[MORPHMET] DA value calculation

[lv xiao]

Dear all,

Question 1: If I have a set of specimens which are object symmetry, how 
could I calculate directional asymmetry *(DA) score* for this set of 
specimen? I noted that after using bilat.symm function in geomorph, 
DA.component could be extracted, which contains two sets of coordinates. I 
guess DA score of the sample could be calculated from DA.component, can 
anyone show me the code necessary to derive DA score, whether in geomorph 
or any other software?

Question 2: A possibly related question is how (appreciated if R code is 
provided) to obtain the *Procrustes distance between two specimens after 
GPA*. I think I can calculate the Procrustes distance between the original 
and reflected and relabled mirrors for each specimen and averaging the 
Procrustes distance across all specimens to obtain DA score for my entire 
sample.

Question3: A third question which is unrelated to the previous two is that 
I noted that Procrustes Variance is used in Morphol.disparity function to 
compare morphological disparity across groups. Procrustes Variance is 
explained in the user manual as "the sum of the diagonal elements of the 
group covariance matrix." But where can I find some more *detailed 
mathematical definition of Procrustes Variance*?

Thank you very much for your help!

Best regards,
Patrick Wen

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[MORPHMET] Is it possible to export .stl file to .ply with colors?

[lv xiao]

Dear all,

I have 3D files in .stl format. I converted these files to .ply file in 
MeshLab (see figure below, the "Color" item cannot be checked):


I further noted that when I import the .ply file into Geomagic design, the 
model appeared in an attrative blue color. In Landmark, the model looked 
yellow to red. In Checkpoint, plain grey.

I want to know is there a way in which I can customize the color of the 
models in either Landmark or Checkpoint software. In particular, I want the 
models in Landmark/Checkpoint appear in the same blue color as in Geomagic 
(Question 1). I am not sure whether this is possible.

I particularly like the blue color in which the 3D models were presented in 
the paper "Evolution of the base of the brain in highly encephalized human 
species". However, I noted that the authors used Edgewarp, which 
unfortunately runs only in Linux system. Is there any GM software that 
allows presentation of 3D models in this blue color (Question 2)?

Best regards,
Patrick

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[MORPHMET] Re: Cannot load STL file into Landmark Editor software

[lv xiao]

Thank you all for your comments. I transformed the .stl file into .ply 
format in MeshLab and the resulting .ply file was successfully loaded into 
Landmark Editor!

Best regards,
Patrick

On Monday, 18 July 2016 10:52:49 UTC+8, lv xiao wrote:
>
> Dear all,
>
> I have 3D dental model files in STL format (a sample file is attached 
> below). I wish to load these files into Landmark Editor (available from 
> http://www.idav.ucdavis.edu/research/EvoMorph) for landmark and 
> semilandmark digitization. However, I do not know why I cannot successfully 
> load these files.
>
> The steps I took was as follows (please help me find out where I was 
> wrong, thank you!):
>
> 1. Open Landmark Editor and create a new project named project.land
>
>
> <https://lh3.googleusercontent.com/-zy06GSff_E4/V4xAnhFuTzI/AL8/cZVsb7PwHQElJHkbnE0ztDFlAEmAu8aPwCLcB/s1600/1.jpg>
>
>
> 2. Click "OK" and the following window appears
>
>
> <https://lh3.googleusercontent.com/-bf0XRzF4-ro/V4xA8sTDVyI/AMA/AlLKHOBCvJMaYHEfHkpTPbZWUn6daqowgCLcB/s1600/2.jpg>
>
>
> 3. Right click the "project" folder and choose "Import"
>
>
> <https://lh3.googleusercontent.com/-r3a2BU1SX6Y/V4xBWSjYdfI/AME/gshC5SbNPKMmKuSq4BGoI6ye6qv1E5i5gCLcB/s1600/3.jpg>
>
>
> 4. Choose the intended STL file and click "open"
>
>
> <https://lh3.googleusercontent.com/-77HZ5q4EMgg/V4xBvZA1lhI/AMM/-CUCHpSbYVIfAvNop48uUa98D7cXu_umQCLcB/s1600/4.jpg>
>
>
> 5. The STL file appears in the leftmost pane as follows
>
>
> <https://lh3.googleusercontent.com/-Zi-IhaB-Co8/V4xCWkXJTeI/AMU/t4bs_juVlz8bkIJsArYeWEKt8neXqJGugCLcB/s1600/5.jpg>
>
>
> 6. BUT The "Load into A" and "Load into B" options are still deactivated
>
>
> <https://lh3.googleusercontent.com/-oWA8wEHvR0I/V4xDB2PVrwI/AMg/XA-ZhtPRP1okaMJUUzVb-mg-jWlBPuAhACLcB/s1600/6.jpg>
>
>
> Therefore, I do not know how should I proceed to load surface files into 
> Landmark Editor.
>
>
> The above steps were performed following the user manual of Landmark 
> Editor available from 
> http://www.idav.ucdavis.edu/research/projects/EvoMorph/supplement/LandmarkDoc_v3_b6.pdf
>
>
> Thank you very much if you could try opening the attached sample.stl file 
> on your Lanmark Editor to help me figure out where I was wrong or if any 
> other files are needed.
>
>
> Best regards,
>
> Patrick
>
>

