/usr/lib/R/site-library/NMF/NEWS is in r-cran-nmf 0.20.6-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 | *************************************************************************
Changes in version 0.20.6
*************************************************************************
FIXES
o fixed new NOTEs in R CMD check (about requireNamespace)
o fixed error in heatmaps due to new version of stringr (>= 1.0.0)
*************************************************************************
Changes in version 0.20
*************************************************************************
NEW FEATURES
o aheatmap gains an argument txt that enables displaying text in each
cell of the heatmap.
FIXES
o now all examples, vignettes and unit tests comply with CRAN policies
on the maximum number of cores to be used when checking packages (2).
*************************************************************************
Changes in version 0.18
*************************************************************************
NEW FEATURES
o aheatmap gains distfun methods 'spearman', 'kendall', and,
for completeness, 'pearson' (for which 'correlation' is now an alias),
which specifies the correlation method to use when computing the
distance matrix.
CHANGES
o In order to fully comply with CRAN policies, internals of the
aheatmap function slightly changed. In particular, this brings an
issue when directly plotting to PDF graphic devices, where a first
blank page may appear. See the dedicated section in the man page
?aheatmap for a work around.
*************************************************************************
Changes in version 0.17.3
*************************************************************************
NEW FEATURES
o add silhouette computation for NMF results, which can be performed on
samples, features or consensus matrix.
The average silhouette width is also computed by the summary methods.
(Thanks to Gordon Robertson for this suggestion)
o New runtime option 'shared.memory' (or 'm') for toggling usage of shared
memory (requires package synchronicity).
CHANGES
o some plots are -- finally -- generated using ggplot2
This adds an Imports dependency to ggplot2 and reshape2.
BUG FIXES
o fix a bug when running parallel NMF computation with
algorithms defined in other packages (this most probably only affected my
own packages, e.g., CellMix)
*************************************************************************
Changes in version 0.17.1
*************************************************************************
CHANGES
o Computations seeded with an NMF object now set slot @seed to 'NMF'
o Added unit tests on seeding with an NMF object
o Removed some obsolete comments
BUG FIXES
o an error was thrown when running multiple sequential NMF
computations with nrun>=50: object '.MODE_SEQ' not found.
(reported by Kenneth Lopiano)
*************************************************************************
Changes in version 0.16.5
*************************************************************************
CHANGES
o Now depends on pkgmaker 0.16
o Disabled shared memory on Mac machines by default, due to un-resolved
bug that occurs with big-matrix descriptors.
It can be restored using nmf.options(shared.memory=TRUE)
o Package version is now shown on startup message
o Re-enabled unit test checks on CRAN, using the new function
pkgmaker::isCHECK, that definitely identifies if tests are run
under R CMD check.
*************************************************************************
* Changes in version 0.15.2 *
*************************************************************************
NEW FEATURES
o New function nmfObject() to update old versions of NMF objects,
eg., saved on disk.
o NMF strategies can now define default values for their parameters,
eg., `seed` to associate them with a seeding method that is not the
default method, `maxIter` to make default runs with more iterations
(for algorithms defined as NMFStrategyIterative), or any other
algorithm-specific parameter.
o new general utility function hasArg2 that is identical to hasArg
but takes the argument name as a character string, so that no
check NOTE is thrown.
CHANGES
o All vignettes are now generated using knitr.
o New dependency to pkgmaker which incorporated many of the
general utility functions, initially defined for the NMF package.
o example check is faster (as requested by CRAN)
o the function selectMethodNMF was renamed into selectNMFMethod to
be consistent with the other related *NMFMethod functions (get, set, etc..)
FIXES
o Fix computation of R-squared in profplot/corplot: now compute from
a linear fit that includes an intercept.
*************************************************************************
* Changes in version 0.8.6 *
*************************************************************************
NEW FEATURES
o Formula based NMF models that can incorporate fixed terms, which may
be used to correct for covariates or define group specific offsets.
CHANGES
o Subsetting an NMF object with a single index now returns an NMF object,
except if argument drop is not missing (i.e. either TRUE or FALSE).
*************************************************************************
* Changes in version 0.6.03 *
*************************************************************************
WARNING
Due to the major changes made in the internal structure of the standard NMF
models, previous NMF fits are not compatible with this version.
