Re: [MORPHMET] geomorph: trajectory analysis error

[Allowen EVIN]

Dear Lawrence,
I think I had a similar issue and for me it was because of the format of 
the grouping factors.
I did as suggested by Mike and create a geomorph data frame first, but 
in the same time I had to transform my vectors into factors based on 
character vectors.

Maybe you can try the following code:
gdf <- geomorph.data.frame(data=data, 
age=as.factor(as.character(classifier$age )), 
species=as.factor(as.character(classifier$species)))

TA <- trajectory.analysis(data ~ age*species, data=gdf)
Have a nice day
Allowen


Le 11/04/2017 22:11, Lawrence Fatica a écrit :

Hi all,
I am trying to use the trajectory.analysis function in geomorph and 
have come across an error I'm not sure how to fix. The command I am 
using is as follows:


trajectory.analysis(proc.coords ~ classifier$age + classifier$species 
+ classifier$age:classifier$species)


in which "proc.coords" is the output from gpagen, and "classifier" is 
a data frame with factors denoting age classes and species.


The error I get is as follows:

Error in procD.fit(f1, data = data, pca = FALSE) :
  Different numbers of specimens in dependent and independent variables

I've double checked that I have Procrustes coordinates for 90 
specimens, age categories for 90 specimens, and species designations 
for 90 specimens. I've gotten this to work in an earlier version of 
geomorph. Am I overlooking something here?


Many thanks,
Lawrence
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Allowen EVIN
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Institut des Sciences de l'Evolution - Montpellier
Equipe: Dynamique de la biodiversité, anthropo-écologie
UMR 5554 CNRS|Université de Montpellier|EPHE|IRD 226|Cirad
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34095 Montpellier | cedex 5 | France
Tel : +33 (0)4 67 14 41 60
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Department of Archaeology, Classics and Egyptology,
University of Liverpool, UK.
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[MORPHMET] RE: Survey for 3D imaging and morphometrics workshop

[Murat Maga]

Hi all,

Thanks for everyone who participated in the survey. While there is quite a bit 
of interest for using 3D volumetric data for many different biology questions, 
people seem to be frustrated with the most mundane of tasks: Getting the data 
into a format and a software that will eventually let them collect morphometric 
data seems to be a major challenge. This really surprised me. That was 
certainly an issue 15 years ago, but it shouldn’t be the case anymore.

I just started a blog (https://blogs.uw.edu/maga/) based on the SOPs of my lab 
and tutorials I used to train students. Currently it has three entries:

  1.  An introduction to the open-source 3D Slicer imaging suite, it is 
capabilities, and how to find help about it.
  2.  A long tutorial of working with data from DigiMorph (Data import, linear 
measurements, landmarking, 3d visualization, down sampling, and segmentation)
  3.  A short tutorial on getting data from MorphoSource into Slicer and how to 
fix DICOM issues.

They are not in the most appealing format, as I copied and pasted from existing 
documents, but I think they are functional enough to get an interested party 
started with his/her project. I did try to put links to the online 
documentation of every module mentioned in tutorials. If something is not clear 
from my description, you can go the source and check it out its details.

Feel free to comment and post specific questions on the blog, so that other can 
benefit from it. I would be particularly interested in knowing other imaging 
repos that cannot be imported into Slicer with the methods described in these 
tutorials. I will try to respond as soon as I can.

Hope this helps some.
M


From: Murat Maga [mailto:m...@uw.edu]
Sent: Wednesday, February 22, 2017 2:19 PM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Survey for 3D imaging and morphometrics workshop

Dear members,

If you are working (or planning to work) with 3D volumetric imaging datasets 
(such CT, or MR) and doing morphometric analyses on them, please consider 
taking this short survey  (6 brief questions) I put together. Should only take 
2 minutes. Survey will be open till March 8th 11PM, PST.

Feedback will be useful to identify the audience and sponsors for a potential a 
short course or a workshop.

https://forms.office.com/Pages/ResponsePage.aspx?id=W9229i_wGkSZoBYqxQYL0lnYz8n5LvRInWGoz5_LAC1URTZOTzdKMllOM1EyVVFZSkI2MlBRVkpKUC4u

Best,
M
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