Re: [MORPHMET] help with "classify" in RRPP

Nicole, I assume that your intention is to summarize a species probability from the several probabilities of specimens, if data sets are combined? (I think you might have used “species” twice but meant “specimen" once, below). If so, there are two ways you could do this. One would be as you

Re: [MORPHMET] Re: semilandmarks in biology

Andrea, I am intrigued by your initial comment about adding covariance that was apparently absent. I tend to think of the problem from the other perspective of not accounting for covariance that should be present. As a thought experiment (that could probably be simulated, and maybe I am not

Re: [MORPHMET] Re: Are more semi landmarks better??

Philipp’s message below felt a little like a déjà vu moment. I checked the Morphmet archives and sure enough, we had a similar thread back in late May/Early June, 2017. Diego, you might want to check that thread, as a lot of what was discussed is relevant to your current questions. Cheers!

[MORPHMET] Re: Conceptual clarification of plotting shape deformation grids in geomorph

gt; abstractness of shape space and coding ;-P Thanks again! > > > Best wishes, > Javier > > > From: Mike Collyer > > Sent: Wednesday, July 25, 2018 2:29:38 PM > To: Javier Santos > Cc: Morphomet Mailing List > Subject: Re: Conceptual clarification of plotting

Re: [MORPHMET] % of overlap of convex hulls in 2D scatterplots

Andrea, There are two ways to do this, one precise and one less precise. The less precise method is to calculate the convex hull areas of three hulls: the two of interest and one comprising the points of both. Subtract the total area of the comprehensive hull from the sum of the two groups

Re: [MORPHMET] help us in multifactor Manova

t; command to quantify effects of interaction, say for example ind$Stages: > ind$Location, Csize: ind$Stages, Csize: ind$Locations... etc. > > Thanks for spending your time and effort! > > Looking forward > > Truly > > Mahen > > > > On Fri, May

Re: [MORPHMET] help us in multifactor Manova

Mahen, Can you be specific with the error statement? It might not me related to the int.first use but more so how you set up your formula. If ind$Stages and ind$Location are in the data frame, you are asking R to create a model matrix from dat in an environment within another environment.

Re: [MORPHMET] 2B PLS question

Angela, The question I believe you are asking is if there is a way to have 2B-PLS work for n-dimensional data (n rows in your data matrix) when you have a s-dimensional phylogenetic covariance matrix (s x s dimensions for s species covariances) and s < n. The phylo-integration function will

Re: [MORPHMET] Issue with sliders file data

Katherine, It appears your issue is that the curves argument in gpagen expects a matrix but is receiving something in a different format (or a matrix with less than 3 columns). You mentioned rebuilding a TPS file and creating sliders, which sounds like you were using TPS software. I’m not

Re: [MORPHMET] pairwise matrix of vector angles in R

diagonal of the > matrix of angles), or to an identical vector in another row (i != j, hence > deposited in an off-diagonal cell). > > I think the line diag(vc) = 0 in Mike's vec.angle.matrix code is meant to do > the same thing for his diagonal values. > > Again, sorry f

Re: [MORPHMET] pairwise matrix of vector angles in R

Dear David, and others, Be careful with the code you just introduced here. There are a couple of mistakes. First, vectors need to be unit length. You code does not transform the vectors to unit length. Second, it’s the arccosine, the cosine of the vector inner product that finds the angle.

Re: [MORPHMET] pairwise matrix of vector angles in R

Andrea, If you already have the matrix of coefficients, geomorph has an internal function that can do what you seek to do. You can try this geomorph:::vec.ang.matrix(myMatrix, type = “r”) # for vector correlations geomorph:::vec.ang.matrix(myMatrix, type = “rad”) # for vector angles in radians

Re: [MORPHMET] Procrustes fit

Andrea, I think it is worth it to do a pedantic review of your exercise for the benefit of the community. First, the differences are not data dependent - they are method dependent. TPSRelw uses partial Procrustes; MorphoJ uses full Procrustes superimposition. PCA would have the exact same

[MORPHMET] geomorph updates

Dear Colleagues, I wish to alert you to a couple of geomorph updates, which are available with an installation of geomorph version 3.0.5, from Github (not yet available on CRAN). These updates include: - A new argument in advanced.procD.lm to choose among different distributions (SS, Rsq, or

[MORPHMET] Re: number of landmarks and sample size

Ilker, Philipp already defined well why - I think - this rationale is incorrect, if not dangerous, especially along the lines of statistical power. As he indicated, using Procrustes residuals as data means a covariance matrix will never be full rank, owing to the invariance in size,

Re: [MORPHMET] number of landmarks and sample size

Dear Lea, I see others have responded to your inquiry, already. I thought I would add an additional perspective. Your question about statistical significance requires asking a follow-up question. What statistical methods would you intend to use to evaluate “significance”? If you are

Re: [MORPHMET] geomorph: trajectory analysis error

Lawrence, I recommend first making a geomorph data frame and using it in your analyses. If the error persists, let us know. These types of errors are often caused by R trying to figure out how to use objects in the global environment, rather that getting the data specifically from a list.

Re: brief comment on non-significance Re: [MORPHMET] procD.allometry with group inclusion

ase of MANCOVAs/vector > angles but certainly in the simpler case of comparisons of means). > > Cheers > > > Andrea > > On 11/12/16 19:17, Mike Collyer wrote: >> Dear Tsung, >> >> The geomorph function, advanced.procD.lm, allows one to extr

Re: [MORPHMET] procD.allometry with group inclusion

s mainly explained by variation in species, and allometry is > absent? > > Regards, > > T.F. > > On Thursday, December 8, 2016 at 6:08:17 PM UTC+8, Mike Collyer wrote: > Dear Tsung, > > The procD.allometry function performs two basic processes when groups are > provided

Re: [MORPHMET] procD.allometry with group inclusion

Dear Tsung, The procD.allometry function performs two basic processes when groups are provided. First, it does a homogeneity of slopes (HOS) test. This test ascertains whether two or more groups have parallel or unique slopes (the latter meaning at least one groups’s slope is different than

[MORPHMET] Re: [geomorph-r-package] Re: geomorph updates

Milena, You must provide a branch reference devtools:::install_github(“geomorphR/geomorph”, ref = “Stable”) should work, but devtools:::install_github(“geomorphR/geomorph”) will not work. Mike > On Oct 28, 2016, at 9:57 AM, Milena Stefanovic wrote: > > > It

[MORPHMET] geomorph updates

Colleagues, I wish to alert you to a small but important update to geomorph. A coding error was found that limited the number of random permutations to 1-100 permutations, irrespective of choice, for one particular analysis type in advanced.procD.lm. This also had implications for the