Re: [MORPHMET] Landmarks coming up funny in MorphoJ

[Guido Rocatti]

Hi Candice,

I think that maybe you should try to organize both coordinate sets directly
using notepad or wordpad and saving the file as a .tps format file. Doing
so, you won't depend on the tpsUtil.
Also, I understand that you have missing data. You can try and estimate
those missing landmarks with the *estimate.missing *function of
the  geomorph package for R. It uses thin-plate spline to interpolate
landmarks, or a linear regression model to predict them (the method
election is up to you).
Once you managed to put both sets together and you obtained your missing
landmarks, you can export your new dataset and open it on MorphoJ.
Hope this helps somehow.

Good Luck.


Guido Rocatti
Lic. en Antropología.
División Antropología, Facultad de Ciencias Naturales y Museo.
Universidad Nacional de La Plata.
CONICET



Libre
de virus. www.avg.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [MORPHMET] Landmarks coming up funny in MorphoJ

[K. James Soda]

Dear Ms. Neves,

Quick addition to Dr. Rohlf's solution.  To change a file extension on a
Windows machine, you will need to do the following:

1) Open a Windows Explorer window.
2) On the ribbon at the top of the window, click "View"
3) Click the box for "File Name Extensions" (in the "Show/Hide" section)

You can now edit the file extension (i.e., change .txt to .tps).

I apologize if that was obvious or if you are not using a Windows machine;
that's hung me up in the past.

Hope this helped,

James

On Mon, Nov 6, 2017 at 4:46 PM, f.james.rohlf <f.james.ro...@stonybrook.edu>
wrote:

> Let it save it as a txt file then just rename the file.
>
> -
> F. James Rohlf
> Depts. of Ecology & Evolution and of Anthropology
> Stony Brook University
>
>  Original message 
> From: Candice Neves <536...@students.wits.ac.za>
> Date: 11/6/17 12:59 PM (GMT-05:00)
> To: Guido Rocatti <guidoroca...@gmail.com>
> Cc: MORPHMET <morphmet@morphometrics.org>
> Subject: Re: [MORPHMET] Landmarks coming up funny in MorphoJ
>
> Hi Guido
>
> Thanks so much for the suggestion, I'll definitely do that. Is there a
> particular way to save a wordpad/notepad file as a .tps format file? I've
> tried to do this before but it kept saving as a .txt file, or would this
> still work?
>
> Thanks for the help
> Candice Neves
>
> On 6 November 2017 at 19:44, Guido Rocatti <guidoroca...@gmail.com> wrote:
>
>> Hi Candice,
>>
>> I think that maybe you should try to organize both coordinate sets
>> directly using notepad or wordpad and saving the file as a .tps format
>> file. Doing so, you won't depend on the tpsUtil.
>> Also, I understand that you have missing data. You can try and estimate
>> those missing landmarks with the *estimate.missing *function of
>> the  geomorph package for R. It uses thin-plate spline to interpolate
>> landmarks, or a linear regression model to predict them (the method
>> election is up to you).
>> Once you managed to put both sets together and you obtained your missing
>> landmarks, you can export your new dataset and open it on MorphoJ.
>> Hope this helps somehow.
>>
>> Good Luck.
>>
>>
>> Guido Rocatti
>> Lic. en Antropología.
>> División Antropología, Facultad de Ciencias Naturales y Museo.
>> Universidad Nacional de La Plata.
>> CONICET
>>
>>
>>
>> <http://www.avg.com/email-signature?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>>  Libre
>> de virus. www.avg.com
>> <http://www.avg.com/email-signature?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>> <#m_-6646032331324499958_m_7371067766444365814_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>
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Re: [MORPHMET] Landmarks coming up funny in MorphoJ

[f.james.rohlf]

Let it save it as a txt file then just rename the file.
-F. James RohlfDepts. of Ecology & Evolution and of 
Anthropology Stony Brook University 
 Original message From: Candice Neves 
<536...@students.wits.ac.za> Date: 11/6/17  12:59 PM  (GMT-05:00) To: Guido 
Rocatti <guidoroca...@gmail.com> Cc: MORPHMET <morphmet@morphometrics.org> 
Subject: Re: [MORPHMET] Landmarks coming up funny in MorphoJ 
Hi Guido
Thanks so much for the suggestion, I'll definitely do that. Is there a 
particular way to save a wordpad/notepad file as a .tps format file? I've tried 
to do this before but it kept saving as a .txt file, or would this still work?
Thanks for the helpCandice Neves
On 6 November 2017 at 19:44, Guido Rocatti <guidoroca...@gmail.com> wrote:
Hi Candice, 
I think that maybe you should try to organize both coordinate sets directly 
using notepad or wordpad and saving the file as a .tps format file. Doing so, 
you won't depend on the tpsUtil. Also, I understand that you have missing data. 
You can try and estimate those missing landmarks with the estimate.missing 
function of the  geomorph package for R. It uses thin-plate spline to 
interpolate landmarks, or a linear regression model to predict them (the method 
election is up to you).Once you managed to put both sets together and you 
obtained your missing landmarks, you can export your new dataset and open it on 
MorphoJ.Hope this helps somehow.
Good Luck.

Guido RocattiLic. en Antropología.División Antropología, Facultad de Ciencias 
Naturales y Museo.Universidad Nacional de La Plata.
CONICET

 

  
Libre de virus. www.avg.com 








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Re: [MORPHMET] Landmarks coming up funny in MorphoJ

[Candice Neves]

Hi Guido

Thanks so much for the suggestion, I'll definitely do that. Is there a
particular way to save a wordpad/notepad file as a .tps format file? I've
tried to do this before but it kept saving as a .txt file, or would this
still work?

Thanks for the help
Candice Neves

On 6 November 2017 at 19:44, Guido Rocatti  wrote:

> Hi Candice,
>
> I think that maybe you should try to organize both coordinate sets
> directly using notepad or wordpad and saving the file as a .tps format
> file. Doing so, you won't depend on the tpsUtil.
> Also, I understand that you have missing data. You can try and estimate
> those missing landmarks with the *estimate.missing *function of
> the  geomorph package for R. It uses thin-plate spline to interpolate
> landmarks, or a linear regression model to predict them (the method
> election is up to you).
> Once you managed to put both sets together and you obtained your missing
> landmarks, you can export your new dataset and open it on MorphoJ.
> Hope this helps somehow.
>
> Good Luck.
>
>
> Guido Rocatti
> Lic. en Antropología.
> División Antropología, Facultad de Ciencias Naturales y Museo.
> Universidad Nacional de La Plata.
> CONICET
>
>
>
> 
>  Libre
> de virus. www.avg.com
> 
> <#m_7371067766444365814_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>

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[MORPHMET] Landmarks coming up funny in MorphoJ

[Candice Neves]

Hi All,

I'm trying to analyze measurement error in MorphoJ but I'm running into a 
problem. When I digitized my landmarks I used tpsDIG2, however I had to 
organize those coordinates into a CSV. file because I digitized them in two 
separate .tps files and tpsUtil wouldn't allow me to open the one that required 
I delete some specimens I didn't landmark (I thus couldn't join the two files 
for analysis). So I collated them in a CSV. However, when I look at the 
outliers in MorphoJ the landmarks come out in a horizontal line instead of in 
the shape of a mandible. I can't analyze this. It doesn't seem to take the 
x,y-coordinate as coordinate pairs, from what I can see it places 26 landmarks 
in a horizontal line, instead of the 13 pairs I digitized. Anyone have any 
suggestions?

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