NEW FEATURES
o The factory function nmfModel has been enhanced and provides new
methods that makes more easier the creation of NMF objects.
See ?nmfModel.
o A new heatmap drawing function 'aheatmap' (for annotated heatmap) is
now used to generate the different heatmaps (basismap, coefmap and consensusmap).
It is a enhancement/fork of the function pheatmap from package pheatmap and draw
-- I think -- very nice heatmaps, providing a convenient and flexible
interface to add annotation tracks to both the columns and rows, with
sensible automatic legends.
CHANGES
o Method nmfModel when called with no arguments does not return anymore
the list of available NMF models, but an empty NMF model.
To list the available models, directly call `nmfModels()`.
o The function `rmatrix` is now a S4 generic function.
It gains methods for generating random matrices based on a template matrix
or an NMF model.
See ?rmatrix.
o The function `rnmf` gains a method to generate a random NMF model
given numerical dimensions.
o The function nmfEstimateRank now returns the fits for each value of the
rank in element 'fit' of the result list.
See ?nmfEstimateRank.
*************************************************************************
* Changes in version 0.5.3 *
*************************************************************************
NEW FEATURES
o The state of the random number generator is systematically stored in the
'NMFfit' object returned by function 'nmf'.
It is stored in a new slot 'rng.seed' and can be access via the new method
'rngSeed' of class 'NMFfit'.
See ?rngSeed for more details.
o The number of cores to use in multicore computations can now also be
specified by the 'p - parallel' runtime option (e.g. 'p4' to use 4 cores).
Note that the value specified in option 'p' takes precedence on the one
passed via argument '.pbackend'.
See section 'Runtime options' in ?nmf for more details.
o Function 'nmfApply' now allows values 3 and 4 for argument 'MARGIN' to
apply a given function to the basis vectors (i.e. columns of the basis matrix W)
and basis profiles (i.e. rows of the mixture coefficients H) respectively.
See ?nmfApply for more details.
o New S4 generic 'basiscor' and 'profcor' to compute the
correlation matrices of the basis vectors and basis profiles respectively
from two NMF models or from an NMF model and a given compatible matrix.
See ?basiscor or ?profcor for more details.
o New S4 generic 'fitcmp' to compare the NMF models fitted by two
different runs of function 'nmf' (i.e. two 'NMFfit' objects).
See ?fitcmp for more details.
o New S4 generic 'canFit' that tells if an NMF method is able to
exactly or partly fit a given NMF model.
See ?canFit for more details.
o New function 'selectMethodNMF' that selects an appropriate NMF method to
fit a given NMF model.
See ?selectMethodNMF for more details.
o The verbosity level can be controlled more finely by the 'v - verbose'
runtime option (e.g. using .options='v1' or 'v2'). The greater is
the level the more information is printed.
The verbose outputs have been cleaned-up and should be more consistent
across the run mode (sequential or multicore).
See section 'Runtime options' in ?nmf for more details.
CHANGES
o The standard update equations have been optimised further, by making
them modify the factor matrices in place. This speeds up the computation
and greatly improves the algorithms' memory footprint.
o The package NMF now depends on the package digest that is used to display
the state of random number generator in a concise way.
o The methods 'metaHeatmap' are split into 3 new S4 generic 'basismap' to
plot a heatmap of the basis matrix [formerly plotted by the call :
'metaHeatmap(object.of.class.NMF, 'features', ...) ], 'coefmap' to plot a
heatmap of the mixture coefficient matrix [formerly plotted by the call :
'metaHeatmap(object.of.class.NMF, 'samples', ...) ], and 'consensusmap' to
plot a heatmap of the consensus matrix associated with multiple runs of NMF
[formerly plotted by the call : 'metaHeatmap(object.of.class.NMFfitX, ...) ].
BUG FIX
o In factory method 'nmfModel': the colnames (resp. rownames) of
matrix W (resp. H) are now correctly set when the rownames of H
(resp. the colnames of W) are not null.
NEWLY DEPRECATED CLASSES, METHODS, FUNCTIONS, DATA SETS
o Deprecated Generics/Methods
1) 'metaHeatmap,NMF' and 'metaHeatmap,NMFfitX' - S4 methods remain
with .Deprecated message.
