Re: [MORPHMET] MorphoJ Text File Formatting

[Carmelo Fruciano]

Alicja Witwicka  ha scritto:


Hello everyone,
I am a complete beginner in geometric morphometrics and I have met  
one problem. Namely, when I try to upload the .tps file created in  
tpsUTIL to MorphoJ software I receive the following communicate:


"Problem with the text file: Line 1 contains less than two entries:
LM=7
Note: A frequent reason for this problem is that the file contains  
delimiters other than commas or tab stops.

Errors occurred in the reading process.
The new dataset could not be created."

I have tried to change the data manually but it does not work.  
Anyway, I have too many specimens to manage that in such a way. Do  
you possibly know where I can find the source of that problem?


Hi Alicja,
Did you select the appropriate format in the import window?
To my understanding, you would get that error if you were importing a  
file in TPS format but you had left the default "text" selected,  
instead of switching to TPS under "File Types" on the "Create new  
dataset" menu.

I hope this helps.
Best,
Carmelo


--
Carmelo Fruciano
Postdoctoral Fellow - Queensland University of Technology - Brisbane,  
Australia

Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/

--
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.

Re: [MORPHMET] curve analysis

[Carmelo Fruciano]

Ioannis Maniakas  ha scritto:

Hello everyone. As I am new in the field of the geometric  
morphometrics, I am expressing my naive problem..
I am trying to analyze differences in the shape of two simple  
separate curves. These describe the radii of circles fitting to the  
condylar margins on the proximal and distal articular surfaces of  
the medial astragalar side respectively.
I think I have followed the standard procedure. The recorded curves  
were resampled (always from a common homologous starting and ending  
position), granting the same number of evenly spaced 50 points (“by  
length” option in tpsDig) across all specimens.


I would double-check that corresponding points across different  
specimens sample the same structure.


Afterwards, the operation of converting into landmarks was conducted  
with the employment of the tpsUtil program resulting in 50 landmark  
configurations.
So, my question is this: can I import their coordinates into Morphoj  
or even Past and ran  the whole analysis there, including the  
superimposition? Or do I have to treat these data in an other way?


No. If these are, in fact, semilandmarks, these should be treated  
accordingly (sliding).


I have tried to make a slider file for both curves (2 landmarks at  
the two ends of the curves and 48 sliding landmarks between). As I  
load these nts files with the tps file with my 50 lanmarks in  
tpsrelw and perform the analysis there, the consensus and the rest  
results are wrong. More specifically, the position of landmarks has  
changed dramatically, as some of them have overslided and there are  
not placed equidistantly.


I would check different criteria for sliding (menu Options of tpsRelW).
Also, there are various discussions of criteria and relative  
advantages you might want to consult, such as

Perez et al 2006 - Journal of Anatomy
Gunz & Mitteroecker 2013 - Hystrix
To memory, the latter explicitly discusses a case which sounds similar  
to yours.



Also, it  seems that right and left specimens are not getting aligned at all.


I guess I would align them separately (unless you want to reflect and  
relabel one of the two sides prior to superimposition, which I imagine  
you'd have to do "manually"/scripting).


This was not the case, when I simply treated them as typical  
landmarks in morphoj..


That is because the Procrustes fit in MorphoJ includes reflection. You  
can find a description of this in the MorphoJ user guide.


I hope this helps,
Carmelo


--
Carmelo Fruciano
Postdoctoral Fellow - Queensland University of Technology - Brisbane,  
Australia

Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/

--
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.

Re: [MORPHMET] MorphoJ Text File Formatting

[Alicja Witwicka]

Dear Colleagues,
Thank for your help! The problem was with dots and commas, I have found the
proper function in tpsDIG. No everything is ok.