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Re: [MORPHMET] Estimating Ontogenetic Trajectories

[lv xiao]

In the botton line of page 53 of Quick Guide to Geomorph v2.1.6 regarding 
trajectory.analysis (Y ~ cov + A * B), A and B are called factors, which 
seems to suggest that A and B are categorical variables. Continuous 
covariates could be included in the formula, but this is only optional. In 
contrast, it seems that there must be two categorical variables (A and B) 
appearing in the formula. 

Following this line of thought, I am wondering if is there the need to 
convert the continuous age variable (age) into a categorical variable 
(age_cat) before applying the trajectory analysis. I am not sure whether 
one should use trajectory.analysis(shape ~ group * age_cat ) 
or trajectory.analysis(shape ~ group * age).

Best regards,
Patrick

On Monday, 24 August 2015 10:56:55 UTC+8, Emma Sherratt wrote:

 Dear Miranda,

 Using procD.lm is the correct function for what you want to do. Since you 
 have just two groups it's a simple Procrustes Anova. Your implementation 
 should be:

 procD.lm(shape~ age*group)

 This will give you:

 Effect of age; where significant means the shape scales allometrically

 Effect of group; where significant means the groups differ in intercept 

 The interaction term of age and group to tell you if the two groups have 
 the same slope (interaction term not significant) or the slopes differ (sig 
 interaction term)

 Then from this you will be able to deduce whether the two groups follow 
 the same allometric trajectory or not. But remember, you are dealing with 
 multivariate regression here so there is no positive or negative allometry, 
 since the slope is a multivariate vector in shape space.

 The same formula into trajectory.analysis should then lead you to where 
 you were hoping to go with that.

 Emma

 On Monday, August 24, 2015, Karban, Miranda E miranda-...@uiowa.edu 
 javascript: wrote:

 Hello morphometricians, 

 I am relatively new to morphometrics, and I am attempting to assess 
 ontogenetic trajectories from a longitudinal sample of growth study x-rays. 
 My subjects are divided into 2 groups, and I would like to determine 
 whether there are developmental differences in cranial shape between these 
 groups. I have precise ages for each subject, so I hope to use age as a 
 variable (following McNulty et al., 2006) rather than centroid size. 

  

 From what I gather from the literature, I can estimate ontogenetic 
 trajectories by regressing the Procrustes aligned shape coordinates onto 
 the independent variable of age. So far, I have attempted to do this in the 
 geomorph package in R using the procD.lm and the trajectory.analysis 
 functions. I am wondering if I am doing this correctly, or if there is a 
 better function to use.

  

 I have tried the following:

 lateral.gpa - gpagen(vaultlandmarks)

 procD.lm(two.d.array(lateral.gpa$coords) ~ age, iter = 999)

  

 where “vaultlandmarks” refers to the 2D landmark and semi-landmark 
 coordinates in my tps file, and “age” refers to a column in my metadata csv 
 file which gives the age of each specimen to the nearest 1/10 of a year. 
 This provides a sum-of-squared Procrustes distances, a mean square, and a 
 highly significant p-value. I am not sure, however, how to compare the 
 results I get from the 2 groups. 

  

 When I try the trajectory.analysis function:

 lateral.gpa - two.d.array(gpagen(vaultlandmarks)$coords)

 trajectory.analysis(lateral.gpa~age)

  

 I get the error message: “Error in trajectory.analysis(lateral.gpa ~ age) 
 :   X-matrix does not specify enough model factors (see help file).”

