shapeR: Collection and Analysis of Otolith Shape Data

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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.

Author
Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
Date of publication
2015-05-20 14:15:42
Maintainer
Lisa Anne Libungan <lisa.libungan@gmail.com>
License
GPL (>= 2)
Version
0.1-5
URLs

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...

Files in this package

shapeR
shapeR/NAMESPACE
shapeR/data
shapeR/data/shape.RData
shapeR/data/datalist
shapeR/data/FISH.csv.gz
shapeR/R
shapeR/R/shapeR.R
shapeR/R/shapeR_functions.R
shapeR/MD5
shapeR/DESCRIPTION
shapeR/man
shapeR/man/cluster.plot.Rd
shapeR/man/enrich.master.list.Rd
shapeR/man/estimate.outline.reconstruction.Rd
shapeR/man/generateShapeCoefficients.Rd
shapeR/man/plotWavelet.Rd
shapeR/man/getWavelet.Rd
shapeR/man/getFourier.Rd
shapeR/man/show.Rd
shapeR/man/getStdFourier.Rd
shapeR/man/smoothout.Rd
shapeR/man/plotWaveletShape.Rd
shapeR/man/FISH.Rd
shapeR/man/outline.reconstruction.plot.Rd
shapeR/man/getStdWavelet.Rd
shapeR/man/setFilter.Rd
shapeR/man/getStdMeasurements.Rd
shapeR/man/plotFourier.Rd
shapeR/man/detect.outline.Rd
shapeR/man/plotFourierShape.Rd
shapeR/man/show.original.with.outline.Rd
shapeR/man/read.master.list.Rd
shapeR/man/write.image.with.outline.Rd
shapeR/man/stdCoefs.Rd
shapeR/man/shape.Rd
shapeR/man/getMeasurements.Rd
shapeR/man/shapeR.Rd
shapeR/man/getMasterlist.Rd
shapeR/man/remove.outline.Rd