# Collection and Analysis of Otolith Shape Data

## Documentation for package ‘shapeR’ version 1.0-2

- 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