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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 otolith shape based on Wavelet reconstruction for three discrete fish populations from Iceland (IC, n = 65), Norway (NO, n = 65) and Scotland (SC, n = 30).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.
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pone.0121102.g002: Mean otolith shape based on Wavelet reconstruction for three discrete fish populations from Iceland (IC, n = 65), Norway (NO, n = 65) and Scotland (SC, n = 30).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.

Mentions: When all the outlines have been captured with high quality, the shape coefficients can be extracted using the function generateShapeCoefficients. Before the Wavelet transformation, the rotation of all otoliths are positioned horizontally along the longest axis of the otoliths and the area is set equal in all (area = 1). Polar coordinates are then collected by drawing a polar axis (radial) horizontally from the otolith centroid (i.e. the mean of the x and y coordinates of the outline) to the right which corresponds to the 0° angle of the otolith outline (Fig. 2). From the 0° angle, radials are collected counter clockwise towards the 360° angle with equidistant angles between successive radials. The Wavelet coefficients are obtained using the functions wd and wr in the wavethresh package [14]. For Fourier, the Normalized Elliptic Fourier technique is performed using the iefourier and efourier functions [17] which both normalizes the otoliths with regards to size and rotation and collects the coefficients. Ten Wavelet levels give a total of 64 Wavelet coefficients using the Daubechies least-asymmetric Wavelet [18] and 12 harmonics give 45 Normalized Elliptic Fourier coefficients (48−3 = 45, the first three coefficients are omitted due to standardisation in relation to size, rotation and starting point). The coefficients are collected with:


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

Libungan LA, Pálsson S - PLoS ONE (2015)

Mean otolith shape based on Wavelet reconstruction for three discrete fish populations from Iceland (IC, n = 65), Norway (NO, n = 65) and Scotland (SC, n = 30).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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121102.g002: Mean otolith shape based on Wavelet reconstruction for three discrete fish populations from Iceland (IC, n = 65), Norway (NO, n = 65) and Scotland (SC, n = 30).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.
Mentions: When all the outlines have been captured with high quality, the shape coefficients can be extracted using the function generateShapeCoefficients. Before the Wavelet transformation, the rotation of all otoliths are positioned horizontally along the longest axis of the otoliths and the area is set equal in all (area = 1). Polar coordinates are then collected by drawing a polar axis (radial) horizontally from the otolith centroid (i.e. the mean of the x and y coordinates of the outline) to the right which corresponds to the 0° angle of the otolith outline (Fig. 2). From the 0° angle, radials are collected counter clockwise towards the 360° angle with equidistant angles between successive radials. The Wavelet coefficients are obtained using the functions wd and wr in the wavethresh package [14]. For Fourier, the Normalized Elliptic Fourier technique is performed using the iefourier and efourier functions [17] which both normalizes the otoliths with regards to size and rotation and collects the coefficients. Ten Wavelet levels give a total of 64 Wavelet coefficients using the Daubechies least-asymmetric Wavelet [18] and 12 harmonics give 45 Normalized Elliptic Fourier coefficients (48−3 = 45, the first three coefficients are omitted due to standardisation in relation to size, rotation and starting point). The coefficients are collected with:

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.