They are replaced by the definition of 3 new S4 generic 'basismap',
'coefmap' and 'consensusmap'. See the related point in section
CHANGES above.
They will be completely removed from the package in the next version.
*************************************************************************
* Changes in version 0.5.1 *
*************************************************************************
BUG FIX
o fix a small bug in method 'rss' to allow argument 'target' to be a
'data.frame'. This was generating errors when computing the summary
measures and especially when the function 'nmfEstimateRank' was called
on a 'data.frame'. Thanks to Pavel Goldstein for reporting this.
*************************************************************************
* Changes in version 0.5 *
*************************************************************************
NEW FEATURES
o Method 'fcnnls' provides a user-friendly interface for the internal
function '.fcnnls' to solve non-nengative linear least square problems,
using the fast combinatorial approach from Benthem and Keenan (2004).
See '?fcnnls' for more details.
o New argument 'callback' in method 'nmf' allows to provide a callback
function when running multiple runs in default mode, that only keeps the
best result. The callback function is applied to the result of each run
before it possibly gets discarding. The results are stored in the
miscellaneous slot '.callback' accessible via the '$' operator (e.g. res$.callback).
See '?nmf' for more details.
o New method 'niter' to retrieve the number of iterations performed to fit
a NMF model. It is defined on objects of class 'NMFfit'.
o New function 'isNMFfit' to check if an object is a result from NMF fitting.
o New function 'rmatrix' to easily generate random matrices, and allow to specify the
distribution from which the entries are drawn. For example:
* 'rmatrix(100, 10)' generates a 100x10 matrix whose entries are drawn
from the uniform distribution
* 'rmatrix(100, 10, rnorm)' generates a 100x10 matrix whose entries are drawn
from the standard Normal distribution.
o New methods 'basisnames' and 'basisnames<-' to retrieve and set the basis vector
names. See '?basisnames'.
CHANGES
o Add a CITATION file that provides the bibtex entries for citing the
BMC Bioinformatics paper for the package
(http://www.biomedcentral.com/1471-2105/11/367), the vignette and manual.
See 'citation('NMF')' for complete references.
o New argument 'ncol' in method 'nmfModel' to specify the target dimensions more
easily by calls like 'nmfModel(r, n, p)' to create a r-rank NMF model that fits a
n x p target matrix.
o The subset method '[]' of objects of class 'NMF' has been changed to be more convenient.
See
BUG FIX
o Method 'dimnames' for objects of class 'NMF' now correctly sets the
names of each dimension.
REMOVED CLASSES, METHODS, FUNCTIONS, DATA SETS
o Method 'extra' has completely been removed.
*************************************************************************
* Changes in version 0.4.8 *
*************************************************************************
BUG FIX
o When computing NMF with the SNMF/R(L) algorithms, an error could
occur if a restart (recomputation of the initial value) for the H
matrix (resp. W matrix) occured at the first iteration.
Thanks to Joe Maisog for reporting this.
*************************************************************************
* Changes in version 0.4.7 *
*************************************************************************
BUG FIX
o When computing the cophenetic correlation coefficient of a diagonal
matrix, the 'cophcor' method was returning 'NA' with a warning from
the 'cor' function. It now correctly returns 1.
Thanks to Joe Maisog for reporting this.
*************************************************************************
* Changes in version 0.4.4 *
*************************************************************************
CHANGES
o The major change is the explicit addition of the synchronicity package into
the suggested package dependencies. Since the publication of versions 4.x
of the bigmemory package, it is used by the NMF package to provide the mutex
functionality required by multicore computations.
Note This is relevant only for Linux/Mac-like platforms as the multicore
package is not yet supported on MS Windows.
Users using a recent version of the bigmemory package (i.e. >=4.x)
DO NEED to install the synchronicity package to be able to run multicore NMF
computations.
Versions of bigmemory prior to 4.x include the mutex functionality.
o Minor enhancement in error messages
o Method 'nmfModel' can now be called with arguments 'rank' and 'target'
swapped. This is for convenience and ease of use.
BUG FIX
o Argument 'RowSideColors' of the 'metaHeatmap' function is now correctly
subset according to the value of argument 'filter'. However the argument
must be named with its complete name 'RowSideColors', not assuming
partial match. See KNOWN ISSUES.
