plotFourier

The mean and standard deviation of the Fourier coefficients

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 described in Haines and Crampton (2000) <doi:10.1111/1475-4983.00148>,
choose from conducting either a Fourier or wavelet see Gençay et al (2001) <doi:10.1016/S0378-4371(00)00463-5> 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.

Lisa Anne Libungan

shapeR

Collection and Analysis of Otolith Shape Data

Snaebjorn Palsson

plotFourier function

<dl><dt>object</dt>
<dd><code>shapeR</code> object</dd>
<dt>coef.index</dt>
<dd>An index vector for which fourier coefficents to be shown. Default is <code>NULL</code> and all coefficients are shown.</dd>
<dt>class.name</dt>
<dd>Column name in master list for partitioning the data into groups and showing the ratio of variance among to the sum of variance among and variance within.</dd>
<dt>useStdcoef</dt>
<dd>Boolean saying if to use the standardized coefficients or not</dd>
<dt>...</dt>
<dd>Additional parameters to be passed to 'plot'</dd></dl>

Arguments

Author

Mean and standard deviation of the Fourier coefficients — plotFourier

<dl>

<dt>object</dt>
<dd><code>shapeR</code> object</dd>


<dt>coef.index</dt>
<dd>An index vector for which fourier coefficents to be shown. Default is <code>NULL</code> and all coefficients are shown.</dd>


<dt>class.name</dt>
<dd>Column name in master list for partitioning the data into groups and showing the ratio of variance among to the sum of variance among and variance within.</dd>


<dt>useStdcoef</dt>
<dd>Boolean saying if to use the standardized coefficients or not</dd>


<dt>...</dt>
<dd>Additional parameters to be passed to 'plot'</dd>

</dl>

plotFourier: Mean and standard deviation of the Fourier coefficients

Description

Usage

Value

Arguments

Author

Examples