All the best,
Alicja Witwicka

On Wed, Apr 26, 2017 at 1:54 AM, Carmelo Fruciano 
wrote:

>
> Alicja Witwicka  ha scritto:
>
> Hello everyone,
>> I am a complete beginner in geometric morphometrics and I have met one
>> problem. Namely, when I try to upload the .tps file created in tpsUTIL to
>> MorphoJ software I receive the following communicate:
>>
>> "Problem with the text file: Line 1 contains less than two entries:
>> LM=7
>> Note: A frequent reason for this problem is that the file contains
>> delimiters other than commas or tab stops.
>> Errors occurred in the reading process.
>> The new dataset could not be created."
>>
>> I have tried to change the data manually but it does not work. Anyway, I
>> have too many specimens to manage that in such a way. Do you possibly know
>> where I can find the source of that problem?
>>
>
> Hi Alicja,
> Did you select the appropriate format in the import window?
> To my understanding, you would get that error if you were importing a file
> in TPS format but you had left the default "text" selected, instead of
> switching to TPS under "File Types" on the "Create new dataset" menu.
> I hope this helps.
> Best,
> Carmelo
>
>
> --
> Carmelo Fruciano
> Postdoctoral Fellow - Queensland University of Technology - Brisbane,
> Australia
> Honorary Fellow - University of Catania - Catania, Italy
> e-mail c.fruci...@unict.it
> http://www.fruciano.it/research/
>
> --
> 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.
>
>

-- 
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.

[MORPHMET] Re: MorphoJ Text File Formatting

[Daniel Jager]

Can you post the entire string from the first specimen?

On Tuesday, April 25, 2017 at 7:38:51 AM UTC-7, Alicja Witwicka wrote:
>
> Hello everyone, 
> I am a complete beginner in geometric morphometrics and I have met one 
> problem. Namely, when I try to upload the .tps file created in tpsUTIL to 
> MorphoJ software I receive the following communicate: 
>
> "Problem with the text file: Line 1 contains less than two entries: 
> LM=7 
> Note: A frequent reason for this problem is that the file contains 
> delimiters other than commas or tab stops. 
> Errors occurred in the reading process. 
> The new dataset could not be created." 
>
> I have tried to change the data manually but it does not work. Anyway, I 
> have too many specimens to manage that in such a way. Do you possibly know 
> where I can find the source of that problem? 
>
> Best regards, 
> Alicja 

-- 
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.

Re: [MORPHMET] MorphoJ Text File Formatting

[Hugo Benítez]

Dear Alicja

This problem is normal when you are trying to open a file that was
digitized in TPS Dig in MorphoJ and when you are creating the project, you
DID NOT select the option TPS  in filetype...

By default MorphoJ when you create a new dataset the filetype is text,
change it for TPS and the problem should be solve!

Let me know if you have any problem later.

Best wishes

Hugo

2017-04-25 4:43 GMT-03:00 Alicja Witwicka :

> Hello everyone,
> I am a complete beginner in geometric morphometrics and I have met one
> problem. Namely, when I try to upload the .tps file created in tpsUTIL to
> MorphoJ software I receive the following communicate:
>
> "Problem with the text file: Line 1 contains less than two entries:
> LM=7
> Note: A frequent reason for this problem is that the file contains
> delimiters other than commas or tab stops.
> Errors occurred in the reading process.
> The new dataset could not be created."
>
> I have tried to change the data manually but it does not work. Anyway, I
> have too many specimens to manage that in such a way. Do you possibly know
> where I can find the source of that problem?
>
> Best regards,
> Alicja
>
> --
> 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.
>



-- 

*Dr. Hugo A. Benítez*
Departamento de Recursos Ambientales
Facultad de Ciencias Agronómicas
Universidad de Tarapacá

Research Associate, University of Cambridge Museum of Zoology
External Researcher Faculty of Agriculture, University of Zagreb

website: http://www.morphoshape.com 
workphone: +56582386136

-- 
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.

[MORPHMET] WORK SHOP - Geometric morphometrics using R - Dean Adams, Michael Collyer, Antigoni Kaliontzopoulou

[Oliver Hooker]

 

Geometric morphometrics using R (GMMR01)

19th - 23rd February 2018 at Margam discovery centre, Wales, UK.

http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

Places 1-10 are priced at £500 per person, 11-20 are £550 per person and 
21-30 are £600 per person.

Course overview: The field of geometric morphometrics (GM) is concerned 
with the quantification and analysis of patterns of shape variation, and 
its covariation with other variables. Over the past several decades these 
approaches have become a mainstay in the field of ecology, evolutionary 
biology, and anthropology, and a panoply of analytical tools for addressing 
specific biological hypotheses concerning shape have been developed. The 
goal of this is to provide participants with a working knowledge of the 
theory of geometric morphometrics, as well as practical training in the 
application of these methods.

