The 'cov' module brings you various specialized analyses (PLS, metric disparity, Collyer Adams model, common alometric component, etc.) using the files produced by other CLIC modules.
Please perform one analysis at a time, closing COV before each new analysis.
Use the WRAP button to read long lines.

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INPUT FILES
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Most of the CLIC files may be called by one or more of the 'cov' functions; the script generally informs you about the kind of INPUT FILE which is relevant for the function to be applied.

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OUTPUT FILES
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From the menu SINGLE MATRIX:
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'..._INFO_COVdst.txt' <- descriptive statistics of a matrix: report
'..._transposed.txt'  <- transposed matrix
'..._XtX.txt' <- transposed matrix X multiplied by the matrix X
'..._PC.txt'  <- variance-covariance matrix based principal components 
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From the menu TWO MATRICES:
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'..._INFO_COVX-Y'    <- substraction matrix X - Y: report 
'..._INFO_COVt2h'    <- T2 of Hotelling: report
'..._INFO_COVcor'    <- correlation between columns of 2 matrices: report
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From the menu SUBDIVIDED MATRIX:
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'..._1.txt', '..._2.txt', etc. <- submatrices from one matrix
'_PROCRUSTESphylip.txt'        <- a matrix of distances between submatrices created from one matrix
'..._W.txt'      <- pooled (or within) variance-covariance matrix
'..._INFO_COV.txt'    <- report saved from 'cov'
'..._INFO_COVpvpca.txt' <- PCA on pooledVCV matrix: report
'..._INFO_COVpwrw.txt'  <- PW and RW of submatrices: report
'..._INFO_COVinfluence' <- influential landmark: report
'..._INFO_COVmd.txt'  <- METRIC DISPARITY (MD) analysis: report
'..._INFO_COVpmd.txt' <- PARTIAL MD analysis: report
'..._INFO_COVqst.txt' <- QST analysis: report
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From the menu ALLOMETRY:
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From the menu PLS:
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From the menu Collyer & Adams, 2007:
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File format
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The CLIC data 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 the 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.