Saturday, April 4, 2015

Geomorph update 2.1.4 Now Available!

Geomorph users,

We have uploaded version 2.1.4 of geomorph to CRAN. The windows and mac binaries have been compiled and the tarball is available*.

Tips & Tricks 8: Examining Replicate Error

Geomorph users,

When starting out in a geometric morphometrics study, the common questions are ones of repeatability and measurement error.

How much of the variation in the Procrustes residuals is due to human (digitizing) error? How much is due to paralax (2D photographs)? How much is due to the threshold choice (3D surface meshes)?

Today we use the Procrustes ANOVA function to learn about how to check for repeatability and in doing so learn also about nested ANOVAs.

Exercise 8 - Examining Replicate Error with procD.lm().


Wednesday, April 1, 2015

ANOVAs and Geomorph

Within geomorph are several functions that perform analysis of variance (ANOVA), including
procD.lm()
procD.pgls()
advanced.procD.lm()
pairwiseD.test()
pairwise.slope.test()
trajectory,analysis()
bilat.symmetry()
plotAllometry()

Wednesday, March 25, 2015

Geomorph and Multivariate Datasets

Did you know that geomorph is not just for landmark-based geometric morphometric (shape) data?

We are committed to providing statistical tools for multivariate AND multidimensional morphometric data.

As laid out in the recent series of papers on Phylogenetic Comparative Methods for high-dimensional data (Adams 2014a, Adams 2014b, Adams 2014c, Adams & Felice 2014), harnessing the R-mode – Q-mode equivalency as first shown by Gower (1966) has allowed us to overcome the issue of greater variables (p) than specimens (n).

Certainly geometric morphometrics has been doing this for many years, using the Procrustes ANOVA (Goodall 1991) which is a distance-based (Q-mode) approach. The distance-based PGLS has a substantially better type I error than previously implemented approaches (Adams & Collyer 2015).

The issue, in short is that when you have p greater than or very close to n, there will be problems; your test will lose power or worse it simply will not work. The solution is to use the functions below that are designed for multivariate datasets (e.g. sets of linear measurements*) as well as multidimensional shape data (from landmark coordinates).

Here is a list of geomorph functions that can take 
multivariate morphometric datasets for statistical analysis:

Monday, March 23, 2015

News So Far for Geomorph v2.1.4beta

Dear geomorph users,

we have so far recognised and fixed the following bugs known to be in geomorph v.2.1.3 on CRAN, and these are available in the GitHub repository of v.2.1.4beta:

  BUG FIXES

  •     Corrected error readland.tps() "Error in pts[i, 1] : subscript out of bounds"
  •     Corrected errors trajectory.analysis()
  •     Corrected an issue with gpagen() that flipped principal axes
  •     Fixed error in read.morphologika() with reading [wireframe] in some morphologika     files (thanks to Marc Jones of Uni of Adelaide for pointing this out)

Thursday, March 19, 2015

Tips & Tricks 7: Plotting PCA with TPS grids

Geomorph users,

Our function plotTangentSpace() performs a Principal Components Analysis (PCA) of shape variation and plots two dimensions of tangent space for a set of Procrustes-aligned specimens and also returns the shape changes associated with the two plotted principal axes. We purposefully restricted the options for this function because plotting in R has almost endless possibilities. That is why we added the 'verbose=TRUE' option, so that the pc scores and pc shapes could be plotted on their own. And users are of course expected to do this for their publications and reports.

In this week's exercise, we explore a few options to do advance of plotting PCAs and TPS grids with geomorph and R base functions. 

Exercise 7 - Plotting Principal Components Analysis Graphs with TPS grids.


Monday, March 16, 2015

Installing Geomorph and R by Source

Since we started having a beta version of geomorph on GitHub, we understand that installation has become a little bit more complex. We were also aware of the issues for Mac Snow Leopard users.

I have written a detailed summary of how to install geomorph via Package Source or GitHub Source on the new geomorph.net Installation Page.

These instructions allow the most recent geomorph version to be available for users from Mac OS10.6 (Snow Leopard) to OS10.10 (Yosemite). Windows users are also covered (including the quirks of installing on shared computers).

Emma