Re: [MORPHMET] Re: Using ImageJ for digitizing on Mac OS X

[Mauro Cavalcanti]

Dear Emma,

Thanks, very helpful indeed.

Best regards,

2015-06-15 18:56 GMT-03:00 Emma Sherratt :

> Dear Edouard,
>
> You can find a comprehensive guide by David Polly here:
> http://www.indiana.edu/~g562/Handouts/Collecting%20Landmarks.pdf
>
> And a few tips on digitizing 2D data can be found here:
> http://www.emmasherratt.com/morphometrics/-goal-gathering-two-dimensional-landmark-coordinates-to-describe-the-shape-of-my-favourite-structure
>
> Best,
>
> Emma
>
> On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote:
>>
>> Hello,
>>
>> Is there a guide for the complete beginner on how to use ImageJ instead
>> of tpsdig, especially on how to set the scale before digitizing?
>>
>> Many thanks
>>
>> Edouard
>>
>>
>> -
>> Edouard Masson-MacLean
>> PhD Candidate
>> Room 119
>> Department of Archaeology
>> School of Geosciences
>> University of Aberdeen
>> St. Mary's, Elphinstone Road
>> Aberdeen, AB24 3UF
>> Scotland, UK
>>
>  --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>



-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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Re: [MORPHMET] Using ImageJ for digitizing on Mac OS X

[Edouard Masson-MacLean]

Great thanks Vincent!

Edouard

Le 15 juin 2015 à 21:41, Vincent Bonhomme  a écrit :

hi there,

Analyze > Set Scale...

+ http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html 


hth
best,

v

2015-06-15 14:59 GMT+02:00 Edouard Masson-MacLean mailto:e.massonmacl...@gmail.com>>:
Hello,

Is there a guide for the complete beginner on how to use ImageJ instead of 
tpsdig, especially on how to set the scale before digitizing?

Many thanks

Edouard


-
Edouard Masson-MacLean
PhD Candidate
Room 119
Department of Archaeology
School of Geosciences
University of Aberdeen
St. Mary's, Elphinstone Road
Aberdeen, AB24 3UF
Scotland, UK

-- 
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.



-- 
vincentbonhomme.fr 

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Re: [MORPHMET] Re: Using ImageJ for digitizing on Mac OS X

[Edouard Masson-MacLean]

Dear Emma

Many thanks for your help that’s very useful

Best

Edouard

Le 15 juin 2015 à 22:56, Emma Sherratt  a écrit :

Dear Edouard,

You can find a comprehensive guide by David Polly here: 
http://www.indiana.edu/~g562/Handouts/Collecting%20Landmarks.pdf

And a few tips on digitizing 2D data can be found here: 
http://www.emmasherratt.com/morphometrics/-goal-gathering-two-dimensional-landmark-coordinates-to-describe-the-shape-of-my-favourite-structure

Best,

Emma

On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote:
Hello,

Is there a guide for the complete beginner on how to use ImageJ instead of 
tpsdig, especially on how to set the scale before digitizing?

Many thanks

Edouard


-
Edouard Masson-MacLean
PhD Candidate
Room 119
Department of Archaeology
School of Geosciences
University of Aberdeen
St. Mary's, Elphinstone Road
Aberdeen, AB24 3UF
Scotland, UK

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org 


To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org 
.

-- 
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[MORPHMET] Re: Using ImageJ for digitizing on Mac OS X

[Emma Sherratt]

Dear Edouard,

You can find a comprehensive guide by David Polly 
here: http://www.indiana.edu/~g562/Handouts/Collecting%20Landmarks.pdf

And a few tips on digitizing 2D data can be found 
here: 
http://www.emmasherratt.com/morphometrics/-goal-gathering-two-dimensional-landmark-coordinates-to-describe-the-shape-of-my-favourite-structure

Best,

Emma

On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote:
>
> Hello,
>
> Is there a guide for the complete beginner on how to use ImageJ instead of 
> tpsdig, especially on how to set the scale before digitizing?
>
> Many thanks
>
> Edouard
>
>
> -
> Edouard Masson-MacLean
> PhD Candidate
> Room 119
> Department of Archaeology
> School of Geosciences
> University of Aberdeen
> St. Mary's, Elphinstone Road
> Aberdeen, AB24 3UF
> Scotland, UK
>