  

 Thank you for any advice or help you might provide.

  

 Best,

 Miranda Karban

 PhD Candidate, University of Iowa

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 -- 

 ~~~

 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.s...@une.edu.au javascript:
 Twitter: @DrEmSherratt

 Caecilians are legless amphibians...

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

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






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[MORPHMET] How to model Shape Changes as the dependent variable for further statistical analysis?

[lv xiao]

Dear all,

*My example:*

I have 150 participants in my sample. At time point 1 (eg., at birth), I 
collected some background information (including both categorical and 
continuous variables) from the participants. Images of the participants 
were taken at time point 2 (eg., 6 months) and time point 3 (eg., 12 
months).

*My aim:*

I wish to investigate whether those background information collected at 
birth predict participants' shape changes from 6 to 12 months.

*Proposed methods:*

Perform between-group PCA (BGPCA) in steps below:

Step 1: Group the shape data by time point. One group for 6 months data, 
and the other for 12 months data;
Step 2: Perform BGPCA (in PCAGen8) and extract the most significant 
principal components (PCs) from scree plot;
Step 3: Extract the PC scores (Save PCA Scores button in PCAGen8)
Step 4: Since each participant appeared in both groups, I can calculate the 
difference of each participant's PC scores between the two groups (time 
points) for each extracted PC;
Step 5: Each participant is then associated with one score reflecting 
his/her shape change along a particular PC (eg., PC 1). This score is then 
used as the dependent variable so   that conventional 
statistical analyses such as simple linear regression and ANOVA, can be 
performed.

*My question:*

Q 1: Is the steps above appropriate?
Q 2: Since the same participants are in both groups (groups differ only in 
the chronological order the shapes were measured), the two groups are 
correlated instead of beingindependent. Will such 
correlation affect the correctness of BGPCA in this example. Is there any 
way out if correlation is indeed a problem?

Thank you very much!

Best regards,
Patrick

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[MORPHMET] Re: Predict shape for a specific value of the predictor using IMP Regress8

[lv xiao]

Hi everyone,

Even though I still could not find a way to obtain the predicted specimen 
at a given value of x in IMP Regress8, I noticed that in tpsRegr, by 
clicking the Visualization button, there would be a pop-up window called 
Regression visualization plot (see attached) in which I was allowed to 
assign any number of x to the box in the upper-left corner, and I can then 
save the predicted shape by choosing save estimates from the file menu.

May I know if this method is correct and if there exists a way to do this 
in IMP Regress8?

Thank you very much for your help.

Best regards,
Patrick

On Friday, 15 May 2015 00:13:45 UTC+8, lv xiao wrote:

 Dear all,

 I am regressing shape variable onto one independent variable using IMP 
 Regress8. Apart from this, I wish to predict shape for a specific value of 
 the independent variable.

 I noted that by choosing *Standardize* in the Call Other Tools menu, 
 I could use* IMP:Standard8* to regress my data on an arbitrarily defined 
 value of x. However, according to the user manual (
 http://www3.canisius.edu/~sheets/UsingStandard6.html), this program adds 
 the residual of each sample to the predicted specimen at that value of x.* 
 What I want is simply the predicted specimen at the value of x, without 
 adding sample residuals.* Would you please provide me some guides on how 
 to obtain the predicted specimen?

 Your help is highly appreciated!

 Best regards,
 Patrick


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[MORPHMET] Re: Error message in tpsSUPER

[lv xiao]

Dear all,

Thanks to Prof. Rohlf, the problem is now solved. The reason for system 
crash is because landmark 28 and 29 are identical in position, leading to 
an infinite amount of bending energy and thus program crash. When one of 
the landmarks is removed, the program worked smoothly.

Best regards,
Patrick WEN

On Wednesday, 13 May 2015 23:00:40 UTC+8, lv xiao wrote:

 Dear Morthometric Wizards,

 I am using tpsSUPER software to create an average image of my specimens. I 
 imported the TPS file Total.TPS as attached into the software and I was 
 able to obtain the average image. However, when I subset this Total 
 document into 4 mutually exclusive and collectively exhaustive parts (part 
