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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.


Mean and standard deviation (sd) of the Wavelet coefficients for all combined otoliths and the proportion of variance among groups or the intraclass correlation (ICC, black solid line).The horizontal axis shows angle in degrees (°) based on polar coordinates (see also Fig. 2) where the centroid of the otolith is the center point of the polar coordinates.
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pone.0121102.g004: Mean and standard deviation (sd) of the Wavelet coefficients for all combined otoliths and the proportion of variance among groups or the intraclass correlation (ICC, black solid line).The horizontal axis shows angle in degrees (°) based on polar coordinates (see also Fig. 2) where the centroid of the otolith is the center point of the polar coordinates.

Mentions: Numbers represent angles in degrees (°) based on polar coordinates (see Fig. 4). The centroid of the otolith (center of the cross) is the center point of the polar coordinates.


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

Libungan LA, Pálsson S - PLoS ONE (2015)

Mean and standard deviation (sd) of the Wavelet coefficients for all combined otoliths and the proportion of variance among groups or the intraclass correlation (ICC, black solid line).The horizontal axis shows angle in degrees (°) based on polar coordinates (see also Fig. 2) where the centroid of the otolith is the center point of the polar coordinates.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121102.g004: Mean and standard deviation (sd) of the Wavelet coefficients for all combined otoliths and the proportion of variance among groups or the intraclass correlation (ICC, black solid line).The horizontal axis shows angle in degrees (°) based on polar coordinates (see also Fig. 2) where the centroid of the otolith is the center point of the polar coordinates.
Mentions: Numbers represent angles in degrees (°) based on polar coordinates (see Fig. 4). The centroid of the otolith (center of the cross) is the center point of the polar coordinates.

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.