Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 2.0.4 dated 2018-04-30 and 2.0.5 dated 2018-07-30
RSDA-2.0.4/RSDA/R/sym.row.plot.R |only RSDA-2.0.4/RSDA/man/sym.radar.plot..Rd |only RSDA-2.0.4/RSDA/man/sym.row.plot.Rd |only RSDA-2.0.5/RSDA/DESCRIPTION | 12 - RSDA-2.0.5/RSDA/MD5 | 58 ++--- RSDA-2.0.5/RSDA/NAMESPACE | 22 +- RSDA-2.0.5/RSDA/R/RSDA.R | 2 RSDA-2.0.5/RSDA/R/classic.to.sym.R | 24 +- RSDA-2.0.5/RSDA/R/data.R | 8 RSDA-2.0.5/RSDA/R/dist.interval.R | 4 RSDA-2.0.5/RSDA/R/plot.sym.data.table.R | 75 ++++--- RSDA-2.0.5/RSDA/R/sym.continuos.plot.R | 42 +--- RSDA-2.0.5/RSDA/R/sym.hist.plot.R | 55 +---- RSDA-2.0.5/RSDA/R/sym.interval.pc.limits.2.j.r | 2 RSDA-2.0.5/RSDA/R/sym.interval.pc.limits.R | 2 RSDA-2.0.5/RSDA/R/sym.interval.pca.limits.new.j.r | 2 RSDA-2.0.5/RSDA/R/sym.interval.plot.R | 50 +--- RSDA-2.0.5/RSDA/R/sym.modal.plot.R | 60 ++--- RSDA-2.0.5/RSDA/R/sym.radar.plot.R | 225 +++++++++++----------- RSDA-2.0.5/RSDA/R/sym.set.plot.R | 58 ++--- RSDA-2.0.5/RSDA/man/USCrime.Rd | 4 RSDA-2.0.5/RSDA/man/classic.to.sym.Rd | 12 - RSDA-2.0.5/RSDA/man/ex1_db2so.Rd | 4 RSDA-2.0.5/RSDA/man/plot.sym.data.table.Rd | 17 + RSDA-2.0.5/RSDA/man/sym.continuos.plot.Rd | 34 --- RSDA-2.0.5/RSDA/man/sym.dist.interval.Rd | 4 RSDA-2.0.5/RSDA/man/sym.hist.plot.Rd | 40 --- RSDA-2.0.5/RSDA/man/sym.interval.plot.Rd | 34 --- RSDA-2.0.5/RSDA/man/sym.modal.plot.Rd | 38 --- RSDA-2.0.5/RSDA/man/sym.radar.data.Rd |only RSDA-2.0.5/RSDA/man/sym.radar.plot.Rd | 29 +- RSDA-2.0.5/RSDA/man/sym.set.plot.Rd | 32 --- 32 files changed, 381 insertions(+), 568 deletions(-)
Title: Scoring Rules for Parametric and Simulated Distribution
Forecasts
Description: Dictionary-like reference for computing scoring rules in a wide
range of situations. Covers both parametric forecast distributions (such as
mixtures of Gaussians) and distributions generated via simulation.
Author: Alexander Jordan, Fabian Krueger, Sebastian Lerch
Maintainer: Fabian Krueger <Fabian.Krueger83@gmail.com>
Diff between scoringRules versions 0.9.4 dated 2017-11-03 and 0.9.5 dated 2018-07-30
scoringRules-0.9.4/scoringRules/inst/doc/crpsformulas.Rmd |only scoringRules-0.9.4/scoringRules/inst/doc/crpsformulas.html |only scoringRules-0.9.4/scoringRules/vignettes/closedforms.bib |only scoringRules-0.9.4/scoringRules/vignettes/crpsformulas.Rmd |only scoringRules-0.9.5/scoringRules/DESCRIPTION | 13 scoringRules-0.9.5/scoringRules/MD5 | 53 scoringRules-0.9.5/scoringRules/NAMESPACE | 15 scoringRules-0.9.5/scoringRules/R/crps.numeric.R | 23 scoringRules-0.9.5/scoringRules/R/header.R | 1 scoringRules-0.9.5/scoringRules/R/header_replication.R | 110 scoringRules-0.9.5/scoringRules/R/logs.numeric.R | 15 scoringRules-0.9.5/scoringRules/R/procs_casestudy.R | 3 scoringRules-0.9.5/scoringRules/R/scores_binom.R |only scoringRules-0.9.5/scoringRules/R/scores_hyper.R |only scoringRules-0.9.5/scoringRules/R/scores_sample_univ.R | 2 scoringRules-0.9.5/scoringRules/build/vignette.rds |binary scoringRules-0.9.5/scoringRules/inst/CITATION |only scoringRules-0.9.5/scoringRules/inst/doc/article.R | 354 ++ scoringRules-0.9.5/scoringRules/inst/doc/article.Rnw | 1305 ++++++++--- scoringRules-0.9.5/scoringRules/inst/doc/article.pdf |binary scoringRules-0.9.5/scoringRules/inst/doc/gettingstarted.Rmd | 8 scoringRules-0.9.5/scoringRules/inst/doc/gettingstarted.html | 12 scoringRules-0.9.5/scoringRules/man/crps.numeric.Rd | 22 scoringRules-0.9.5/scoringRules/man/gdp_mcmc.Rd | 2 scoringRules-0.9.5/scoringRules/man/logs.numeric.Rd | 15 scoringRules-0.9.5/scoringRules/man/print.casestudy.Rd |only scoringRules-0.9.5/scoringRules/man/print.mcstudy.Rd |only scoringRules-0.9.5/scoringRules/man/scores_binom.Rd |only scoringRules-0.9.5/scoringRules/man/scores_hyper.Rd |only scoringRules-0.9.5/scoringRules/man/summary.casestudy.Rd |only scoringRules-0.9.5/scoringRules/man/summary.mcstudy.Rd |only scoringRules-0.9.5/scoringRules/vignettes/article.Rnw | 1305 ++++++++--- scoringRules-0.9.5/scoringRules/vignettes/bibliography.bib | 217 + scoringRules-0.9.5/scoringRules/vignettes/gettingstarted.Rmd | 8 34 files changed, 2649 insertions(+), 834 deletions(-)
Title: Test and Detection of Explosive Behaviors for Time Series
Description: Provides the Augmented Dickey-Fuller test and its variations to check the existence of bubbles (explosive behavior) for time series, based on the article by Peter C. B. Phillips, Shuping Shi and Jun Yu (2015a) <doi:10.1111/iere.12131>. Some functions may take a while depending on the size of the data used, or the number of Monte Carlo replications applied.
