Geomorph 1.1-5 Now available!

December 13, 2013
By

(This article was first published on geomorph, and kindly contributed to R-bloggers)

Geomorph users,

We have uploaded version 1.1-5 to CRAN. The windows binary has been compiled and the tarball is available. The MAC OSX binary may take a few days (mac users can install the package from source using the tar.gz file). The PDF of helpfiles has not yet been updated - as of 10am CST Dec 13 2013.

In this new version, there are some edits to existing function as well as a new function! In summary:


  • The 2d and 3d digitizing functions have had their helpfiles spruced up! Video tutorials of digitizing in geomorph are coming later this month.
  • The functions digit.curves and curves2d have got new names: define.sliders.2d and define.sliders.3d. This should help clear up any confusion regarding what these functions do (details below).
  • For better visualization, functions plotAllometry and plotTangetSpace now have a "group" option, where the groups are plotted in different colors. Simply type groups = mygroup, where 'mygroup' is a vector containing the labels for each specimen (order must match order of specimens). The plotTangetSpace example now contains this option, so go check it out!
  • There's a new function! compare.evol.rates - the function compares rates of morphological evolution for two or more groups of species on a phylogeny, under a Brownian motion model of evolution. This function is based on a new method in Systematic Biology: Adams 2014 Quantifying and Comparing Phylogenetic Evolutionary Rates for Shape and other High-Dimensional Phenotypic Data.(doi: 10.1093/sysbio/syt105) first published online 12/10/13. This approach generalizes comparative methods for single-valued traits (e.g., O’Meara et al. 2006) for the case of high-dimensional multivariate data.

define.sliders.2d and define.sliders.3d

These two functions are designed to aid the user in creating a landmark address file (curveslide.csv), within which landmarks that will be treated as sliding semilandmarks during Generalized Procrustes superimposition are defined. The input is a matrix of 2d or 3d coordinates for one specimen. These coordinates can be digitized with the geomorph digitizing functions, or they can come from external digitizing software.

For both functions, the procedure is as follows:
Say we have a file, spec, with 10 landmarks distributed around a closed-boundary of an object. 1 to 6 are fixed (type I landmarks) and 7 to 10 are semilandmarks.
nsliders = 4 (number of the digitized landmarks in spec to be defined as curve sliding semilandmarks).

Landmark '7' is the first sliding semilandmark, and it will slide between landmarks 6 and 8 along a curve. Then select landmark 6, then 7 then 8. The file created will have the first row will be:
 6  7  8
Landmark 8 is also a slider, to slide between 7 and 9, so select 7 then 8 then 9. Now the file has a new line:
 6  7  8
 7  8  9
Repeat the process until nsliders have been defined. Then you have a curveslide.csv file with nsliders lines that looks like this:
 before slide after
 6  7  8
 7  8  9
 8  9  10
 9  10 1
See that because the landmarks of our specimen were digitized on a closed-boundary circuit, the last slider slides between 9 (a slider) and 1 (a fixed landmark).

In define.sliders.3d, an extra option is available. If the matrix of coordinates also contains landmarks that are surface sliding semilandmarks (as made using buildtemplate and digitsurface), then the file of landmarks addresses (surfslide.csv) should be in the working directory and choose surfsliders = TRUE
So for example spec has 20 landmarks: 1 to 6 are fixed (type I landmarks) and 7 to 10 are curve sliding semilandmarks and 11 to 20 are surface sliding landmarks. Then surfside.csv is a vector: 11 12 13 14 15 16 17 18 19 20.
For 2d and 3d digitizing, It is good practice to digitize all of the fixed (type I landmarks) first, then the curve slider semilandmarks and surface slider semilandmarks. 
More information on surface and curve sliding semilandmarks can be found in the geomorph help files and references within.

Happy Holidays!

Emma

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