KNOWN ISSUES
o In the 'metaHeatmap' function, when argument 'filter' is not 'FALSE':
arguments 'RowSideColors', 'labRow', 'Rowv' that are intended to the
'heatmap.plus'-like function (and are used to label the rows) should be
named using their complete name (i.e. not assuming partial match),
otherwise the filtering is not applied to these argument and an error
is generated.
This issue will be fixed in a future release.
*************************************************************************
* Changes in version 0.4.3 *
*************************************************************************
CHANGES
o function 'nmfEstimateRank' has been enhanced:
-run options can be passed to each internal call to the 'nmf' function.
See ?nmfEstiamteRank and ?nmf for details on the supported options.
- a new argument 'stop' allows to run the estimation with fault tolerance,
skipping runs that throw an error. Summary measures for these runs are set
to NAs and a warning is thrown with details about the errors.
o in function 'plot.NMF.rank': a new argument 'na.rm' allows to remove from
the plots the ranks for which the measures are NAs (due to errors during the
estimation process with 'nmfEstimateRank').
BUG FIX
o Method 'consensus' is now exported in the NAMESPACE file.
Thanks to Gang Su for reporting this.
o Warnings and messages about loading packages are now suppressed.
This was particularly confusing for users that do not have the packages
and/or platform required for parallel computation: warnings were printed
whereas the computation was -- sequentially -- performed without
problem.
Thanks to Joe Maisog for reporting this.
*************************************************************************
* Changes in version 0.4.1 *
*************************************************************************
BUG FIX
o The 'metaHeatmap' function was not correctly handling row labels
when argument filter was not FALSE. All usual row formating in heatmaps
(label and ordering) are now working as expected.
Thanks to Andreas Schlicker, from The Netherlands Cancer Institute for
reporting this.
o An error was thrown on some environments/platforms (e.g. Solaris)
where not all the packages required for parallel computation were not
available -- even when using option 'p' ('p' in lower case), which
should have switched the computation to sequential.
This is solved and the error is only thrown when running NMF with
option 'P' (capital 'P').
o Not all the options were passed (e.g. 't' for tracking) in sequential
mode (option '-p').
o verbose/debug global nmf.options were not restored if a numerical random
seed were used.
CHANGES
o The 'metaHeatmap' function nows support passing the name of a filtering
method in argument 'filter', which is passed to method 'extractFeatures'.
See ?metaHeatmap.
o Verbose and debug messages are better handled. When running a parallel
computation of multiple runs, verbose messages from each run are shown only
in debug mode.
*************************************************************************
* Changes in version 0.4 *
*************************************************************************
NEW FEATURES
o Part of the code has been optimised in C++ for speed and memory efficiency:
- the multiplicative updates for reducing the KL divergence and the euclidean
distance have been optimised in C++. This significantly reduces the
computation time of the methods that make use of them: 'lee', 'brunet',
'offset', 'nsNMF' and 'lnmf'.
Old R version of the algorithm are still accessible with the suffix '.R#'.
- the computation of euclidean distance and KL divergence are implemented
in C++, and do not require the duplication of the original matrices as done
in R.
o Generic 'dimnames' is now defined for objects of class 'NMF' and returns
a list with 3 elements: the row names of the basis matrix, the column names
of the mixture coefficient matrix , and the column names of the basis matrix.
This implies that methods 'rownames' and 'columnames' are also available for
'NMF' objects.
o A new class structure has been developed to handle the results of multiple
NMF runs in a cleaner and more structured way:
- Class 'NMFfitX' defines a common interface for multiple NMF runs of a
single algorithm.
- Class 'NMFfitX1' handles the sub-case where only the best fit is returned.
In particular, this class allows to handle such results as if coming
from a single run.
- Class 'NMFfitXn' handles the sub-case where the list of all the fits
is returned.
- Class 'NMFList' handles the case of heterogeneous NMF runs (different
algorithms, different factorization rank, different dimension, etc...)
o The vignette contains more examples and details about the use of package.
o The package is compatible with both versions 3.x and 4.x of the bigmemory
package. This package is used when running multicore parallel computations.
With version 4.x of bigmemory, the synchronicity package is also required as
it provides the mutex functionality that used to be provided by bigmemory 3.x.
BUG FIX
o Running in multicore mode from the GUI on MacOS X is not allowed anymore as
it is not safe and were throwing an error ['The process has forked and ...'].