Author: Pedro Araujo <pharaujo1094@gmail.com>
Gustavo Lacerda <gustavolacerdas@gmail.com>
Peter C.B. Phillips <peter.phillips@yale.edu>
Shu-Ping Shi <shuping.shi@mq.edu.au>
Maintainer: Pedro Araujo <pharaujo1094@gmail.com>
Diff between MultipleBubbles versions 0.1.0 dated 2018-01-29 and 0.2.0 dated 2018-07-30
DESCRIPTION | 12 +++--- MD5 | 26 ++++++------- NAMESPACE | 26 ++++++------- R/ADF_IC.R | 6 +-- R/GSADF.R | 101 +++++++++++++++++++++++++++--------------------------- man/ADF_FL.Rd | 52 +++++++++++++-------------- man/ADF_IC.Rd | 59 ++++++++++++++++--------------- man/DGP.Rd | 44 +++++++++++------------ man/badf.Rd | 62 ++++++++++++++++----------------- man/bsadf.Rd | 58 +++++++++++++++---------------- man/gsadf.Rd | 62 ++++++++++++++++++--------------- man/sadf.Rd | 56 ++++++++++++++--------------- man/sadf_gsadf.Rd | 56 ++++++++++++++--------------- man/sp_data.Rd | 28 +++++++------- 14 files changed, 328 insertions(+), 320 deletions(-)
More information about MultipleBubbles at CRAN
Permanent link
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on
top of the 'libuv' C library.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
libuv project contributors [cph] (libuv library),
Joyent, Inc. and other Node contributors [cph] (libuv library),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between fs versions 1.2.4 dated 2018-07-26 and 1.2.5 dated 2018-07-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/file.cc | 1 + tests/testthat/test-list.R | 16 ++++++++++++---- 5 files changed, 24 insertions(+), 11 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package includes tests for trend detection
(Cox-Stuart Trend Test, Mann-Kendall Trend Test,
(correlated) Hirsch-Slack Test,
partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope,
partial Pearson and Spearman correlation trend test),
change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test,
Buishand U Test, Standard Normal Homogeinity Test),
detection of non-randomness (Wallis-Moore Phase Frequency Test,
Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 1.1.0 dated 2018-01-03 and 1.1.1 dated 2018-07-30
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- R/csmk.test.R | 21 +++++++++++---------- R/mk.test.R | 7 +++---- R/mult.mk.test.R | 9 ++++----- R/partial.cor.trend.test.R | 8 ++++---- R/rrod.test.R | 8 ++++++-- R/sea.sens.slope.R | 6 +++--- R/sens.slope.R | 5 +++-- R/smk.test.R | 7 +++---- build/vignette.rds |binary inst/NEWS.Rd | 10 ++++++++++ inst/doc/trend.pdf |binary man/csmk.test.Rd | 13 ++++++------- man/mk.test.Rd | 7 +++---- man/mult.mk.test.Rd | 9 ++++----- man/partial.cor.trend.test.Rd | 8 ++++---- man/rrod.test.Rd | 8 ++++++-- man/sea.sens.slope.Rd | 6 +++--- man/sens.slope.Rd | 5 +++-- man/smk.test.Rd | 7 +++---- 21 files changed, 103 insertions(+), 89 deletions(-)
Title: Simple Metrics to Summarize Growth Curves
Description: This is a simple package that fits the logistic equation to
microbial growth curve data (e.g., repeated absorbance measurements
taken from a plate reader over time). From this fit, a variety of
metrics are provided, including the maximum growth rate,
the doubling time, the carrying capacity, the area under the logistic
curve, and the time to the inflection point.
Author: Kathleen sprouffske [aut, cre]
Maintainer: Kathleen sprouffske <sprouffske@gmail.com>
Diff between growthcurver versions 0.2.1 dated 2016-03-29 and 0.3.0 dated 2018-07-30
DESCRIPTION | 16 MD5 | 26 R/helpers.R | 2 R/summarize-growth-by-plate.R | 4 R/utils.R | 6 README.md | 1 build/vignette.rds |binary inst/doc/Growthcurver-vignette.html | 1081 +++++++++++++++++++++--------------- man/NAtT.Rd | 1 man/SummarizeGrowth.Rd | 1 man/SummarizeGrowthByPlate.Rd | 1 man/gcfit.Rd | 3 man/gcvals.Rd | 1 man/growthdata.Rd | 1 14 files changed, 683 insertions(+), 461 deletions(-)
Title: Enhanced Foreign Function Interface Supporting Long Vectors
Description: Provides .C64(), which is an enhanced version of .C()
and .Fortran() from the foreign function interface. .C64() supports long
vectors, arguments of type 64-bit integer, and provides a mechanism to
avoid unnecessary copies of read-only and write-only arguments. This
makes it a convenient and fast interface to C/C++ and Fortran code.
