is that landmark 40 which I used to create the >> > comb fan for both the tail and the head is too far from both of >> them >> > so it doesn't bypass the bending. >> > 4. I'm affraid I don't fully understand why landmark 40 can not be >> > treated as a fixed landmark. In the book of Zelditch 2004, she says >> > that one of the basic differences between fixed-landmark and >> > semi-landmark is the degree of freedom, while fixed has two because >> > it is docked on both X and Y axes while semi only on one of them >> > (depending on the nature of the specific fan). Please correct me if >> > I'm wrong, but what if I use the side line of the larvae (which is >> > an anatomical/homologous feature) as my X axis and use the Y >> > component of landmark 1 (dorsal connection of the tail fin) to dock >> > landmark 40 on the Y axis? Is it wrong because of the dependency of >> > landmark 40 on landmark 1 regarding the Y coordinate? >> >> I think Don has covered these two very well. >> >> > 5. Emma Sherratt told me she straightened the bent tail-body using TPS >> > software in her paper Sherratt et al. 2017 - Nature ecology & >> > evolution. In the supplementary material of her paper she wrote: >> > "To correct for dorso-ventral bending in the landmark >> configurations >> > (caused by the joint of the tail with the head/body), we used the >> > ‘unbend specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The >> > landmark configurations for each specimen were transformed using >> the >> > quadratic approach, straightening from the eye (1) along the >> > notochord landmarks (46 to 55) to the tip of the tail (8)." >> > Jim mentioned this unbending function here before. I read the help >> > about unbending specimens and thought I can use landmarks 20 (tail >> > tip), 48 (head tip) and several semi-landmarks I can digitize using >> > the comb fan (equally spaced) along the side line of the larvae, in >> > order to create the quadratic curve (while the side line "helper" >> > semi-landmarks can be later omitted from the dataset - I saw >> > Fruciano et al. 2016). Does this sound good? >> > I bet that this can basically solve the problems I mentioned in 3 & >> > 4, since then I can digitized the whole body contour. >> >> That function is great but, as everything, relies on a set of >> assumptions (see also Fruciano 2016 - Development Genes and Evolution >> for a brief discussion). In your case: >> - that you can consistently identify those points along an hypothetical >> line (which you would remove after the unbending) >> - that your arching is well represented by the chosen function >> >> You are the best judge on whether these assumptions are satisfied in >> your case or not. >> I suggested the Valentin et al. (2008 - Journal of Fish Biology) >> approach because it's more flexible (less stringent assumptions, which >> obviously doesn't mean assumption-free) and therefore more generally >> applicable. But, of course, the approach in tpsUtil can be a great >> solution if it's appropriate to your data. >> >> Best, >> Carmelo >> >> > -- 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.
