Collection and Analysis of Otolith Shape Data

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Documentation for package ‘shapeR’ version 1.0-1

• DESCRIPTION file.
• Package NEWS.

Help Pages

cluster.plot	Plot data clusters
detect.outline	Detect otolith outline
enrich.master.list	Link information in the info.file to the coefficients obtained from the otolith images
estimate.outline.reconstruction	Estimate the outline reconstruction based on Fourier/wavelet compared to the outlines that have not been transformed
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 filter
getStdMeasurements	Get simple shape variables after standardization, filtered according to filter
getStdWavelet	Get standardized wavelet coefficients, filtered according to filter
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
shapeR-class	shapeR
show-method	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 checking