Author: Kaspar Moesinger [aut],
Florian Gerber [cre, ctb],
Reinhard Furrer [ctb]
Maintainer: Florian Gerber <florian.gerber@math.uzh.ch>
Diff between dotCall64 versions 0.9-5.2 dated 2018-01-11 and 1.0-0 dated 2018-07-30
dotCall64-0.9-5.2/dotCall64/NEWS.md |only dotCall64-1.0-0/dotCall64/DESCRIPTION | 8 +++--- dotCall64-1.0-0/dotCall64/MD5 | 10 +++---- dotCall64-1.0-0/dotCall64/NEWS |only dotCall64-1.0-0/dotCall64/R/dotCall64.R | 9 +++--- dotCall64-1.0-0/dotCall64/inst/CITATION | 38 ++++++++++++++--------------- dotCall64-1.0-0/dotCall64/man/dotCall64.Rd | 9 +++--- 7 files changed, 38 insertions(+), 36 deletions(-)
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.7-0 dated 2018-01-12 and 0.7-1 dated 2018-07-30
DESCRIPTION | 12 ++-- MD5 | 34 ++++++------ NAMESPACE | 7 -- R/Summary.R | 2 R/array.R | 3 + R/as.R | 5 + build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 14 +++++ inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.R | 18 ++++-- inst/doc/log1mexp-note.Rnw | 90 +++++++++++++++++++--------------- inst/doc/log1mexp-note.pdf |binary man/Rmpfr-package.Rd | 22 +------- man/base-copies.Rd |only tests/arith-ex.R | 5 + tests/lowlevel.R | 40 +++++++++++++++ vignettes/log1mexp-note.Rnw | 90 +++++++++++++++++++--------------- 19 files changed, 212 insertions(+), 130 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES can be
used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public
key) encryption or EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 1.0.1 dated 2018-03-03 and 1.0.2 dated 2018-07-30
DESCRIPTION | 6 - LICENSE | 2 MD5 | 44 +++++++------- NEWS | 9 ++ R/cert.R | 5 - build/vignette.rds |binary inst/doc/bignum.Rmd | 2 inst/doc/bignum.html | 33 +++++----- inst/doc/crypto_hashing.html | 11 ++- inst/doc/keys.html | 45 +++++++------- inst/doc/secure_rng.html | 21 +++--- man/certificates.Rd | 5 - man/openssl.Rd | 1 man/rand_bytes.Rd | 1 man/read_key.Rd | 3 src/ssl.c | 109 ++++++++++++++++++++++++------------ tests/testthat.R | 4 - tests/testthat/test_keys_dsa.R | 2 tests/testthat/test_keys_ecdsa.R | 2 tests/testthat/test_keys_ecdsa384.R | 2 tests/testthat/test_keys_ecdsa521.R | 2 tests/testthat/test_keys_rsa.R | 2 vignettes/bignum.Rmd | 2 23 files changed, 188 insertions(+), 125 deletions(-)
Title: Functions for the Logitnormal Distribution
Description: Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between logitnorm versions 0.8.36 dated 2018-05-17 and 0.8.37 dated 2018-07-30
DESCRIPTION | 6 MD5 | 32 - NEWS.md | 6 R/logitnorm.R | 740 ++++++++++++++++++++-------------------- inst/doc/logitnorm.html | 4 inst/unitTests/runitLogitnorm.R | 11 man/dlogitnorm.Rd | 12 man/logit.Rd | 2 man/plogitnorm.Rd | 3 man/qlogitnorm.Rd | 3 man/rlogitnorm.Rd | 8 man/twCoefLogitnorm.Rd | 12 man/twCoefLogitnormCi.Rd | 8 man/twCoefLogitnormE.Rd | 16 man/twCoefLogitnormMLE.Rd | 20 - man/twCoefLogitnormN.Rd | 34 - man/twSigmaLogitnorm.Rd | 20 - 17 files changed, 486 insertions(+), 451 deletions(-)
Title: Modify Data Using Externally Defined Modification Rules
Description: Data cleaning scripts typically contain a lot of 'if this change that'
type of statements. Such statements are typically condensed expert knowledge.
With this package, such 'data modifying rules' are taken out of the code and
become in stead parameters to the work flow. This allows one to maintain, document,
and reason about data modification rules as separate entities.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between dcmodify versions 0.1.1 dated 2017-10-06 and 0.1.2 dated 2018-07-30
DESCRIPTION | 9 ++++----- MD5 | 11 ++++++----- NEWS |only R/modifier.R | 9 ++++++--- build/vignette.rds |binary inst/doc/introduction.html | 16 ++++++++-------- tests/testthat/test_modifier.R | 8 +++++++- 7 files changed, 31 insertions(+), 22 deletions(-)
Title: A Partial Clustering Algorithm
Description: Provide the CrossClustering algorithm (Tellaroli et al. (2016)
<doi:10.1371/journal.pone.0152333>), which is a partial clustering algorithm
that combines the Ward's minimum variance and Complete Linkage algorithms,
providing automatic estimation of a suitable number of clusters and
identification of outlier elements.
Author: Paola Tellaroli [cre, aut],
Marco Bazzi [aut],
Michele Donato [aut],
Livio Finos [aut],
Philippe Courcoux [aut],
Corrado Lanera [aut]
Maintainer: Paola Tellaroli <paola.tellaroli@gmail.com>
Diff between CrossClustering versions 3.0 dated 2016-03-29 and 4.0.3 dated 2018-07-30
CrossClustering-3.0/CrossClustering/R/CrossClustering.R |only CrossClustering-3.0/CrossClustering/R/geneinlista.R |only CrossClustering-3.0/CrossClustering/R/proportion.function.R |only CrossClustering-3.0/CrossClustering/inst |only CrossClustering-3.0/CrossClustering/man/CrossClustering.Rd |only CrossClustering-3.0/CrossClustering/man/geneinlista.Rd |only CrossClustering-3.0/CrossClustering/man/proportion.function.Rd |only CrossClustering-4.0.3/CrossClustering/DESCRIPTION | 64 ++ CrossClustering-4.0.3/CrossClustering/MD5 | 57 +- CrossClustering-4.0.3/CrossClustering/NAMESPACE | 21 CrossClustering-4.0.3/CrossClustering/NEWS.md |only CrossClustering-4.0.3/CrossClustering/R/CrossClustering-internal.R | 252 +++++----- CrossClustering-4.0.3/CrossClustering/R/ari.R |only CrossClustering-4.0.3/CrossClustering/R/cc_crossclustering.R |only CrossClustering-4.0.3/CrossClustering/R/cc_get_cluster.R |only CrossClustering-4.0.3/CrossClustering/R/cc_test_ari.R |only CrossClustering-4.0.3/CrossClustering/R/cc_test_ari_permutation.R |only CrossClustering-4.0.3/CrossClustering/R/consensus_cluster.R |only CrossClustering-4.0.3/CrossClustering/R/data.R |only CrossClustering-4.0.3/CrossClustering/R/dependencies.R |only CrossClustering-4.0.3/CrossClustering/R/reverse_table.R |only CrossClustering-4.0.3/CrossClustering/R/utils-pipe.R |only CrossClustering-4.0.3/CrossClustering/R/utils.R |only CrossClustering-4.0.3/CrossClustering/README.md |only CrossClustering-4.0.3/CrossClustering/data |only CrossClustering-4.0.3/CrossClustering/man/ari.Rd |only CrossClustering-4.0.3/CrossClustering/man/cc_crossclustering.Rd |only CrossClustering-4.0.3/CrossClustering/man/cc_get_cluster.Rd |only CrossClustering-4.0.3/CrossClustering/man/cc_test_ari.Rd |only CrossClustering-4.0.3/CrossClustering/man/cc_test_ari_permutation.Rd |only CrossClustering-4.0.3/CrossClustering/man/chain_effect.Rd |only CrossClustering-4.0.3/CrossClustering/man/consensus_cluster.Rd |only CrossClustering-4.0.3/CrossClustering/man/is_zero.Rd |only CrossClustering-4.0.3/CrossClustering/man/nb_data.Rd |only CrossClustering-4.0.3/CrossClustering/man/pipe.Rd |only CrossClustering-4.0.3/CrossClustering/man/prune_zero_tail.Rd |only CrossClustering-4.0.3/CrossClustering/man/reverse_table.Rd |only CrossClustering-4.0.3/CrossClustering/man/toy.Rd |only CrossClustering-4.0.3/CrossClustering/man/twomoons.Rd |only CrossClustering-4.0.3/CrossClustering/man/worms.Rd |only CrossClustering-4.0.3/CrossClustering/tests |only 41 files changed, 242 insertions(+), 152 deletions(-)
More information about CrossClustering at CRAN
Permanent link
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing as
described in "J. Polzehl and V. Spokoiny (2006)
<DOI:10.1007/s00440-005-0464-1>",
"J. Polzehl and V. Spokoiny (2004) <DOI:10.20347/WIAS.PREPRINT.998>"
and "J. Polzehl, K. Papafitsoros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>",
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 1.9-6 dated 2016-09-15 and 2.2-0 dated 2018-07-30
aws-1.9-6/aws/src/Makevars |only aws-2.2-0/aws/DESCRIPTION | 23 aws-2.2-0/aws/MD5 | 75 +- aws-2.2-0/aws/NAMESPACE | 13 aws-2.2-0/aws/R/Classes.r | 605 ++++++++++------- aws-2.2-0/aws/R/ICIsmooth.r | 817 ++++++++++++++--------- aws-2.2-0/aws/R/TGVTV.r |only aws-2.2-0/aws/R/aws.r | 1331 +++++++++++++++++++++++--------------- aws-2.2-0/aws/R/awsgaussian.r | 720 +++++++++++++------- aws-2.2-0/aws/R/awsirregular.r | 673 +++++++++++-------- aws-2.2-0/aws/R/awspropagation.r | 885 +++++++++++++++---------- aws-2.2-0/aws/R/awssegment.r | 730 +++++++++++++------- aws-2.2-0/aws/R/lpaws.r | 1060 ++++++++++++++++++------------ aws-2.2-0/aws/R/misc.r | 914 +++++++------------------- aws-2.2-0/aws/R/nlmean.r |only aws-2.2-0/aws/R/paws.r |only aws-2.2-0/aws/R/quality.r |only aws-2.2-0/aws/R/utilities.r | 881 +++++++++++++++---------- aws-2.2-0/aws/R/vaws.r | 452 +++++++----- aws-2.2-0/aws/R/vpaws.r |only aws-2.2-0/aws/build |only aws-2.2-0/aws/cleanup |only aws-2.2-0/aws/configure |only aws-2.2-0/aws/configure.ac |only aws-2.2-0/aws/inst/CITATION | 19 aws-2.2-0/aws/man/ICIcombined.Rd | 34 aws-2.2-0/aws/man/ICIsmooth.Rd | 25 aws-2.2-0/aws/man/TV_denoising.Rd |only aws-2.2-0/aws/man/aws-class.Rd | 3 aws-2.2-0/aws/man/aws-package.Rd | 50 - aws-2.2-0/aws/man/aws.Rd | 41 - aws-2.2-0/aws/man/awsweights.Rd |only aws-2.2-0/aws/man/kernsm.Rd | 22 aws-2.2-0/aws/man/nlmeans.Rd |only aws-2.2-0/aws/man/paws.Rd |only aws-2.2-0/aws/man/qmeasures.Rd |only aws-2.2-0/aws/man/vaws.Rd |only aws-2.2-0/aws/man/vpaws.Rd |only aws-2.2-0/aws/src/ICIsmooth.f | 42 - aws-2.2-0/aws/src/Makevars.in |only aws-2.2-0/aws/src/Makevars.win |only aws-2.2-0/aws/src/awslp.f | 138 +-- aws-2.2-0/aws/src/caws.f | 452 ++++++++++-- aws-2.2-0/aws/src/cawsmask.f | 10 aws-2.2-0/aws/src/init.c |only aws-2.2-0/aws/src/misc.f | 16 aws-2.2-0/aws/src/nlmeans.f |only aws-2.2-0/aws/src/pcaws.f |only aws-2.2-0/aws/src/pcaws2.f |only aws-2.2-0/aws/src/segment.f | 10 50 files changed, 5974 insertions(+), 4067 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <http://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.6 dated 2018-05-14 and 0.6.1 dated 2018-07-30
DESCRIPTION | 14 +++++----- MD5 | 18 ++++++------- NEWS.md | 5 +++ build/vignette.rds |binary inst/doc/udpipe-annotation.html | 20 ++++++--------- inst/doc/udpipe-train.html | 20 ++++++--------- inst/doc/udpipe-tryitout.html | 18 ++++++------- inst/doc/udpipe-usecase-postagging-lemmatisation.html | 18 ++++++------- inst/doc/udpipe-usecase-topicmodelling.html | 20 ++++++--------- src/udpipe.cpp | 24 +++++++++--------- 10 files changed, 76 insertions(+), 81 deletions(-)
More information about NitrogenUptake2016 at CRAN
Permanent link
More information about DecisionAnalysis at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-22 0.7.7
2016-04-25 0.7.5
2014-11-25 0.6.2
2013-02-09 0.6.1
2013-02-07 0.6
2012-02-06 0.5.5
2011-10-19 0.5.2
2011-01-20 0.5
2010-05-17 0.4.5
2010-04-19 0.4.4
2010-03-01 0.4.3
2009-11-03 0.4
2009-07-31 0.3.3
2009-07-02 0.3
2009-04-15 0.2
2008-11-30 0.1.1
2008-11-06 0.1
Title: Stineman, a Consistently Well Behaved Method of Interpolation
Description: A consistently well behaved method of interpolation based on piecewise rational functions using Stineman's algorithm.
