dyn.cor: Dynamical Correlation and Covariance
In longitudinal: Analysis of Multiple Time Course Data

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/dyn.cor.R

The functions estimate dynamical correlation and covariance, and related quantities.

dyn.cor(x, lambda, verbose=TRUE)
dyn.var(x, lambda.var, verbose=TRUE)
dyn.cov(x, lambda, lambda.var, verbose=TRUE)
dyn.invcor(x, lambda, verbose=TRUE)
dyn.invcov(x, lambda, lambda.var, verbose=TRUE)
dyn.pvar(x, lambda, lambda.var, verbose=TRUE)
dyn.pcor(x, lambda, verbose=TRUE)

`x`	a data matrix
`lambda`	the correlation shrinkage intensity (range 0-1). If `lambda` is not specified (the default) it is estimated using an analytic formula from Sch\"afer and Strimmer (2005) and Opgen-Rhein and Strimmer (2006a,b). For `lambda=0` the empirical correlations are recovered. See also `cor.shrink`.
`lambda.var`	the variance shrinkage intensity (range 0-1). If `lambda.var` is not specified (the default) it is estimated using an analytic formula from Sch\"afer and Strimmer (2005) and Opgen-Rhein and Strimmer (2006a,b). For `lambda.var=0` the empirical variances are recovered. See also `var.shrink`.
`verbose`	report progress while computing (default: TRUE)

The dynamical correlation and related quantities implemented here follow the definition of Opgen-Rhein and Strimmer (2006a,b). This approach is derived from a FDA perspective. Essentially, it takes account of the distances between the various time points by assigning weights to samples. If these weights are all equal the usual iid estimators are obtained.

For details about the analytic shrinkage procedure consult Opgen-Rhein and Strimmer (2006b) and Sch\"afer and Strimmer (2005) as well as the help page of cov.shrink.

dyn.cor returns the dynamical correlation matrix. dyn.var returns the vector of dynamical variances. dyn.cov returns the dynamical covariance matrix.

dyn.invcor returns the inverse dynamical correlation matrix. dyn.invcov returns the inverse dynamical covariance matrix.

dyn.pvar returns the vector of partial dynamical variances. dyn.pcor returns the partial dynamical correlation matrix.

Rainer Opgen-Rhein and Korbinian Strimmer (https://strimmerlab.github.io).

Opgen-Rhein, R., and K. Strimmer. 2006a. Inferring gene dependency networks from genomic longitudinal data: a functional data approach. REVSTAT 4:53-65.

Opgen-Rhein, R., and K. Strimmer. 2006b. Using regularized dynamic correlation to infer gene dependency networks from time-series microarray data. The 4th International Workshop on Computational Systems Biology, WCSB 2006 (June 12-13, 2006, Tampere, Finland).

Schaefer, J., and Strimmer, K. (2005). A shrinkage approach to large-scale covariance estimation and implications for functional genomics. Statist. Appl. Genet. Mol. Biol. 4:32. <DOI:10.2202/1544-6115.1175>

dyn.weights, cov.shrink, pcor.shrink

# load "longitudinal" library
library("longitudinal")

# load tcell data
data(tcell)
get.time.repeats(tcell.34)


# dynamical partial correlation 
# (this takes into account of the unequal spacings between time points) 
dynpc <- dyn.pcor(tcell.34, lambda=0)

# static partial correlation
statpc <- pcor.shrink(tcell.34, lambda=0)

# this is NOT the same
sum((dynpc - statpc)^2)