Re: [MORPHMET] Landmark Editor documentation missing

[José Manuel Barreiro]

Thanks a lot guys for your quick responses. I wish you p values smaller than 
0.05!
Jose

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[MORPHMET] Stats course - Geometric Morphometrics using R - Dean Adams - 5-9 June 2017 - Scotland

[Oliver Hooker]

Geometric Morphometrics Using R (GMMR01)

This course is being delivered by Prof. Dean Adams, Prof. Michael Collyer 
and Dr. Antigoni Kaliontzopoulou

This course will run from 5th - 9th June 2017 at Millport Field centre on 
the Isle of Cumbare, Scotland. Please note that although the course is held 
on an island it is extremely accessible and easy to reach using public 
transport.

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.

Course cost is £520 for students and academic staff and £630 for people 
working in industry.
Accommodation package available for £275, includes all accommodation, meals 
and refreshments.

Course Programme

Sunday 5th Meet at Millport field centre at approximately 18:30.

Monday 6th – Classes from 09:00 to 18:001:
1: Morphometrics: History, Introduction and Data Types
2: Review of matrix algebra and multivariate statistics
3: Superimposition
4: Software demonstration and lab practicum

Tuesday 7th – Classes from 09:00 to 18:00
1: Shape spaces, shape variables, PCA
2: GPA with semi-landmarks
3: Shape covariation
4: Software demonstration and lab practicum

Wednesday 8th – Classes from 09:00 to 18:00
1: Phylogenetic shape variation
2: Group Differences & Trajectory Analysis
3: Allometry
4: Software demonstration and lab practicum

Thursday 9th – Classes from 09:00 to 18:00
1: Assymetry
2: Missing Data
3: Integration and Modularity
4: Disparity
5: Software demonstration and lab practicum

Friday 10th – Classes from 09:00 to 16:00
1: Future Directions
2: Lab Practicum
3: Student Presentations

Please send inquiries to oliverhoo...@prstatistics.com or visit the website 
*www.prstatistics.com* 

Please feel free to distribute this information anywhere you think suitable

Upcoming courses - email for details oliverhoo...@prstatistics.com

1.   ADVANCING IN STATISTICAL MODELLING USING R (December 2016, 
April 2017, December 2017

http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr05/

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

2.   SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (November 2016, 
July 2017)

http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae04/

3.   STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR 
USING R (February 2017)

http://www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm03/

4.   GENETIC DATA ANALYSIS USING R (TBC)

5.   BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS (July 2017)

http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

6.   APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS 
(November 2017)

7.   INTRODUCTION TO STATISTICS AND R FOR BIOLOGISTS (April 2017)

http://www.prstatistics.com/course/introduction-to-statistics-and-r-for-biologists-irfb02/

8.   INTRODUCTION TO PYTHON FOR BIOLOGISTS (TBC)

9.   TIME SERIES MODELS FOR ECOLOGISTS AND CLIMATOLOGISTS (TBC)

10. ADVANCES IN MULTIVAIRAITE ANALYSIS OF SPATIAL 

[MORPHMET] Re: old Morpheus et al. does truss, missing landmarks etc.

[dslice]

And be careful, in general, with missing data imputation. It should be used 
sparingly. Parameter estimates for substituted data are generally unbiased, 
but variance estimates are underestimated - it looks like you have more 
data that your really do. 

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[MORPHMET] Re: old Morpheus et al. does truss, missing landmarks etc.

[dslice]

Andrea is correct. I am currently immersed in a complete graphics rewrite 
facilitated by an enormous amount of initial work by Detelina Stoyanova. 
She developed a generic data-side API to the nuts-and-bolts OpenGL 
underpinning. I am currently integrating that into Morpheus, then must move 
all current and a lot of new graphics over to it. Once that is done, more 
computational things will be added to the new Morpheus. The current 
Morpheus supports basic mean substitution either with or without and 
initial GPA. See Process|Points|Missing Data|Impute. 

GPA mean substitution performs an initial GPA, does the mean substitution 
for the superimposed data, then undoes the GPA putting the data back to 
where it was. This is most probably what you would want to do for landmark 
data, but the direct mean-substitution (data untouched prior to mean 
computation) is provided based on the philosophy of Morpheus et al. 
allowing you to do individual steps, not forcing them on you.

There is no capacity at this time to import MorphoJ data. That will be 
looked at, I am sure, once the current graphics stuff is complete.

