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

[f.james.rohlf]

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 

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

[Carmelo Fruciano]

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
>