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ShapeR: an R package to study otolith shape variation among fish populations.

Libungan LA, Pálsson S - PLoS ONE (2015)

Bottom Line: ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland.

ABSTRACT
ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations. 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.

No MeSH data available.


Quality of the a) Wavelet and b) Fourier outline reconstruction.The red vertical lines show the level of Wavelet and number of Fourier harmonics needed for a 98.5% accuracy of the reconstruction.
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pone.0121102.g003: Quality of the a) Wavelet and b) Fourier outline reconstruction.The red vertical lines show the level of Wavelet and number of Fourier harmonics needed for a 98.5% accuracy of the reconstruction.

Mentions: As seen in Fig. 3, the quality increases as expected with the number of Wavelet/Fourier coefficients used.


ShapeR: an R package to study otolith shape variation among fish populations.

Libungan LA, Pálsson S - PLoS ONE (2015)

Quality of the a) Wavelet and b) Fourier outline reconstruction.The red vertical lines show the level of Wavelet and number of Fourier harmonics needed for a 98.5% accuracy of the reconstruction.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4372608&req=5

pone.0121102.g003: Quality of the a) Wavelet and b) Fourier outline reconstruction.The red vertical lines show the level of Wavelet and number of Fourier harmonics needed for a 98.5% accuracy of the reconstruction.
Mentions: As seen in Fig. 3, the quality increases as expected with the number of Wavelet/Fourier coefficients used.

Bottom Line: ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland.

ABSTRACT
ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations. 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.

No MeSH data available.