Author: Tomas Johannesson & Halldor Bjornsson, Icelandic Met. Office;
Gabor Grothendieck
Maintainer: Tomas Johannesson <tj@vedur.is>
Diff between stinepack versions 1.3 dated 2009-03-20 and 1.4 dated 2018-07-30
DESCRIPTION | 20 +++++++++++--------- MD5 |only NAMESPACE |only man/stinterp.Rd | 2 +- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Manipulation of Linear Systems of (in)Equalities
Description: Variable elimination (Gaussian elimination, Fourier-Motzkin elimination),
Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution,
projecting a vector on the convex polytope described by a system of (in)equations,
simplify systems by removing spurious columns and rows and collapse implied equalities,
test if a matrix is totally unimodular, compute variable ranges implied by linear
(in)equalities.
Author: Mark van der Loo [aut, cre],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between lintools versions 0.1.1.4 dated 2017-06-06 and 0.1.2 dated 2018-07-30
DESCRIPTION | 7 ++--- MD5 | 24 ++++++++--------- NEWS | 7 +++++ R/compact.R | 57 +++++++++++++++++++++++++++++++++--------- build/vignette.rds |binary inst/doc/project.html | 4 +- man/compact.Rd | 5 ++- src/R_all_finite.c | 4 +- src/R_dc_spa.c | 9 ------ src/R_sc_arith.c | 16 ++--------- src/R_spa.c | 7 ----- src/R_sparseConstraints.c | 17 ++---------- tests/testthat/test_compact.R | 35 +++++++++++++++++++++++++ 13 files changed, 120 insertions(+), 72 deletions(-)
Title: Integration of Multiple Data Sets with Clustering Techniques
Description: Several integrative data methods in which information of objects from different data sources can be combined are included in the IntClust package. As a single data source is limited in its point of view, this provides more insight and the opportunity to investigate how the variables are interconnected. Clustering techniques are to be applied to the combined information. For now, only agglomerative hierarchical clustering is implemented. Further, differential gene expression and pathway analysis can be conducted on the clusters. Plotting functions are available to visualize and compare results of the different methods.
Author: Marijke Van Moerbeke
Maintainer: Marijke Van Moerbeke <marijke.vanmoerbeke@uhasselt.be>
Diff between IntClust versions 0.0.2 dated 2016-03-31 and 0.1.0 dated 2018-07-30
IntClust-0.0.2/IntClust/R/ADC.R |only IntClust-0.0.2/IntClust/R/ADEC.R |only IntClust-0.0.2/IntClust/R/ADECa.R |only IntClust-0.0.2/IntClust/R/ADECb.R |only IntClust-0.0.2/IntClust/R/ADECc.R |only IntClust-0.0.2/IntClust/R/BinFeaturesPlot.R |only IntClust-0.0.2/IntClust/R/BoxPlotDistance.R |only IntClust-0.0.2/IntClust/R/CEC.R |only IntClust-0.0.2/IntClust/R/CECa.R |only IntClust-0.0.2/IntClust/R/CECb.R |only IntClust-0.0.2/IntClust/R/CECc.R |only IntClust-0.0.2/IntClust/R/CategoricalFeaturesPlot.R |only IntClust-0.0.2/IntClust/R/CharacteristicsFeatures.R |only IntClust-0.0.2/IntClust/R/ChooseCluster.R |only IntClust-0.0.2/IntClust/R/Cluster.R |only IntClust-0.0.2/IntClust/R/ClusterCols.R |only IntClust-0.0.2/IntClust/R/ClusterPlot.R |only IntClust-0.0.2/IntClust/R/ColorPalette.R |only IntClust-0.0.2/IntClust/R/ColorsNames.R |only IntClust-0.0.2/IntClust/R/CompareInteractive.R |only IntClust-0.0.2/IntClust/R/ComparePlot.R |only IntClust-0.0.2/IntClust/R/CompareSilCluster.R |only IntClust-0.0.2/IntClust/R/CompareSvsM.R |only IntClust-0.0.2/IntClust/R/ContFeaturesPlot.R |only IntClust-0.0.2/IntClust/R/DetermineWeight_SilClust.R |only IntClust-0.0.2/IntClust/R/DetermineWeight_SimClust.R |only IntClust-0.0.2/IntClust/R/DiffGenes.R |only IntClust-0.0.2/IntClust/R/DiffGenesSelection.R |only IntClust-0.0.2/IntClust/R/Distance.R |only IntClust-0.0.2/IntClust/R/FeatSelection.R |only IntClust-0.0.2/IntClust/R/FeaturesOfCluster.R |only IntClust-0.0.2/IntClust/R/FindCluster.R |only IntClust-0.0.2/IntClust/R/FindElement.R |only IntClust-0.0.2/IntClust/R/FindGenes.R |only IntClust-0.0.2/IntClust/R/Geneset.intersect.R |only IntClust-0.0.2/IntClust/R/Geneset.intersectSelection.R |only IntClust-0.0.2/IntClust/R/HeatmapPlot.R |only IntClust-0.0.2/IntClust/R/HeatmapSelection.R |only IntClust-0.0.2/IntClust/R/IntClust-internal.R |only IntClust-0.0.2/IntClust/R/LabelCols.R |only IntClust-0.0.2/IntClust/R/Labelplot.R |only IntClust-0.0.2/IntClust/R/Normalization.R |only IntClust-0.0.2/IntClust/R/PathwayAnalysis.R |only IntClust-0.0.2/IntClust/R/Pathways.R |only IntClust-0.0.2/IntClust/R/PathwaysIter.R |only IntClust-0.0.2/IntClust/R/PathwaysSelection.R |only