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.

AuthorLisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
Date of publication2015-05-20 14:15:42
MaintainerLisa Anne Libungan <lisa.libungan@gmail.com>
LicenseGPL (>= 2)
Version0.1-5
https://github.com/lisalibungan/shapeR, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102

View on CRAN

Man pages

cluster.plot: Plot data clusters

detect.outline: Detect otolith outline

enrich.master.list: Link information in the info.file to the coefficients...

estimate.outline.reconstruction: Estimate the outline reconstruction based on Fourier/wavelet...

FISH: An example data file

generateShapeCoefficients: Get wavelet/Fourier coefficients and basic shape variables

getFourier: Get Fourier coefficients, filtered according to filter

getMasterlist: Get filtered master.list values

getMeasurements: Get simple shape variables, filtered according to filter

getStdFourier: Get standardized Fourier coefficients, filtered according to...

getStdMeasurements: Get simple shape variables after standardization, filtered...

getStdWavelet: Get standardized wavelet coefficients, filtered according to...

getWavelet: Get wavelet coefficients, filtered according to filter

outline.reconstruction.plot: Plot outline reconstruction

plotFourier: Mean and standard deviation of the Fourier coefficients

plotFourierShape: Mean otolith shape based on Fourier reconstruction

plotWavelet: Mean and standard deviation of the wavelet coefficients

plotWaveletShape: Mean otolith shape based on wavelet reconstruction

read.master.list: Read updated master list

remove.outline: Remove otolith outline

setFilter: Set a filter to analyze the shape data

shape: An example shapeR instance including 160 images.

shapeR: shapeR

show: Show a shapeR object

show.original.with.outline: Show the extracted outline on top of the original image

smoothout: Contour smoothing

stdCoefs: Standardize coefficients

write.image.with.outline: Write outlines on top of the original images for quality...

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.