 1, 2, 3, and 4 as attached) using tpsUtil Delete/reorder specimens 
 function, it is strage to note that while Part 1.TPS and Part 3.TPS 
 still worked smoothly, errors appeared when clicking the Unwarp button 
 for the Part 2.TPS and Part 4.TPS files. 

 The error message that appeared is also in the attachment. Would you 
 please help me figure out where on earth has gone wrong?

 Thank you very much for your help! Please feel free to contace me if you 
 need any further information.

 Best regards,
 Patrick WEN


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Re: [MORPHMET] Re: Error message in tpsSUPER

[lv xiao]

Dear Prof. Rohlf,

I tried on the software and learnt that the location of the face appearing
in the photo can be adjusted using the Image adjustments function in the
Options menu. Thank you very much again for your help!

Best regards,
PhD Candidate,
The University of Hong Kong
Yi Feng WEN

2015-05-14 14:21 GMT+08:00 lv xiao lxia...@gmail.com:

 Dear all,

 Thanks to Prof. Rohlf, the problem is now solved. The reason for system
 crash is because landmark 28 and 29 are identical in position, leading to
 an infinite amount of bending energy and thus program crash. When one of
 the landmarks is removed, the program worked smoothly.

 Best regards,
 Patrick WEN


 On Wednesday, 13 May 2015 23:00:40 UTC+8, lv xiao wrote:

 Dear Morthometric Wizards,

 I am using tpsSUPER software to create an average image of my specimens.
 I imported the TPS file Total.TPS as attached into the software and I was
 able to obtain the average image. However, when I subset this Total
 document into 4 mutually exclusive and collectively exhaustive parts (part
 1, 2, 3, and 4 as attached) using tpsUtil Delete/reorder specimens
 function, it is strage to note that while Part 1.TPS and Part 3.TPS
 still worked smoothly, errors appeared when clicking the Unwarp button
 for the Part 2.TPS and Part 4.TPS files.

 The error message that appeared is also in the attachment. Would you
 please help me figure out where on earth has gone wrong?

 Thank you very much for your help! Please feel free to contace me if you
 need any further information.

 Best regards,
 Patrick WEN

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[MORPHMET] How to cite the companion workbook in scientific publications?

[lv xiao]

Dear all,

I want to cite the book *A Practical Companion to Geometric Morphometrics 
for Biologists: Running analyses in freely-available software*. 

May I know whether I should cite this workbook as a book (but no 
information on year, pubulisher or place published) or directly refer to 
the website http://booksite.elsevier.com/9780123869036/content/Workbook.pdf 
?

*Would you please provide the complete reference *so that I may directly 
use it in my publication?

Thank you!
Patrick

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[MORPHMET] TMorphGen8 creates one more linear variable than I asked for in the protocol file

[lv xiao]

Hi everyone,

I am using TMorphGen8 embedded in CoordGen8 to calculate traditional linear 
measurements.

I imported my dataset and then loaded the protocol for linear measurements.

### my protoco l###
1 7 12
2 31 32
3  33 34
## end of protocol ##

The protocol above indicates that* I asked for 3 linear measurements*, 
i.e., the linear distance between landmark 7 and 12, 31 and 32, and 33 and 
34.* HOWEVER, in the ouput file, I got four columns.* I checked and found 
that the first three columns are what I asked for, while I am really 
confused about what the fourth column stands for.

*Could you please tell me what the numbers in the 4th column means?*

I have attached my datafile in TPS format, protocol file as well as the 
output for your reference. 

Thank you very much for your help.

Best regards,
Patrick

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data file.TPS
Description: Binary data
1   7   12
2   31  32
3   33  34
78.2111 186.451 165.067 393.816  
67.3313 160.036 136.129 340.88  
69.8328 164.388 132.994 357.205  
65.7193 162.959 130.028 340.784  
76.3864 185.733 141.887 393.402  

[MORPHMET] Re: TMorphGen8 creates one more linear variable than I asked for in the protocol file

[lv xiao]

Dear ALL,

Thanks to Prof. Sheets' and Prof. Swiderski's help, I now understand that 
the 4th column indicates centroid size.

Best regards,
Patrick

On Tuesday, 14 April 2015 15:41:01 UTC+8, lv xiao wrote:

 Hi everyone,

 I am using TMorphGen8 embedded in CoordGen8 to calculate traditional 
 linear measurements.

 I imported my dataset and then loaded the protocol for linear measurements.

 ### my protoco l###
 1 7 12
 2 31 32
 3  33 34
 ## end of protocol ##

 The protocol above indicates that* I asked for 3 linear measurements*, 
