fcnnls  R Documentation 
This function solves the following nonnegative least square linear problem using normal equations and the fast combinatorial strategy from Van Benthem et al. (2004):
min Y  X K_F, s.t. K>=0
where Y and X are two real matrices of dimension n x p and n x r respectively, and ._F is the Frobenius norm.
The algorithm is very fast compared to other approaches, as it is optimised for handling multiple righthand sides.
fcnnls(x, y, ...) ## S4 method for signature 'matrix,matrix' fcnnls(x, y, verbose = FALSE, pseudo = TRUE, ...)
... 
extra arguments passed to the internal
function 
verbose 
toggle verbosity (default is

x 
the coefficient matrix 
y 
the target matrix to be approximated by X K. 
pseudo 
By default ( 
Within the NMF
package, this algorithm is used
internally by the SNMF/R(L) algorithm from Kim et
al. (2007) to solve general Nonnegative Matrix
Factorization (NMF) problems, using alternating
nonnegative constrained leastsquares. That is by
iteratively and alternatively estimate each matrix
factor.
The algorithm is an active/passive set method, which rearrange the righthand side to reduce the number of pseudoinverse calculations. It uses the unconstrained solution K_u obtained from the unconstrained least squares problem, i.e. min Y  X K_F^2 , so as to determine the initial passive sets.
The function fcnnls
is provided separately so that
it can be used to solve other types of nonnegative least
squares problem. For faster computation, when multiple
nonnegative least square fits are needed, it is
recommended to directly use the function
.fcnnls
.
The code of this function is a port from the original MATLAB code provided by Kim et al. (2007).
A list containing the following components:
x 
the estimated optimal matrix K. 
fitted 
the fitted matrix X K. 
residuals 
the residual matrix Y  X K. 
deviance 
the residual sum of squares between the fitted matrix X K and the target matrix Y. That is the sum of the square residuals. 
passive 
a r x p logical matrix containing the passive set, that is the set of entries in K that are not null (i.e. strictly positive). 
pseudo 
a logical that
is 
signature(x = "matrix", y =
"matrix")
: This method wraps a call to the internal
function .fcnnls
, and formats the results in a
similar way as other lestsquares methods such as
lm
.
signature(x = "numeric", y =
"matrix")
: Shortcut for fcnnls(as.matrix(x), y,
...)
.
signature(x = "ANY", y = "numeric")
:
Shortcut for fcnnls(x, as.matrix(y), ...)
.
Original MATLAB code : Van Benthem and Keenan
Adaption of MATLAB code for SNMF/R(L): H. Kim
Adaptation to the NMF package framework: Renaud Gaujoux
Original MATLAB code from Van Benthem and Keenan, slightly modified by H. Kim:(http://www.cc.gatech.edu/~hpark/software/fcnnls.m)
Van Benthem M and Keenan MR (2004). "Fast algorithm for the solution of largescale nonnegativityconstrained least squares problems." _Journal of Chemometrics_, *18*(10), pp. 441450. ISSN 08869383, <URL: http://dx.doi.org/10.1002/cem.889>, <URL: http://doi.wiley.com/10.1002/cem.889>.
Kim H and Park H (2007). "Sparse nonnegative matrix factorizations via alternating nonnegativityconstrained least squares for microarray data analysis." _Bioinformatics (Oxford, England)_, *23*(12), pp. 1495502. ISSN 14602059, <URL: http://dx.doi.org/10.1093/bioinformatics/btm134>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/17483501>.
nmf
## Define a random nonnegative matrix matrix n < 200; p < 20; r < 3 V < rmatrix(n, p) ## Compute the optimal matrix K for a given X matrix X < rmatrix(n, r) res < fcnnls(X, V) ## Compute the same thing using the MoorePenrose generalized pseudoinverse res < fcnnls(X, V, pseudo=TRUE) ## It also works in the case of single vectors y < runif(n) res < fcnnls(X, y) # or res < fcnnls(X[,1], y)
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