IntClust-0.0.2/IntClust/R/PlotPathways.R |only IntClust-0.0.2/IntClust/R/PreparePathway.R |only IntClust-0.0.2/IntClust/R/ProfilePlot.R |only IntClust-0.0.2/IntClust/R/ReorderToReference.R |only IntClust-0.0.2/IntClust/R/SNF.R |only IntClust-0.0.2/IntClust/R/SNFa.R |only IntClust-0.0.2/IntClust/R/SNFb.R |only IntClust-0.0.2/IntClust/R/SNFc.R |only IntClust-0.0.2/IntClust/R/SelectnrClusters.R |only IntClust-0.0.2/IntClust/R/SharedComps.R |only IntClust-0.0.2/IntClust/R/SharedGenesPathsFeat.R |only IntClust-0.0.2/IntClust/R/SharedSelection.R |only IntClust-0.0.2/IntClust/R/SharedSelectionLimma.R |only IntClust-0.0.2/IntClust/R/SharedSelectionMLP.R |only IntClust-0.0.2/IntClust/R/SimilarityHeatmap.R |only IntClust-0.0.2/IntClust/R/SimilarityMeasure.R |only IntClust-0.0.2/IntClust/R/TrackCluster.R |only IntClust-0.0.2/IntClust/R/Ultimate.R |only IntClust-0.0.2/IntClust/R/WeightedClust.R |only IntClust-0.0.2/IntClust/R/WeightedSimClust.R |only IntClust-0.0.2/IntClust/R/WonM.R |only IntClust-0.0.2/IntClust/R/distanceheatmaps.R |only IntClust-0.0.2/IntClust/data/Colors2.RData |only IntClust-0.0.2/IntClust/data/GS.RData |only IntClust-0.0.2/IntClust/inst/doc/IntClustVignette.R |only IntClust-0.0.2/IntClust/inst/doc/IntClustVignette.Rnw |only IntClust-0.0.2/IntClust/inst/doc/IntClustVignette.pdf |only IntClust-0.0.2/IntClust/man/ADECa.Rd |only IntClust-0.0.2/IntClust/man/ADECb.Rd |only IntClust-0.0.2/IntClust/man/ADECc.Rd |only IntClust-0.0.2/IntClust/man/BinFeaturesPlot.Rd |only IntClust-0.0.2/IntClust/man/CECa.Rd |only IntClust-0.0.2/IntClust/man/CECb.Rd |only IntClust-0.0.2/IntClust/man/CECc.Rd |only IntClust-0.0.2/IntClust/man/Colors2.Rd |only IntClust-0.0.2/IntClust/man/DetermineWeight._SimClust.Rd |only IntClust-0.0.2/IntClust/man/IntClust-package.Rd |only 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IntClust-0.0.2/IntClust/vignettes/InteractiveCluster.pdf |only IntClust-0.0.2/IntClust/vignettes/InteractiveMethod.pdf |only IntClust-0.0.2/IntClust/vignettes/SimilarityHeatmap_MCF7W.pdf |only IntClust-0.0.2/IntClust/vignettes/Tracking.pdf |only IntClust-0.1.0/IntClust/DESCRIPTION | 17 IntClust-0.1.0/IntClust/MD5 | 327 +++++----- IntClust-0.1.0/IntClust/NAMESPACE | 93 ++ IntClust-0.1.0/IntClust/R/Functions.R |only IntClust-0.1.0/IntClust/R/IntClust.R |only IntClust-0.1.0/IntClust/R/data.R |only IntClust-0.1.0/IntClust/build/partial.rdb |only IntClust-0.1.0/IntClust/build/vignette.rds |binary IntClust-0.1.0/IntClust/data/Colors1.RData |binary IntClust-0.1.0/IntClust/data/GeneInfo.rda |binary IntClust-0.1.0/IntClust/data/datalist | 2 IntClust-0.1.0/IntClust/data/fingerprintMat.rda |binary IntClust-0.1.0/IntClust/data/geneMat.rda |binary IntClust-0.1.0/IntClust/data/targetMat.rda |binary IntClust-0.1.0/IntClust/inst/EnsembleClusteringC.m |only IntClust-0.1.0/IntClust/inst/EnsembleClusteringH.m |only IntClust-0.1.0/IntClust/inst/EnsembleClusteringM.m |only IntClust-0.1.0/IntClust/inst/LinkBasedClusteringasrs.m |only IntClust-0.1.0/IntClust/inst/LinkBasedClusteringcts.m |only IntClust-0.1.0/IntClust/inst/LinkBasedClusteringsrs.m |only IntClust-0.1.0/IntClust/inst/LinkCluE.m |only IntClust-0.1.0/IntClust/inst/LinkCluETest.m |only IntClust-0.1.0/IntClust/inst/MetisAlgorithm.m |only IntClust-0.1.0/IntClust/inst/MetisAlgorithm_euclideaneuclidean.m |only IntClust-0.1.0/IntClust/inst/REFERENCES.bib |only IntClust-0.1.0/IntClust/inst/asrs.m |only IntClust-0.1.0/IntClust/inst/ceevalmutual.m |only IntClust-0.1.0/IntClust/inst/checkcl.m |only IntClust-0.1.0/IntClust/inst/checks.m |only IntClust-0.1.0/IntClust/inst/clHC.m |only IntClust-0.1.0/IntClust/inst/clbtocl.m |only IntClust-0.1.0/IntClust/inst/clcgraph.m |only IntClust-0.1.0/IntClust/inst/cleval.m |only IntClust-0.1.0/IntClust/inst/clhgraph.m |only IntClust-0.1.0/IntClust/inst/clstoclbs.m |only IntClust-0.1.0/IntClust/inst/cltoclb.m |only IntClust-0.1.0/IntClust/inst/clusterensemble.m |only IntClust-0.1.0/IntClust/inst/cmetis.m |only IntClust-0.1.0/IntClust/inst/crEnsemble.m |only IntClust-0.1.0/IntClust/inst/cspa.m |only IntClust-0.1.0/IntClust/inst/cts.m |only IntClust-0.1.0/IntClust/inst/doc/IntClust_Vignette.R |only IntClust-0.1.0/IntClust/inst/doc/IntClust_Vignette.Rnw |only IntClust-0.1.0/IntClust/inst/doc/IntClust_Vignette.pdf |only IntClust-0.1.0/IntClust/inst/evalmutual.m |only IntClust-0.1.0/IntClust/inst/fastchangem.m |only IntClust-0.1.0/IntClust/inst/hgpa.m |only IntClust-0.1.0/IntClust/inst/hmetis.m |only IntClust-0.1.0/IntClust/inst/ints.m |only IntClust-0.1.0/IntClust/inst/mapasc.m |only