RE: [MORPHMET] Error in estimate.missing (package geomorph)

2017-01-31 Thread Adams, Dean [EEOBS]
Pere,

I agree that there is likely some issue in the data array and how it is 
configured, but it is difficult to troubleshoot without knowing more and seeing 
the input data.

If you communicate with me off-line I am willing to take a look for you.

Best,

Dean

Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

From: Pere Ibáñez [mailto:perei...@gmail.com]
Sent: Tuesday, January 31, 2017 5:34 AM
To: MORPHMET 
Subject: [MORPHMET] Error in estimate.missing (package geomorph)

I have an array (p x k x n) of landmark corrdinates for a set of specimens. 
Some of them have missing landmarks (NA). I am trying to estimate these 
landmarks using:

estimate.missing(nameofmyarray, method = "Reg")

And I get this error:

Error in incomplete[lndmk, , i] <- tmp : replacement has length zero

Any ideas of what is happening? I followed the exact same procedure with other 
arrays of landmarks and it worked. There is probably something wrong with this 
array, but I have no idea of what...

Thanks!
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[MORPHMET] Workshop: UWashington.EvolQuantGenetics.Jun5-9

2017-01-31 Thread Joe Felsenstein
(note: this course will have about one lecture on the analysis of
morphometrics on phylogenies)


Evolutionary Quantitative Genetics Workshop

Friday Harbor Laboratories, University of Washington, 5-9 June 2017


Non-credit workshop.
Participants arrive at Friday Harbor Labs on Sunday, June 4, lectures and
exercises occur June 5-9, and participants depart on Saturday, June 10, 2017.

Application deadline March 1, 2017.
Application forms and details here:
  http://tinyurl.com/EQG2017
Web page:
  http://depts.washington.edu/fhl/studentSummer2017.html#SumB-genetics

Instructors:

Dr. Joe Felsenstein
Department of Genome Sciences
University of Washington, Seattle
j...@gs.washington.edu

Dr. Stevan J. Arnold
Department of Integrative Biology
Oregon State University, Corvallis
stevan.arn...@oregonstate.edu


Previous versions of this 5-day workshop were given at the National
Evolutionary Synthesis Center (NESCENT) at Duke University in Durham, North
Carolina from 2011-2013, and then at the National Institute for Mathematical
and Biological Synthesis (NIMBioS) at the University of Tennessee in Knoxville
from 2014-2016. Like past versions, the Friday Harbor version will review the
basics of theory in the field of evolutionary quantitative genetics and its
connections to evolution observed at various time scales. The aim of the
workshop is to build a bridge between the traditionally separate disciplines of
quantitative genetics and comparative methods.

Quantitative genetic theory for natural populations was developed considerably
in the period from 1970 to 1990 and up to the present, and it has been applied
to a wide range of phenomena including the evolution of differences between the
sexes, sexual preferences, life history traits, plasticity of traits, as well
as the evolution of body size and other morphological measurements. Textbooks
have not kept pace with these developments, and currently few universities
offer courses in this subject aimed at evolutionary biologists. Evolutionary
biologists need to understand this field because of the ability to collect
large amounts of data by computer, the development of statistical methods for
changes of traits on evolutionary trees and for changes in a single species
through time, and the realization that quantitative characters will not soon be
fully explained by genomics. This workshop aims to fill this need by reviewing
basic aspects of theory and illustrating how that theory can be tested with
data, both from single species and with multiple-species phylogenies.
Participants will use R, an open-source statistical programming language, to
build and test evolutionary models.

The workshop involves lectures and in-class computer exercises. You can
consult the 2016 tutorial website for examples, it will be found at
  http://www.nimbios.org/tutorials/TT_eqg2016
The intended participants for this
tutorial are graduate students, post-docs, and junior faculty members in
evolutionary biology. The workshop can accommodate up to 35 participants. Guest
instructors will include:

* Marguerite Butler, Biology, Univ. Hawai'i, Mānoa
* Patrick Carter, Evolutionary Physiology, Washington State University, Pullman
* Adam Jones, Biology, Texas A University, College Station
* Brian O'Meara, Ecology & Evolutionary Biology, Univ. of Tennessee, Knoxville
* Josef Uyeda, Biological Sciences, Virginia Tech, Blacksburg

Cost: $1000 to be paid to Friday Harbor Laboratories. This fee will cover
housing and meals at FHL and all other workshop expenses, except travel.
Participants who have been admitted to attend will make their payment prior to
arrival at FHL. Details of payment by credit card or check will be provided
once the applicant has been admitted to attend.


J.F.

Joe Felsenstein j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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[MORPHMET] Error in estimate.missing (package geomorph)

2017-01-31 Thread Pere Ibáñez
I have an array (p x k x n) of landmark corrdinates for a set of specimens. 
Some of them have missing landmarks (NA). I am trying to estimate these 
landmarks using:

estimate.missing(nameofmyarray, method = "Reg")

And I get this error:

Error in incomplete[lndmk, , i] <- tmp : replacement has length zero

Any ideas of what is happening? I followed the exact same procedure with 
other arrays of landmarks and it worked. There is probably something wrong 
with this array, but I have no idea of what...

Thanks!

-- 
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[MORPHMET] Procrustes ANOVA for FA Analysis

2017-01-31 Thread Kate Rusk
Hello everyone,

I am a bit confused about how to properly import and classify data for a 
Procrustes ANOVA in MorphoJ. Here is some more information about my data:

15 3D landmarks on human faces (object symmetry)
479 individuals
15 landmarks from 5 individuals digitized a second time
Sex and age as additional main effects

I realize I need to include a classifier that indicates a repeat (to be added 
as an Error classifier), but I am unsure how to import these data. So far, I 
have imported 1) the original data text file which includes the identifier and 
the XYZ coordinates for the original 15 landmarks and 2) a classifier text file 
which includes sex and age as covariates. I have separate XYZ coordinates for 
the repeat landmarks, but I don't know how these should be imported to 
implement the "repeat" classifier. 

Any assistance you could provide would be greatly appreciated! 

Thanks very much,
Kate

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