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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.


Otolith shape of samples from three herring populations in the NE-Atlantic using Canonical analysis of Principal Coordinates with the Wavelet coefficients.Canonical scores on the first two discriminating axes CAP1 and CAP2 are shown. Black letters represent the mean canonical value for each population, Iceland (IC), Norway (NO) and Scotland (SC) and smaller letters represent individual fish showing the first letter of each population. Interval surrounding the mean canonical values present one standard error (mean +/- 1SE).
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pone.0121102.g005: Otolith shape of samples from three herring populations in the NE-Atlantic using Canonical analysis of Principal Coordinates with the Wavelet coefficients.Canonical scores on the first two discriminating axes CAP1 and CAP2 are shown. Black letters represent the mean canonical value for each population, Iceland (IC), Norway (NO) and Scotland (SC) and smaller letters represent individual fish showing the first letter of each population. Interval surrounding the mean canonical values present one standard error (mean +/- 1SE).

Mentions: For visualizing the clustering of the CAP results using the Wavelet coefficients in two dimensions (Fig. 5):


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

Libungan LA, Pálsson S - PLoS ONE (2015)

Otolith shape of samples from three herring populations in the NE-Atlantic using Canonical analysis of Principal Coordinates with the Wavelet coefficients.Canonical scores on the first two discriminating axes CAP1 and CAP2 are shown. Black letters represent the mean canonical value for each population, Iceland (IC), Norway (NO) and Scotland (SC) and smaller letters represent individual fish showing the first letter of each population. Interval surrounding the mean canonical values present one standard error (mean +/- 1SE).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121102.g005: Otolith shape of samples from three herring populations in the NE-Atlantic using Canonical analysis of Principal Coordinates with the Wavelet coefficients.Canonical scores on the first two discriminating axes CAP1 and CAP2 are shown. Black letters represent the mean canonical value for each population, Iceland (IC), Norway (NO) and Scotland (SC) and smaller letters represent individual fish showing the first letter of each population. Interval surrounding the mean canonical values present one standard error (mean +/- 1SE).
Mentions: For visualizing the clustering of the CAP results using the Wavelet coefficients in two dimensions (Fig. 5):

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.