Collection and Analysis of Otolith Shape Data
Plot data clusters
Detect otolith outline
Link information in the info.file to the coefficients obtained from th...
Estimate the outline reconstruction based on Fourier/wavelet compared ...
An example data file
Get wavelet/Fourier coefficients and basic shape variables
Get Fourier coefficients, filtered according to filter
Get filtered master.list values
Get simple shape variables, filtered according to filter
Get standardized Fourier coefficients, filtered according to filter
Get simple shape variables after standardization, filtered according t...
Get standardized wavelet coefficients, filtered according to filter
Get wavelet coefficients, filtered according to filter
Plot outline reconstruction
Mean and standard deviation of the Fourier coefficients
Mean otolith shape based on Fourier reconstruction
Mean and standard deviation of the wavelet coefficients
Mean otolith shape based on wavelet reconstruction
Read updated master list
Remove otolith outline
Set a filter to analyze the shape data
shapeR: Otholith analysis
shapeR
Show the extracted outline on top of the original image
Show a shapeR object
Contour smoothing
Standardize coefficients
Write outlines on top of the original images for quality checking
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 described in Haines and Crampton (2000) <doi:10.1111/1475-4983.00148>, choose from conducting either a Fourier or wavelet see Gençay et al (2001) <doi:10.1016/S0378-4371(00)00463-5> 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.
Useful links