Thursday, June 25, 2015

Geomorph update 2.1.6 Now Available!

Geomorph users,

We have uploaded version 2.1.6 of geomorph* to CRAN. The windows and mac binaries have been compiled and the tarball is available.

Thursday, June 18, 2015

Tips & Tricks 9: Shape Changes and Hypothetical Shapes

Geomorph users,

This month's tips and tricks was prompted by a user email from Tim Astrop, thanks Tim!


How can I create a hypothetical shape representing a point in shape space?

Today we will use some relatively simple R code to create a shape based on position in a Principal Component (PC) shape space and visualise this shape as a change from the mean using plotRefToTarget().

Exercise 9 - Creating hypothetical shapes


Tuesday, June 9, 2015

advanced.procD.lm for pairwise tests and model comparisons

In geomorph 2.1.5, we decided to deprecate the functions, pairwiseD.test and pairwise.slope.test.   Our reason for this was two-fold.  First, recent updates by CRAN rendered these functions unstable.  These functions depended on the model.frame family of base functions, which were updated by CRAN.  We tried to find solutions but the updated pairwise functions were worse than non-functioning functions, as they sometimes provided incorrect results (owing to strange sorting of rows in design matrices).  We realized that we were in a position that required a complete overhaul of these functions, if we wanted to maintain them.  Second, because advanced.procD.lm was already capable of pairwise tests and did not suffer from the same issues, we realized we did not have to update the other functions, but could instead help users understand how to use advancd.procD.lm.  Basically, this blog post is a much better use of time than trying again and again to fix broken functions.  Before reading on, if you have not already read the blog post on ANOVA in geomorph, it would probably be worth your time to read that post first.

Sunday, May 24, 2015

Geomorph update 2.1.5 Now Available!

Geomorph users,

We have uploaded version 2.1.5 of geomorph* to CRAN. The windows and mac binaries have been compiled and the tarball is available.

Sunday, May 3, 2015

Geomorph beta in development (2.1.5)

Dear geomorph users,

We've been busy adding some new functions to the forthcoming v.2.1.5, currently in beta stage and available on gitHub (installed using: devtools::install_github("EmSherratt/geomorph",ref = "Develop")). Users be aware that we strongly discourage you from publishing results with this version, unless you check with us first.

NEW Functions:

  •  gridPar function to customise plots of plotRefToTarget
  •  digit.curves function to calculate equidistant semilandmarks along 2D and 3D curves
  •  define.sliders interactive function for defining sliding semilandmarks for 2D and 3D curves, plus an automatic mode when given a sequence of semilandmarks along a curve.

Feedback most welcome!

Emma, Mike and Dean.

p.s. Twitter users can follow me with @DrEmSherratt to send quick comments or suggestions.

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().