parallelpam

Description

Application of the Partitioning-Around-Medoids (PAM) clustering algorithm described in Schubert, E. and Rousseeuw, P.J.: "Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms." Information Systems, vol. 101, p. 101804, (2021). <doi:10.1016/j.is.2021.101804>. It uses a binary format for storing and retrieval of matrices developed for the 'jmatrix' package but the functionality of 'jmatrix' is included here, so you do not need to install it. Also, it is used by package 'scellpam', so if you have installed it, you do not need to install this package. PAM can be applied to sets of data whose dissimilarity matrix can be very big. It has been tested with up to 100.000 points. It does this with the help of the code developed for other package, 'jmatrix', which allows the matrix not to be loaded in 'R' memory (which would force it to be of double type) but it gets from disk, which allows using float (or even smaller data types). Moreover, the dissimilarity matrix is calculated in parallel if the computer has several cores so it can open many threads. The initial part of the PAM algorithm can be done with the BUILD or LAB algorithms; the BUILD algorithm has been implemented in parallel. The optimization phase implements the FastPAM1 algorithm, also in parallel. Finally, calculation of silhouette is available and also implemented in parallel.

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Found the following file with non-ASCII characters:
  Fatal error: cannot create 'R_TempDir'
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.

Error(s) in re-building vignettes:
  ...
Warning in gzfile(file, mode) :
  cannot open compressed file '/tmp/Rtmp2wLiMN/libloc_216_4b2a3c4b2ff61586.rds', probable reason 'No space left on device'
Error in gzfile(file, mode) : cannot open the connection
Calls: <Anonymous> ... rownames -> %||% -> <Anonymous> -> saveRDS -> gzfile
Execution halted

installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb

installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/parallelpam.Rcheck/00install.out' for details.

installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb

installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb

installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb

installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb

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