On Monday, November 14, 2016 at 2:34:31 AM UTC-5, alcardini wrote:
>
> Not exactly: another user-friendly option is the 'old Morpheus et 
> al.', which estimates missing landmarks (with coordinates, for 
> instance, coded in NTS as - - -, for each 3D landmark) 
> using mean substitution, regression, tps or mirror reflection. The 
> last option is a bit more complicated, I believe, and I never tried 
> it, but the other 3 are easy to select: import the NTS file and first 
> use the command SET FULLPRECISION ON; then try the command LIST PMISS 
> OPTIONS, and then SET PMISS IMPUTATION REGRESSION (for instance); 
> finally use SUPER GPA followed by PMISS IMPUTE; if you restore scale 
> (SUPER RESTORE SCALE), you'll get size back in the data (and also 
> estimated for specimens with missing landmarks). 
> You just need to re-export the nts file and remove, in the first line, 
> the code (1 -) for the missing landmarks (replace with simply 0): 
> check any description of NTS in the TPS Series and you'll see what I 
> mean. 
>
> In a couple of my old papers (the one with Thorington on marmots 
> ontogeny, 2007, and the one with Elton, 2008, BJLS on guenon skulls - 
> pdfs in my webpage) there might be something on this and how we 
> estimated the accuracy of missing landmarks estimates. Much more on 
> this topic is in several papers by Gunz and the others from the 
> Viennese school (including, if I am correct, one of their two papers 
> in the Hystrix, 2013, open access special issue). 
>
>
> As someone was also interested in the truss method (implemented in the 
> old Morpheus et al. as well), I've uploaded the software here: 
> https://www.dropbox.com/sh/ee5gu0qiqe6hz0v/AABLZkLs98uD8aXr79VaxbWma?dl=0 
> That should be the  latest version I have, which Dennis gave us in 
> Vienna 10 years ago. To be honest, I suspect it's still on the web, in 
> its official page, but haven't check the link for a while. 
>
> Dennis can help more with the 'secret commands', and check if I made 
> mistakes above. 
> There should be a few other people on the list with experience on 
> this, and certainly someone who has used the mirror reflection option 
> (on which, I can't help). 
>
>
> Good luck. Cheers 
>
> Andrea 
>
>
> On 13/11/2016, Murat Maga  wrote: 
> > MorphoJ handles missing landmarks, but I don't think it has a function 
> to 
> > estimate them. SO without an estimation of your landmark position, your 
> > options are either to drop the sample from the analysis (if you want to 
> > retain full set of landmarks) or to remove the landmark from your 
> analysis 
> > (to keep full set of individuals). 
> > 
> > You can also experiment with trying to estimate them based on reflection 
> (if 
> > it is a symmetrical structure) or based on bunch of reference samples. 
> Both 
> > Morpho and gemorph in R have functions for estimating missing landmarks. 
> See 
> > if they give you reliable estimates, and then you can proceed with your 
> > analysis. 
> > 
> > Otherwise your options are limited to those two. 
> > M 
> > 
> > 
> > -Original Message- 
> > From: Rosa Perez [mailto:rmper...@ncsu.edu] 
> > Sent: Saturday, November 12, 2016 9:53 PM 
> > To: MORPHMET  
> > Subject: [MORPHMET] Re: Problem with missing data using MorphoJ 
> > 
> > On Thursday, August 11, 2016 at 4:06:01 PM UTC-4, Jade Racine wrote: 
> >> Dear all, 
> >> 
> >> 
> >> 
> >> I digitized 108 craniofacial landmarks on human skulls from an 
> >> archaeological context using a MicroScribe G2X. I have a lot of random 
> >> missing values due to postmortem damage. I am currently trying to 
> >> analyze my data using MorphoJ. I followed the instructions from the 
> >> user’s guide, entering "-" in the data files for missing values. I 
> >> then combined the dorsal and ventral views 

[MORPHMET] paper on multivariate heritability

[Mark Belk]

Dear morphometricians,

Just wanted to bring your attention to a paper that we published last spring in 
the journal Development Genes and Evolution that illustrates a new approach to 
the analysis of heritability of shape (multivariate trait).  Chris Klingenberg 
made an announcement about the special issue on size and shape last spring.  
Calculating multivariate heritability has been a difficult problem to approach 
because it requires a multivariate linear mixed model.  The approach 
illustrated in this paper is statistically rigorous and it may be of interest 
to the broader moprphometrics community.

Mark C. Belk, and G. Bruce Schaalje.  2016.  Multivariate heritability of shape 
in June sucker (Chasmistes liorus) and Utah sucker (Catostomus ardens): shape 
as a functional trait for discriminating closely related species.  Development 
Genes and Evolution 226:197-207.

http://link.springer.com/journal/427/226/3/page/1
 or
http://link.springer.com/article/10.1007/s00427-016-0547-2/fulltext.html

Best,
Mark

Mark C. Belk, Professor of Biology
Brigham Young University
Editor, Western North American Naturalist
801-422-4154

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[MORPHMET] Landmark Editor documentation missing

[José Manuel Barreiro]

Hi everyone,
I am trying to use the Landmar Editor by the UC Davis group 
(http://www.idav.ucdavis.edu/research/EvoMorph) but I can not download the 
documentation. The links in their webpage do not work, I've been trying all 
week. Do you guys have the documentation pdf? and if you do cold you share it?
Thanks a lot.

Jose

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