shapeR: Collection and Analysis of Otolith Shape Data

Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.

Version: 0.1-5
Depends: R (≥ 3.0.2)
Imports: gplots, jpeg, pixmap, wavethresh, methods, vegan, MASS
Published: 2015-05-20
Author: Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
Maintainer: Lisa Anne Libungan <lisa.libungan at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/lisalibungan/shapeR, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102
NeedsCompilation: no
CRAN checks: shapeR results

Downloads:

Reference manual: shapeR.pdf
Package source: shapeR_0.1-5.tar.gz
Windows binaries: r-devel: shapeR_0.1-5.zip, r-release: shapeR_0.1-5.zip, r-oldrel: shapeR_0.1-5.zip
OS X Mavericks binaries: r-release: shapeR_0.1-5.tgz, r-oldrel: shapeR_0.1-5.tgz
Old sources: shapeR archive

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