Thanks to Stephen Henderson from the UCL Cancer Institute (UK) for reporting this.
o Function 'nmf' now restores the random seed to its original value as before its call
with a numeric seed. This behaviour can be disabled with option 'restore.seed=FALSE' or '-r'
NEWLY DEPRECATED CLASSES, METHODS, FUNCTIONS, DATA SETS
o Deprecated Generics/Methods
1) 'errorPlot' - S4 generic/methods remains with .Deprecated message.
It is replaced by a definition of the 'plot' method for signatures
'NMFfit,missing' and 'NMFList,missing'
It will be completely removed from the package in the next version.
o Deprecated Class
1) 'NMFSet' - S4 class remains for backward compatibility, but is not
used anymore. It is replaced by the classes 'NMFfitX1', 'NMFfitXn',
'NMFList'.
*************************************************************************
* Changes in version 0.3 *
*************************************************************************
NEW FEATURES
o Now requires R 2.10
o New list slot 'misc' in class 'NMF' to be able to define new NMF models,
without having to extend the S4 class. Access is done by methods '$' and '$<-'.
o More robust and convenient interface 'nmf'
o New built-in algorithm : PE-NMF [Zhang (2008)]
o The vignette and documentation have been enriched with more examples and
details on the functionalities.
o When possible the computation is run in parallel on all the available cores.
See option 'p' or 'parallel=TRUE' in argument '.options' of function 'nmf'.
o Algorithms have been optimized and run faster
o Plot for rank estimation: quality measure curves can be plotted together
with a set of reference measures.
The reference measures could for example come from the rank estimation of
randomized data, to investigate overfitting.
o New methods '$' and '$<-' to access slot 'extra' in class 'NMFfit'
These methods replace method 'extra' that is now defunct.
o Function 'randomize' allows to randomise a target matrix or
'ExpressionSet' by permuting the entries within each columns using a
different permutation for each column. It is useful when checking for
over-fitting.
CHANGES
o The 'random' method of class 'NMF' is renamed 'rnmf', but is still
accessible through name 'random' via the 'seed' argument in the
interface method 'nmf'.
NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS
o Defunct Generics/Methods
1) 'extra' - S4 generic/methods remains with .Defunct message.
It will be completely removed from the package in the next version.
*************************************************************************
* Changes in version 0.2.4 *
*************************************************************************
CHANGES
o Class 'NMFStrategy' has a new slot 'mixed', that specify if the algorithm
can handle mixed signed input matrices.
o Method 'nmf-matrix,numeric,function' accepts a new parameter 'mixed' to
specify if the custom algorithm can handle mixed signed input matrices.
*************************************************************************
* Changes in version 0.2.3 *
*************************************************************************
NEW FEATURES
o Package 'Biobase' is not required anymore, and only suggested.
The definition and export of the NMF-BioConductor layer is done at
loading.
o 'nmfApply' S4 generic/method: a 'apply'-like method for objects of
class 'NMF'.
o 'predict' S4 method for objects of class 'NMF': the method replace the now
deprecated 'clusters' method.
o 'featureNames' and 'sampleNames' S4 method for objects of class 'NMFSet'.
o sub-setting S4 method '[' for objects of class 'NMF': row subsets are
applied to the rows of the basis matrix, column subsets are applied to
the columns of the mixture coefficient matrix.
CHANGES
o method 'featureScore' has a new argument 'method' to allow choosing between
different scoring schema.
o method 'extractFeatures' has two new arguments: 'method' allows choosing
between different scoring and selection methods; 'format' allows to specify
the output format.
NOTE: the default output format has changed. The default result is now a
list whose elements are integer vectors (one per basis component) that
contain the indices of the basis-specific features. It is in practice what
one is usually interested in.
BUG FIXES
o Methods 'basis<-' and 'coef<-' were not exported by file NAMESPACE.
o Method 'featureNames' was returning the column names of the mixture
coefficient matrix, instead of the row names of the basis matrix.
o 'metaHeatmap' with argument 'class' set would throw an error.
NEWLY DEPRECATED CLASSES, METHODS, FUNCTIONS, DATA SETS
o Deprecated Generics/Methods
1) clusters - S4 generic/methods remain with .Deprecated message
|