Re: [MORPHMET] Use of PIC (Phylogenetic Independent Contrast)

2016-02-20 Thread K. James Soda
Dear Ms. Llopis, It is my understanding that you are correct, Brownian evolution is a generally considered an assumption in PIC (see Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15). Its inclusion is important to Felsenstein's formulation because it

Re: [MORPHMET] Interpreting PCA results

2017-05-14 Thread K. James Soda
Dear David, Great question! I disagree with the statement that the samples' variance in shape space is not biologically real or, perhaps more accurately, is less real than the variance in any other space. As far as I see it, the basic strategy in any biostatistical study, be it GM or otherwise,

Re: [MORPHMET] Does a research sample need to be normally distributed (male/female ratio) for PCA?

2017-05-27 Thread K. James Soda
Dear Dr. Hadi, I would just like to add one additional comment to your question about the need for normal distributions in PCA. Dr. Mitteroecker is (of course) correct that PCA does not make any distributional assumptions, but you mentioned in passing that confidence ellipses are being placed

Re: [MORPHMET] Landmarks coming up funny in MorphoJ

2017-11-06 Thread K. James Soda
Dear Ms. Neves, Quick addition to Dr. Rohlf's solution. To change a file extension on a Windows machine, you will need to do the following: 1) Open a Windows Explorer window. 2) On the ribbon at the top of the window, click "View" 3) Click the box for "File Name Extensions" (in the "Show/Hide"

Re: [MORPHMET] How to project shape difference onto different PC

2018-05-18 Thread K. James Soda
Dear Dr. Hu, Let me begin by restating how I understand the question: You have completed a PCA on a morphological data set in which there are two subsets of interest. Now you would like to decompose the difference between the two subsets into differences along individual PCs. Here is my two cents

Re: [MORPHMET] Pillai Tr

2018-08-23 Thread K. James Soda
Dear Dr. Rodriguez, When you said Goodman, did you mean Goodall? If so, these statistics arise from two different types of tests. Both have their advantages and their drawbacks. Goodall's F-test is a shape-specific test for differences between groups, if I am not mistaken. The advantage is that

Re: [MORPHMET] How can I test the project for identification of unknown crania?

2018-04-02 Thread K. James Soda
Dear Dr. Ibrahim, As you note, standard LDA does not usually permit nested groupings. In this scenario, you would either need to have one LDA for sex and one LDA for ancestry OR you could have one LDA that classifies into compound sex-ancestry groups (i.e., male-Malay, female-Malay,

Re: [MORPHMET] A question regarding "target shape"

2018-10-31 Thread K. James Soda
Dear Mr. Ardón, Good question. Whenever we make shape comparisons in GM, be that via displacement vector or deformation grid (which is what you’re doing), we can typically only compare two shapes at a time. One shape is called the reference (or starting shape, in this case). This is the shape

Re: [MORPHMET] Dennis Slice

2019-06-17 Thread K. James Soda
Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University phone: 515-294-3834 On Mon, Jun 17, 2019 at 3:53 AM K. James Soda wrote: > Hello Everyone, > > Since Friday afternoon, I have struggl

Re: [MORPHMET] Dennis Slice

2019-06-17 Thread K. James Soda
Hello Everyone, Since Friday afternoon, I have struggled to put into words the kind of adviser Dennis Slice was to his students to supplement the elegant testimonies to his abilities as a researcher, but words fail me. I do not know how I can properly portray the care and compassion that he

[MORPHMET] Migrating to the New Morphmet (aka morphmet2)

2019-07-02 Thread K. James Soda
Hello Everyone, Quick update on the state of morphmet: Over the weekend, I lost some administrative control over the 2014 version of morphmet. Fearing that this was an indication that it would go down soon, I started sending out invitations for a new version. At this point, most members who were

[MORPHMET] Morphmet in the Future

2019-06-29 Thread K. James Soda
Dear Fellow Morphometricians, I want to give a quick comment about the future of morphmet after Dennis's passing so that any necessary changes will not come as a surprise. Please rest assure that it is not a question of whether morphmet will continue but rather if any different procedures will be