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```
### partial.R (2008-11-14)
###
### Partial Correlation and Partial Variance
###
###
### Copyright 2003-2008 Juliane Schaefer and Korbinian Strimmer
###
### This file is part of the `corpcor' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 3, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE. See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
#
# partial correlation matrix
#
# input: covariance matrix or correlation matrix
# ouput: partial correlation matrix
#
cor2pcor = function(m, tol)
{
# invert, then negate off-diagonal entries
m = -pseudoinverse(m, tol=tol)
diag(m) = -diag(m)
# standardize and return
return(cov2cor(m))
}
#
# backtransformation to correlation matrix
#
# input: partial correlation matrix
# ouput: correlation matrix
pcor2cor = function(m, tol)
{
# negate off-diagonal entries, then invert
m = -m
diag(m) = -diag(m)
m = pseudoinverse(m, tol=tol)
# standardize and return
return(cov2cor(m))
}
########################################################
# partial correlation
pcor.shrink = function(x, lambda, w, verbose=TRUE)
{
pc = -invcor.shrink(x, lambda, w, verbose=verbose)
diag(pc) = -diag(pc)
spv = 1/diag(pc) # standardized partial variances (i.e. pvar/var)
pc = cov2cor(pc) # partial correlations
attr(pc, "spv") = spv
return(pc)
}
# partial variances
pvar.shrink = function(x, lambda, lambda.var, w, verbose=TRUE)
{
prec = invcov.shrink(x, lambda, lambda.var, w, verbose=verbose)
pvar = 1/diag(prec)
attr(pvar, "lambda") = attr(prec, "lambda")
attr(pvar, "lambda.estimated") = attr(prec, "lambda.estimated")
attr(pvar, "lambda.var") = attr(prec, "lambda.var")
attr(pvar, "lambda.var.estimated") = attr(prec, "lambda.var.estimated")
return( pvar )
}
```

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