The 'fog' module is designed to process an outline-based study. It performs the following:
- Elliptic Fourier Analysis
- Normalization based on the semi-major axis of H1 ellipse (NEF coefficients)
- Procrustes superimposition of recomputed shapes (only for graphical output)
- Principal component analyses of NEF coefficients.
- Discriminant analyses of NEF coefficients.
- Discriminant analyses of amplituds.
- Quantile box of size variation (perimeter, or rootsquared area of H1 ellipse).
- Allometric analysis.
- Help for using R (J. Claude's book).
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INPUT FILE
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'coord_[date]_OTL.txt'
(for instance 'coord_March15_OTL.txt', see the COO 'o.help')
or,
'coord_[date]_OTL_FOG.txt'
(an output file of 'fog' secondarily used as an input file)
The DATA of an ..._OTL.txt file are as follows:
col. 1: the number of points of the digitized line; this number includes the centroid point (note that lines may contain a different number of points).
col. 2 and 3: the x,y coordinates of the centroid point
next columns: the x,y coordinates of the digitized line (pseudo-landmarks)
The DATA of an ..._OTL_FOG.txt file are as follows:
col. 1 perimeter of the digitized line
col. 2 and 3: Ao and Co coefficients
next columns: 28 sets (28 harmonics), generally, of the 4 EFD (Elliptic Fourier Descriptors, or coefficients, named a,b,c,d).
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OUTPUT FILES
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ending by:
'..._OTL_FOG.txt' perimeter, Ao, Co, EFD
'..._OTL_FOGnef.txt' Normalized EFD (NEF), including H1 EFD
'..._OTL_FOGnefcp.txt' principal components of NEF
'..._OTL_FOGnefdf.txt' discriminant factors of NEF
'..._OTL_PER.txt' perimeter of the outline
'..._OTL_ARE.txt' root squared area of the H1 ellipse
'..._OTL_HAMP.txt' amplitudes of each harmonic, one by harmonic
'..._OTL_HAMPnef.txt' the "normalized" amplitudes, one by harmonic
'..._OTL_HAMPnefdf.txt' the discriminant factors derived from the "normalized" amplitudes
'..._OTL_POW.txt' power of each harmonic
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File formats
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As for the 'mog' input file, the internal format is as follows:
- The first row is a free comment, next rows are the data.
- The first row is mandatory.
- Data (next rows) are organized as a table without headers
- Empty rows are allowed, except the first one (see above).
- Columns are separated by a tabulation.
Exceptions to this CLIC data format are:
1. The 'coord_[date].txt' file, which is the natural 'coo' output file: it has an internal format close to the TPS format of Rohlf.
2. The CLIC data base format ('..._OTL_DB.txt'): there are headers!
3. The CLIC distance matrix format ('..._MAHAphylip.txt', etc.): except for the first row (the comment), its format depends on the external software to which it is destinated.