Listing and Retrieving NMF Algorithms


nmfAlgorithm lists access keys or retrieves NMF algorithms that are stored in registry. It allows to list


nmfAlgorithm(name = NULL, version = NULL, all = FALSE, ...)


Access key. If not missing, it must be a single character string that is partially matched against the available algorithms in the registry. In this case, if all=FALSE (default), then the algorithm is returned as an NMFStrategy object that can be directly passed to nmf. An error is thrown if no matching algorithm is found. If missing or NULL, then access keys of algorithms -- that match the criteria version, are returned. This argument is assumed to be regular expression if all=TRUE or version is not NULL.
version of the algorithm(s) to retrieve. Currently only value 'R' is supported, which searched for plain R implementations.
a logical that indicates if all algorithm keys should be returned, including the ones from alternative algorithm versions (e.g. plain R implementations of algorithms, for which a version based on optimised C updates is used by default).
extra arguments passed to getNMFMethod when name is not NULL and all=FALSE. It is not used otherwise.


an NMFStrategy-class object if name is not NULL and all=FALSE, or a named character vector that contains the access keys of the matching algorithms. The names correspond to the access key of the primary algorithm: e.g. algorithm ‘lee’ has two registered versions, one plain R (‘.R#lee’) and the other uses optimised C updates (‘lee’), which will all get named ‘lee’.


# list all main algorithms
##  [1] "brunet"    "KL"        "lee"       "Frobenius" "offset"   
##  [6] "nsNMF"     "ls-nmf"    "pe-nmf"    "snmf/r"    "snmf/l"   
## [11] "siNMF"
# list all versions of algorithms
##  [1] ".R#brunet" "brunet"    "KL"        ".R#lee"    "lee"      
##  [6] "Frobenius" ".R#offset" "offset"    ".R#nsNMF"  "nsNMF"    
## [11] ".M#brunet" "ls-nmf"    "pe-nmf"    "snmf/r"    "snmf/l"   
## [16] ".siNMF"    "siNMF"
# list all plain R versions
##      brunet         lee      offset       nsNMF 
## ".R#brunet"    ".R#lee" ".R#offset"  ".R#nsNMF"

See also

Other regalgo: canFit