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

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Re: [MORPHMET] Landmark Editor --> MorphoJ problem

[Emma Sherratt]

Ari,

This issue is probably due to having spaces in the names of your specimens.
Find and replace with _ then try again

Emma


On Monday, June 15, 2015, a.l.schulz  wrote:

> Hello All,
>
> I need to ask a rather silly question for which I imagine there is a
> simple solution ... but I just can't figure it out. I've created a landmark
> file in IDAV Landmark Editor and exported an NTSYSpc (.dta) file for it. I
> then tried to upload that into MorphoJ, but to no avail. I keep getting the
> message "There appear to be too many row labels in the file." I then tried
> to create the same dataset using text files exported from Landmark Editor
> but got roughly the same message. I have opened the files and looked at
> them and as far as I can tell there is nothing wrong.
>
> Has anyone else encountered and overcome this issue? For the time being I
> am stumped.
>
> Best,
> Ari
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org
> 
> .
>


-- 

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

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to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] Using ImageJ for digitizing on Mac OS X

[Vincent Bonhomme]

hi there,

Analyze > Set Scale...

+
http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html

hth
best,

v

2015-06-15 14:59 GMT+02:00 Edouard Masson-MacLean :

> Hello,
>
> Is there a guide for the complete beginner on how to use ImageJ instead of
> tpsdig, especially on how to set the scale before digitizing?
>
> Many thanks
>
> Edouard
>
>
> -
> Edouard Masson-MacLean
> PhD Candidate
> Room 119
> Department of Archaeology
> School of Geosciences
> University of Aberdeen
> St. Mary's, Elphinstone Road
> Aberdeen, AB24 3UF
> Scotland, UK
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>



-- 
vincentbonhomme.fr 

-- 
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to morphmet+unsubscr...@morphometrics.org.

[MORPHMET] Using ImageJ for digitizing on Mac OS X

[Edouard Masson-MacLean]

Hello,

Is there a guide for the complete beginner on how to use ImageJ instead of 
tpsdig, especially on how to set the scale before digitizing?

Many thanks

Edouard


-
Edouard Masson-MacLean
PhD Candidate
Room 119
Department of Archaeology
School of Geosciences
University of Aberdeen
St. Mary's, Elphinstone Road
Aberdeen, AB24 3UF
Scotland, UK

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

[MORPHMET] Landmark Editor --> MorphoJ problem

[a.l.schulz]

Hello All,

I need to ask a rather silly question for which I imagine there is a simple 
solution ... but I just can't figure it out. I've created a landmark file 
in IDAV Landmark Editor and exported an NTSYSpc (.dta) file for it. I then 
tried to upload that into MorphoJ, but to no avail. I keep getting the 
message "There appear to be too many row labels in the file." I then tried 
to create the same dataset using text files exported from Landmark Editor 
but got roughly the same message. I have opened the files and looked at 
them and as far as I can tell there is nothing wrong.

Has anyone else encountered and overcome this issue? For the time being I 
am stumped.

Best,
Ari

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

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Re: [MORPHMET] Re: physignal in geomorph

[Emma Sherratt]

Anneke,

I'm gad you've managed to solve your issue but I need to say that making
your data a 3D array shouldn't be the fix.

> library(geomorph)
Loading required package: rgl
> data(plethspecies)
> Y.gpa<-gpagen(plethspecies$land)#GPA-alignment
>
> #Test for phylogenetic signal in shape using data in a 3D array
> physignal(plethspecies$phy, Y.gpa$coords, method="Kmult",iter=99)
$phy.signal
  [,1]
[1,] 0.9572538

$pvalue
 [,1]
[1,] 0.04

> #Test for phylogenetic signal in shape using data in a 2D matrix
> physignal(plethspecies$phy, two.d.array(Y.gpa$coords),
method="Kmult",iter=99)
$phy.signal
  [,1]
[1,] 0.9572538

$pvalue
 [,1]
[1,] 0.02

So there must have been something wrong with your 2D matrix to not work
previously. Check that it is numeric, check that the rownames were assigned
properly, and that it contained only the data you wanted to input.

