Re: [MORPHMET] Re: Digitizing landmarks on live larvae

[andrea cardini]

I start with a "disclaimer" (and many apologies!): I read only the last 
two messages (by Jim and Carmelo), as I am stuck with teaching in this 
period.


I'd like only to suggest a reference on N vs the number of variables (in 
morphometrics but not necessarily only in this field). It's a difficult 
but very important and most interesting paper on this issue:
Bookstein, 2017, Evolutionary Biology: A Newly Noticed Formula Enforces 
Fundamental Limits on Geometric Morphometric Analyses

DOI 10.1007/s11692-017-9424-9

Cheers

Andrea

On 14/03/18 04:05, 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 
Date: 3/12/18 9:51 PM (GMT-10:00)
To: MORPHMET 
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
  

Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae

[Avi Koplovich]

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  
> Date: 3/12/18 9:51 PM (GMT-10:00) 
> To: MORPHMET  
> 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 
>> > 

RE: [MORPHMET] digitizing very variable leaves

['Tina Klenovšek' via MORPHMET]

Thanks to everyone who answered.

Dear Dr. Rohlf,
I assumed great variability would be a problem.
I was thinking the best way of digitizing would be to draw a curve on the 
outline of each leaf (simple and lobed leaves). Resample curves by length with 
approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf 
tip and base, would be fixed others could be defined as semi-landmarks. Is this 
sensible?
Alternatively, we could analyse simple and lobed leaves separately.
Thank you a lot for your help.

Tina


From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu]
Sent: Wednesday, March 14, 2018 3:59 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves

An assumption of the usual GMM methods is that shape variation is "small". I 
think these leaves exceed this quite a bit! Another problem is landmarks. How 
to match leaves with and without lobes?

__
F. James Rohlf, Distinguished Prof. Emeritus
Dept. Anthropology and Ecology & Evolution
Stonybrook University

 Original message 
From: 'Tina Klenovšek' via MORPHMET 
Date: 3/12/18 10:56 AM (GMT-10:00)
To: morphmet@morphometrics.org
Subject: [MORPHMET] digitizing very variable leaves

Hello everyone,

we would like to digitize tree leaves that are very variable (from simple oval 
to strongly lobed on one tree).

1.)I am wondering if TpsDig can do some kind of automatic digitizing like 
the LeafAnalyser software: 
http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes 
a defined number of landmarks on the leaf outline...

LeafAnalyser does not seem flexible or precise enough. Or I can’t use it 
properly. Any experience?


2.)Is it possible/sensible to put objects that are so differently shaped 
(photos attached) into the same group or is it better to analyse simple and 
lobed leaves separately?


I apologize if similar questions have been already answered...

Kind regards,
Tina







[cid:image002.jpg@01D3BA4C.D9433EA0]

doc. dr. Tina Klenovšek, koordinatorica doktorskega
študijskega programa Ekološke znanosti
Univerza v Mariboru | University of Maribor
Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija
T: +386 41 808 366
E: tina.klenov...@um.si, 
www.fnm.um.si



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