-------- Original Message --------
Subject: Re: error in digitising landmarks
Date: Thu, 3 Feb 2011 18:12:26 -0500
From: Nicolas Jaramillo-O <[email protected]>
Reply-To: [email protected]
To: [email protected]
Dear Claudia.
The CLIC package (by Jean-Pierre Dujardin;
http://www.mpl.ird.fr/morphometrics/clic/index.html) has the VAR
module which computes the repeatability of two sets of measurements;
that is, it allows to know your precision by repeating two times the
same measurements on the same individuals, and calculating the
variance between them. You can see the repeatability value for
centroid-size, relative warps, and residual coordinates. From these
last you can know the worse landmarks.
sincerely yours,
sincerely yours,
Nicolas Jaramillo-O
2011/2/3 morphmet <[email protected]>:
-------- Original Message --------
Subject: RE: error in digitising landmarks
Date: Thu, 3 Feb 2011 16:05:36 -0500
From: Carmelo Fruciano <[email protected]>
To: [email protected]
morphmet <[email protected]> ha scritto:
-------- Original Message --------
Subject: RE: error in digitising landmarks
Date: Thu, 3 Feb 2011 15:00:52 -0500
From: Garrido-Varas, Claudia <[email protected]>
To: [email protected] <[email protected]>
Dear Carmelo,
Thank you very much for your email. I will try what you say.
Yes, I said reliable because the landmarks that I am using have been
chosen by myself, so, I want to test them and want to test my
personal error, and see that maybe I should use only the ones that
have the least error.
Well, the problem there is how you do set up a threshold to remove
certain landmarks and keep others. In the "exploratory" procedure I
suggested the decision of which landmarks should be removed is
subjective (nonetheless, it can be useful to have a look at those plots)
Once that I know I have picked up the proper landmarks I will
compare the shape change in different individuals, see if sex has an
impact and look at bilateral asymmetry.
Another thing that I would like to ask is if I need to have a scale,
because in the morhoJ program one never needs to input which pair of
landmarks are the ones of the scale, I get very confused in how
centroid size can be computed if I don't give the scale.
If you performed the digitization with TpsDig2, you can set up the
scale from there, using the appropriate part of the "Image Tools"
option (refer to the program manual, it's explained very well there).
If you save your data as a TPS file, this adds a SCALE line for each
specimen (assuming that you entered scale for each specimen), which
you can check by opening the TPS file with a text editor (such as
Windows Notepad). Then, if you wish to use MorphoJ you can import the
TPS containing the scale as a new dataset and perform the Procustes
superimposition there (calculating also centroid size; take a look at
the program guide that is online).
In your particular case, it sounds not particularly important to have
a scale and calculate centroid size because your dataset is currently
made of only one specimen and you are probably going to have a look at
plots of landmarks after superimposition. Moreover, using a single
picture the presence of the scale is not so important (it is important
when you deal with multiple specimens and then one picture is slightly
different than the next one so you can compute centroid size values
that are in the same units for all the specimens).
All the best
Carmelo
--
Carmelo Fruciano
Dipartimento di Biologia
University of Catania
Tel. +39 095 7306023
Cell. +39 349 5822831
e-mail [email protected]
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