FYI, in geomorph, we use the 3D array format to specify that the data are
coordinate data, and the 2D matrix for multivariate data, not necessarily
shape data. This allows several of the functions to be used with non-shape,
multivariate datasets.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians




On 15 June 2015 at 20:24, Anneke van Heteren 
wrote:

> Dear all
>
> Thank you very much to those who have replied to my question. It turned
> out that my data was a 2D matrix instead of a 3D array and that that was
> causing the problem.
>
> Best wishes,
>
> Anneke
>
>
> On Thursday, June 11, 2015 at 1:41:55 PM UTC+2, Anneke van Heteren wrote:
>>
>> Dear friends and colleagues
>>
>>
>>
>> I am trying to run physignal in geomorph (R), but I am running into a
>> problem I do not understand. Here is the code I am using and the error
>> message:
>>
>> > physignal(ursid_phyl, Regr_res_av, iter=99)
>>
>> Error in match.names(clabs, names(xi)) :
>>
>>   names do not match previous names
>>
>>
>>
>> However:
>>
>> > name.check(ursid_phyl,Regr_res_av)
>>
>> [1] "OK"
>>
>>
>>
>> But:
>>
>> > match(ursid_phyl,Regr_res_av)
>>
>> [1] NA NA NA NA
>>
>> > match(Regr_res_av,ursid_phyl)
>>
>>  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
>>
>> [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
>>
>>
>>
>> This suggested to me that physignal might need the columns to carry the
>> same names rather than the rows (as my phylogeny is list of 4 and I have 15
>> landmarks=45 variables), but when I transposed my data, I get a different
>> error message:
>>
>> > trans_regr_res_av <-t(Regr_res_av)
>>
>> > physignal(ursid_phyl, trans_regr_res_av, iter=99)
>>
>> Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) :
>>
>>   Number of taxa in data matrix and tree are not not equal.
>>
>>
>>
>> I do not know what I could try next to calculate physignal. Any help
>> would be appreciated. This is the phylogeny that I am using:
>>
>>
>>
>> (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3);
>>
>>
>> Thanks in advance.
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Anneke van Heteren
>>
>>
>>
>>
>>  --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>

-- 
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[MORPHMET] Re: physignal in geomorph

[Anneke van Heteren]

Dear all

Thank you very much to those who have replied to my question. It turned out 
that my data was a 2D matrix instead of a 3D array and that that was 
causing the problem.

Best wishes,

Anneke

On Thursday, June 11, 2015 at 1:41:55 PM UTC+2, Anneke van Heteren wrote:
>
> Dear friends and colleagues
>
>  
>
> I am trying to run physignal in geomorph (R), but I am running into a 
> problem I do not understand. Here is the code I am using and the error 
> message: 
>
> > physignal(ursid_phyl, Regr_res_av, iter=99)
>
> Error in match.names(clabs, names(xi)) : 
>
>   names do not match previous names
>
>  
>
> However:
>
> > name.check(ursid_phyl,Regr_res_av)
>
> [1] "OK"
>
>  
>
> But:
>
> > match(ursid_phyl,Regr_res_av)
>
> [1] NA NA NA NA
>
> > match(Regr_res_av,ursid_phyl)
>
>  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
>
> [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
>
>  
>
> This suggested to me that physignal might need the columns to carry the 
> same names rather than the rows (as my phylogeny is list of 4 and I have 15 
> landmarks=45 variables), but when I transposed my data, I get a different 
> error message:
>
> > trans_regr_res_av <-t(Regr_res_av)
>
> > physignal(ursid_phyl, trans_regr_res_av, iter=99)
>
> Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) : 
>
>   Number of taxa in data matrix and tree are not not equal.
>
>  
>
> I do not know what I could try next to calculate physignal. Any help would 
> be appreciated. This is the phylogeny that I am using:
>
>
>
> (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3);
>
>
> Thanks in advance. 
>
>  
>
> Best wishes,
>
>  
>
> Anneke van Heteren
>
>  
>
>
>

-- 
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