The course is organized in both theoretical and practical sessions. The 
theoretical sessions will provide a comprehensive introduction to the 
methods of landmark-based geometric morphometrics, which aims at providing 
the participants with a solid theoretical background for understanding the 
procedures used in shape data analysis. Practical sessions will include 
worked examples, giving the participants the opportunity to gain hands-on 
experience in the treatment of shape data using the R package geomorph. 
These sessions focus on the generation of shape variables from primary 
landmark data, the statistical treatment of shape variation with respect to 
biological hypotheses, and the visualization of patterns of shape variation 
and of the shapes themselves for interpretation of statistical findings, 
using the R language for statistical programming. While practice datasets 
will be available, it is strongly recommended that participants come with 
their own datasets.

Note: Because this is a geometric morphometrics workshop in R, it is 
required that participants have some working knowledge in R. The practical 
sessions of the course will focus on GM-based analyses, and not basic R 
user-interfacing. It is therefore strongly recommended that participants 
refresh their R skills prior to attending the workshop.

If you have any questions please feel free to email 
oliverhoo...@prstatistics.com alternatively you canfind out more details 
and/or book using the link below

http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01

 

1.   ADVANCING IN STATISTICAL MODELLING FOR EVOLUTIONARY BIOLOGISTS AND 
ECOLOGISTS USING R #ADVR

17th – 21st April 2017, Scotland, Dr. Luc Bussiere, Dr. Ane Timenes Laugen

*http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr06/*
 


 

2.   MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE

19th – 23rd June, Canada, Prof. Subhash Lele, Dr. Peter Solymos

*http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/*
 


 

3.   TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME

26th – 30th June, Canada, Dr. Andrew Parnell

*http://www.prstatistics.com/course/time-series-models-foe-ecologists-tsme01/* 


 

4.   META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES 
#METR01

24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena Kulinskaya

*http://www.prstatistics.com/course/meta-analysis-in-ecology-evolution-and-environmental-sciences-metr01/*
 


 

5.   SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE

7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James 
Grecian

*http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/*
 


 

6.   ECOLOGICAL NICHE MODELLING USING R #ENMR

16th – 20th October 2017, Scotland, Dr. Neftali Sillero

*http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/* 


 

7.   GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR

23rd – 27th October, Wales, Dr. Thibaut Jombart, Zhian Kavar

*http://www.prstatistics.com/course/genetic-data-analysis-exploration-using-r-gdar03/*
 


 

8.   STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY 
BIOLOGISTS USING R #SEMR

23rd – 27th October, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck

[MORPHMET] curve analysis

[Ioannis Maniakas]

Hello everyone. As I am new in the field of the geometric morphometrics, I am 
expressing my naive problem.. 
I am trying to analyze differences in the shape of two simple separate curves. 
These describe the radii of circles fitting to the condylar margins on the 
proximal and distal articular surfaces of the medial astragalar side 
respectively. 
I think I have followed the standard procedure. The recorded curves were 
resampled (always from a common homologous starting and ending position), 
granting the same number of evenly spaced 50 points (“by length” option in 
tpsDig) across all specimens. Afterwards, the operation of converting into 
landmarks was conducted with the employment of the tpsUtil program resulting in 
50 landmark configurations. 
So, my question is this: can I import their coordinates into Morphoj or even 
Past and ran  the whole analysis there, including the superimposition? Or do I 
have to treat these data in an other way? 
I have tried to make a slider file for both curves (2 landmarks at the two ends 
of the curves and 48 sliding landmarks between). As I load these nts files with 
the tps file with my 50 lanmarks in tpsrelw and perform the analysis there, the 
consensus and the rest results are wrong. More specifically, the position of 
landmarks has changed dramatically, as some of them have overslided and there 
are not placed equidistantly. Also, it  seems that right and left specimens are 
not getting aligned at all.
This was not the case, when I simply treated them as typical landmarks in 
morphoj..
Please any help would be very welcome. 

-- 
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.