Package: shapeR 0.1-5

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.

Authors:Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]

shapeR_0.1-5.tar.gz
shapeR_0.1-5.zip(r-4.5)shapeR_0.1-5.zip(r-4.4)shapeR_0.1-5.zip(r-4.3)
shapeR_0.1-5.tgz(r-4.4-any)shapeR_0.1-5.tgz(r-4.3-any)
shapeR_0.1-5.tar.gz(r-4.5-noble)shapeR_0.1-5.tar.gz(r-4.4-noble)
shapeR_0.1-5.tgz(r-4.4-emscripten)shapeR_0.1-5.tgz(r-4.3-emscripten)
shapeR.pdf |shapeR.html
shapeR/json (API)

# Install 'shapeR' in R:
install.packages('shapeR', repos = c('https://lisalibungan.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lisalibungan/shaper/issues

Datasets:
  • FISH - An example data file
  • shape - An example shapeR instance including 160 images.
  • shape - An example shapeR instance including 160 images.

On CRAN:

4.43 score 9 stars 20 scripts 224 downloads 3 mentions 26 exports 16 dependencies

Last updated 7 years agofrom:75a5b53928. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 12 2024
R-4.5-winNOTEOct 12 2024
R-4.5-linuxNOTEOct 12 2024
R-4.4-winNOTEOct 12 2024
R-4.4-macNOTEOct 12 2024
R-4.3-winNOTEOct 12 2024
R-4.3-macNOTEOct 12 2024

Exports:cluster.plotdetect.outlineenrich.master.listestimate.outline.reconstructiongenerateShapeCoefficientsgetFouriergetMasterlistgetMeasurementsgetStdFouriergetStdMeasurementsgetStdWaveletgetWaveletoutline.reconstruction.plotplotFourierplotFourierShapeplotWaveletplotWaveletShaperead.master.listremove.outlinesetFiltershapeRshowshow.original.with.outlinesmoothoutstdCoefswrite.image.with.outline

Dependencies:bitopscaToolsclustergplotsgtoolsjpegKernSmoothlatticeMASSMatrixmgcvnlmepermutepixmapveganwavethresh

Readme and manuals

Help Manual

Help pageTopics
Plot data clusterscluster.plot
Detect otolith outlinedetect.outline
Link information in the info.file to the coefficients obtained from the otolith imagesenrich.master.list
Estimate the outline reconstruction based on Fourier/wavelet compared to the outlines that have not been transformedestimate.outline.reconstruction
An example data fileFISH
Get wavelet/Fourier coefficients and basic shape variablesgenerateShapeCoefficients
Get Fourier coefficients, filtered according to filtergetFourier
Get filtered master.list valuesgetMasterlist
Get simple shape variables, filtered according to filtergetMeasurements
Get standardized Fourier coefficients, filtered according to filtergetStdFourier
Get simple shape variables after standardization, filtered according to filtergetStdMeasurements
Get standardized wavelet coefficients, filtered according to filtergetStdWavelet
Get wavelet coefficients, filtered according to filtergetWavelet
Plot outline reconstructionoutline.reconstruction.plot
Mean and standard deviation of the Fourier coefficientsplotFourier
Mean otolith shape based on Fourier reconstructionplotFourierShape
Mean and standard deviation of the wavelet coefficientsplotWavelet
Mean otolith shape based on wavelet reconstructionplotWaveletShape
Read updated master listread.master.list
Remove otolith outlineremove.outline
Set a filter to analyze the shape datasetFilter
An example shapeR instance including 160 images.shape
shapeRshapeR-package shapeR shapeR-class
Show a shapeR objectshow,shapeR-method
Show the extracted outline on top of the original imageshow.original.with.outline
Contour smoothingsmoothout
Standardize coefficientsstdCoefs
Write outlines on top of the original images for quality checkingwrite.image.with.outline