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.
- Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
- Date of publication
- 2015-05-20 14:15:42
- Lisa Anne Libungan <email@example.com>
- GPL (>= 2)
- Plot data clusters
- Detect otolith outline
- Link information in the info.file to the coefficients...
- Estimate the outline reconstruction based on Fourier/wavelet...
- 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...
- Get simple shape variables after standardization, filtered...
- Get standardized wavelet coefficients, filtered according to...
- 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
- An example shapeR instance including 160 images.
- Show a shapeR object
- Show the extracted outline on top of the original image
- Contour smoothing
- Standardize coefficients
- Write outlines on top of the original images for quality...
Files in this package