 i.e., the linear distance between landmark 7 and 12, 31 and 32, and 33 and 
 34.* HOWEVER, in the ouput file, I got four columns.* I checked and found 
 that the first three columns are what I asked for, while I am really 
 confused about what the fourth column stands for.

 *Could you please tell me what the numbers in the 4th column means?*

 I have attached my datafile in TPS format, protocol file as well as the 
 output for your reference. 

 Thank you very much for your help.

 Best regards,
 Patrick


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[MORPHMET] Re: Save Procrustes vs Save Procrustes Data, tab delimited, labels and Header

[lv xiao]

Is anyone willing to help me with the above question? Your help is highly 
appreciated.

Thank you!
Patrick

On Wednesday, 11 February 2015 16:29:50 UTC+8, lv xiao wrote:

 Dear Morphometrics Wizards,

 I am using CoordGen8 to perform Procrustes superimposition. My sample size 
 is 20 and there are 19 landmarks for each specimen.

 May I know the differences between the document saved using Save 
 Procrustes button in the deep blue *Save coordinates* box and the 
 documents saved using Save Procrustes Data, tab delimited, labels and 
 Header button in the drop-down list from the *File Options* menu?

 If Save Procrustes generates the coordinates after Procrustes 
 superimposition, what does the Save Procrustes Data, tab delimited, labels 
 and Header generate?

 Best regards,
 Patrick


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[MORPHMET] Save Procrustes vs Save Procrustes Data, tab delimited, labels and Header

[lv xiao]

Dear Morphometrics Wizards,

I am using CoordGen8 to perform Procrustes superimposition. My sample size 
is 20 and there are 19 landmarks for each specimen.

May I know the differences between the document saved using Save 
Procrustes button in the deep blue *Save coordinates* box and the 
documents saved using Save Procrustes Data, tab delimited, labels and 
Header button in the drop-down list from the *File Options* menu?

If Save Procrustes generates the coordinates after Procrustes 
superimposition, what does the Save Procrustes Data, tab delimited, labels 
and Header generate?

Best regards,
Patrick

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[MORPHMET] How to create Group Membership List?

[lv xiao]

Dear Morphometrics Wizards,

I am using PCAGen8 and I noted that there is a purple push-button named Load 
Group Membership List in the software. However, I don't know how I can build 
this Group Membership List at all!

I checked CoordGen8_Win but can't find anywhere to generate such a list. Can 
anyone help me with this???

More specifically, my original data contains 20 images with equal number of 
boys (10) and girls (10). Can I just create a single column in Excel with the 
first 10 rows being 1 and the last 10 rows being 2 and save the document as a 
.csv file?

Your help is highly appreciated!

Best regards,
Patrick 

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[MORPHMET] Re: How to create Group Membership List?

[lv xiao]

Hi Gabi,

Thank you very much for your generous help. The problem has been solved 
based on your suggestions.

Thank you!
Patrick

On Thursday, 29 January 2015 05:38:10 UTC+8, gnavas wrote:

 Hi Patrick,

 I generate the list in excel as you suggest and then save it as a *.txt* 
 file the way you described, so simply 10 successive 1 and 10 successive 2 
 for a total of 20 rows. PCAGen8 will then generate different symbols for 
 your 2 groups. I suggest you make sure that your pictures are all in that 
 particular order, since I have had issues with tpsdig renumbering my 
 sequential pix, in which case you just adjust where your 1 and 2 group 
 memberships go in your list (they may not be sequential in that case, but 
 the program will at least assign them correctly). 

 I hope this was helpful.

 Gabi



 On Wednesday, January 28, 2015 at 4:50:12 AM UTC-8, lv xiao wrote:

 Dear Morphometrics Wizards, 

 I am using PCAGen8 and I noted that there is a purple push-button named 
 Load Group Membership List in the software. However, I don't know how I 
 can build this Group Membership List at all! 

 I checked CoordGen8_Win but can't find anywhere to generate such a list. 
 Can anyone help me with this??? 

 More specifically, my original data contains 20 images with equal number 
 of boys (10) and girls (10). Can I just create a single column in Excel 
 with the first 10 rows being 1 and the last 10 rows being 2 and save the 
 document as a .csv file? 

 Your help is highly appreciated! 

 Best regards, 
 Patrick 



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