IntClust-0.1.0/IntClust/inst/mapdense.m |only IntClust-0.1.0/IntClust/inst/mcla.m |only IntClust-0.1.0/IntClust/inst/metis.m |only IntClust-0.1.0/IntClust/inst/norml.m |only IntClust-0.1.0/IntClust/inst/onetomax.m |only IntClust-0.1.0/IntClust/inst/relabelCl.m |only IntClust-0.1.0/IntClust/inst/run_EnsembleClusteringC.sh |only IntClust-0.1.0/IntClust/inst/run_EnsembleClusteringH.sh |only IntClust-0.1.0/IntClust/inst/run_EnsembleClusteringM.sh |only IntClust-0.1.0/IntClust/inst/run_LinkBasedClusteringasrs.sh |only IntClust-0.1.0/IntClust/inst/run_LinkBasedClusteringcts.sh |only IntClust-0.1.0/IntClust/inst/run_LinkBasedClusteringsrs.sh |only IntClust-0.1.0/IntClust/inst/run_MetisAlgorithm.sh |only IntClust-0.1.0/IntClust/inst/sgraph.m |only IntClust-0.1.0/IntClust/inst/showBar.m |only IntClust-0.1.0/IntClust/inst/simbjac.m |only IntClust-0.1.0/IntClust/inst/simxjac.m |only IntClust-0.1.0/IntClust/inst/srs.m |only IntClust-0.1.0/IntClust/inst/stod.m |only IntClust-0.1.0/IntClust/inst/valid_CA.m |only IntClust-0.1.0/IntClust/inst/valid_DbDunn.m |only IntClust-0.1.0/IntClust/inst/valid_RandIndex.m |only IntClust-0.1.0/IntClust/inst/valid_compactness.m |only IntClust-0.1.0/IntClust/inst/valid_sumsqures.m |only IntClust-0.1.0/IntClust/inst/weightCl.m |only IntClust-0.1.0/IntClust/inst/wgraph.m |only IntClust-0.1.0/IntClust/man/ABC.SingleInMultiple.Rd |only IntClust-0.1.0/IntClust/man/ADC.Rd | 93 -- IntClust-0.1.0/IntClust/man/ADEC.Rd | 109 +-- IntClust-0.1.0/IntClust/man/BinFeaturesPlot_MultipleData.Rd |only IntClust-0.1.0/IntClust/man/BinFeaturesPlot_SingleData.Rd |only IntClust-0.1.0/IntClust/man/BoxPlotDistance.Rd | 137 +--- IntClust-0.1.0/IntClust/man/CEC.Rd | 149 +--- IntClust-0.1.0/IntClust/man/CVAA.Rd |only IntClust-0.1.0/IntClust/man/CharacteristicFeatures.Rd | 127 +-- IntClust-0.1.0/IntClust/man/ChooseCluster.Rd | 156 ++-- IntClust-0.1.0/IntClust/man/Cluster.Rd | 123 +-- IntClust-0.1.0/IntClust/man/ClusterCols.Rd |only IntClust-0.1.0/IntClust/man/ClusterPlot.Rd | 92 +- IntClust-0.1.0/IntClust/man/ClusteringAggregation.Rd |only IntClust-0.1.0/IntClust/man/ColorPalette.Rd | 34 - IntClust-0.1.0/IntClust/man/Colors1.Rd | 16 IntClust-0.1.0/IntClust/man/ColorsNames.Rd | 52 - IntClust-0.1.0/IntClust/man/CompareInteractive.Rd | 156 ++-- IntClust-0.1.0/IntClust/man/ComparePlot.Rd | 163 ++-- IntClust-0.1.0/IntClust/man/CompareSilCluster.Rd | 152 ++-- IntClust-0.1.0/IntClust/man/CompareSvsM.Rd | 146 ++-- IntClust-0.1.0/IntClust/man/ConsensusClustering.Rd |only IntClust-0.1.0/IntClust/man/ContFeaturesPlot.Rd | 109 +-- IntClust-0.1.0/IntClust/man/DetermineWeight_SilClust.Rd | 195 ++--- IntClust-0.1.0/IntClust/man/DetermineWeight_SimClust.Rd |only IntClust-0.1.0/IntClust/man/DiffGenes.Rd | 141 +--- IntClust-0.1.0/IntClust/man/DiffGenesSelection.Rd |only IntClust-0.1.0/IntClust/man/Distance.Rd | 66 -- IntClust-0.1.0/IntClust/man/EHC.Rd |only IntClust-0.1.0/IntClust/man/EnsembleClustering.Rd |only IntClust-0.1.0/IntClust/man/EvidenceAccumulation.Rd |only IntClust-0.1.0/IntClust/man/FeatSelection.Rd |only IntClust-0.1.0/IntClust/man/FeaturesOfCluster.Rd | 93 +- IntClust-0.1.0/IntClust/man/FindCluster.Rd | 67 -- IntClust-0.1.0/IntClust/man/FindElement.Rd | 56 - IntClust-0.1.0/IntClust/man/FindGenes.Rd | 59 - IntClust-0.1.0/IntClust/man/GS.Rd | 31 IntClust-0.1.0/IntClust/man/GeneInfo.Rd | 27 IntClust-0.1.0/IntClust/man/Geneset.intersect.Rd | 89 +- IntClust-0.1.0/IntClust/man/Geneset.intersectSelection.Rd |only IntClust-0.1.0/IntClust/man/HBGF.Rd |only IntClust-0.1.0/IntClust/man/HeatmapPlot.Rd | 118 +-- IntClust-0.1.0/IntClust/man/HeatmapSelection.Rd | 137 ++-- IntClust-0.1.0/IntClust/man/HierarchicalEnsembleClustering.Rd |only IntClust-0.1.0/IntClust/man/IntClust.Rd |only IntClust-0.1.0/IntClust/man/LabelCols.Rd |only IntClust-0.1.0/IntClust/man/LabelPlot.Rd | 58 - IntClust-0.1.0/IntClust/man/LinkBasedClustering.Rd |only IntClust-0.1.0/IntClust/man/M_ABC.Rd |only IntClust-0.1.0/IntClust/man/Normalization.Rd | 34 - IntClust-0.1.0/IntClust/man/PathwayAnalysis.Rd | 157 ++-- IntClust-0.1.0/IntClust/man/Pathways.Rd | 193 ++--- IntClust-0.1.0/IntClust/man/PathwaysIter.Rd | 164 ++--- IntClust-0.1.0/IntClust/man/PathwaysSelection.Rd |only IntClust-0.1.0/IntClust/man/PlotPathways.Rd | 67 -- IntClust-0.1.0/IntClust/man/PreparePathway.Rd | 84 +- IntClust-0.1.0/IntClust/man/ProfilePlot.Rd | 149 +--- IntClust-0.1.0/IntClust/man/ReorderToReference.Rd | 116 +-- IntClust-0.1.0/IntClust/man/SNF.Rd | 129 +-- IntClust-0.1.0/IntClust/man/SelectnrClusters.Rd | 143 ++-- IntClust-0.1.0/IntClust/man/SharedComps.Rd | 57 - IntClust-0.1.0/IntClust/man/SharedGenesPathsFeat.Rd | 114 +-- IntClust-0.1.0/IntClust/man/SharedSelection.Rd |only IntClust-0.1.0/IntClust/man/SharedSelectionLimma.Rd |only IntClust-0.1.0/IntClust/man/SharedSelectionMLP.Rd |only IntClust-0.1.0/IntClust/man/SimilarityHeatmap.Rd | 120 +-- IntClust-0.1.0/IntClust/man/SimilarityMeasure.Rd | 65 - IntClust-0.1.0/IntClust/man/TrackCluster.Rd | 202 ++---- IntClust-0.1.0/IntClust/man/WeightedClust.Rd | 132 +--- IntClust-0.1.0/IntClust/man/WonM.Rd | 109 +-- IntClust-0.1.0/IntClust/man/distanceheatmaps.Rd |only IntClust-0.1.0/IntClust/man/f.clustABC.MultiSource.Rd |only IntClust-0.1.0/IntClust/man/f.gsample.Rd |only IntClust-0.1.0/IntClust/man/f.rmv.Rd |only IntClust-0.1.0/IntClust/man/f.t.Rd |only IntClust-0.1.0/IntClust/man/fingerprintMat.Rd | 20 IntClust-0.1.0/IntClust/man/geneMat.Rd | 21 IntClust-0.1.0/IntClust/man/targetMat.Rd | 21 IntClust-0.1.0/IntClust/vignettes/IntClustComparePlot.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustFP.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustPathwayPlot.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustPathwaysPlot.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustProfilePlot.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustTP.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustTrackingPlot.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustVignette-ClusterPlotF.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClustVignette-ClusterPlotT.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClust_Biblio.bib |only IntClust-0.1.0/IntClust/vignettes/IntClust_ClusterPlot_F.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClust_ClusterPlot_T.pdf |only IntClust-0.1.0/IntClust/vignettes/IntClust_Vignette.Rnw |only 270 files changed, 2496 insertions(+), 2991 deletions(-)
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Minimally adjust the values of numerical records in a data.frame, such
that each record satisfies a predefined set of equality and/or inequality
constraints. The constraints can be defined using the 'validate' package.
The core algorithms have recently been moved to the 'lintools' package,
refer to 'lintools' for a more basic interface and access to a version
of the algorithm that works with sparse matrices.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.2.1 dated 2017-06-14 and 0.2.3 dated 2018-07-30
DESCRIPTION | 11 +++++------ MD5 | 18 +++++++++--------- NEWS | 9 +++++++-- R/match_restrictions.R | 5 ++++- src/R_all_finite.c | 4 ++-- src/R_dc_spa.c | 9 +-------- src/R_sc_arith.c | 16 ++++------------ src/R_spa.c | 7 +------ src/R_sparseConstraints.c | 19 +++++-------------- tests/testthat/test_match_restrictions.R | 8 +++++++- 10 files changed, 45 insertions(+), 61 deletions(-)
Title: Generalized Linear Latent Variable Models
Description: Generalized linear latent variable model (gllvm) for analyzing multivariate data.
Estimation is performed using either Laplace approximation or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>).
Details for gllvm, see Hui et al. (2015) <doi:10.1111/2041-210X.12236>
and (2017) <doi:10.1080/10618600.2016.1164708> and Niku et al. (2017)
<doi:10.1007/s13253-017-0304-7>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 0.1.0 dated 2017-12-20 and 1.0 dated 2018-07-30
DESCRIPTION | 10 MD5 | 44 +- NAMESPACE | 12 R/TMBtrait.R | 801 +++++++++++++++++++++++--------------------- R/anova.gllvm.R |only R/coef.gllvm.R | 3 R/coefplot.gllvm.R | 44 +- R/confint.gllvm.R | 101 ++--- R/getResidualCor.gllvm.R | 20 - R/gllvm.R | 115 +++--- R/gllvm.TMB.R | 380 +++++++++++--------- R/gllvm.VA.R | 124 +++--- R/gllvm.auxiliary.R | 224 +++++------- R/logLik.gllvm.R | 2 R/ordiplot.gllvm.R | 39 +- R/print.gllvm.R | 9 R/residuals.gllvm.R | 21 - R/summary.gllvm.R | 13 man/anova.gllvm.Rd |only man/coefplot.gllvm.Rd | 13 man/getResidualCor.gllvm.Rd | 6 man/gllvm.Rd | 44 +- man/ordiplot.gllvm.Rd | 14 src/gllvm.cpp | 221 ++++++------ 24 files changed, 1222 insertions(+), 1038 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.2.8 dated 2017-07-08 and 2.2.10 dated 2018-07-30
emil-2.2.10/emil/DESCRIPTION | 20 +++++------ emil-2.2.10/emil/MD5 | 54 +++++++++++++++---------------- emil-2.2.10/emil/NAMESPACE | 2 - emil-2.2.10/emil/R/RcppExports.R | 6 +-- emil-2.2.10/emil/R/caret.r | 4 ++ emil-2.2.10/emil/R/cforest.r | 13 +++++++ emil-2.2.10/emil/R/glmnet.r | 3 + emil-2.2.10/emil/R/lda.r | 5 ++ emil-2.2.10/emil/R/modeling.r | 9 +++++ emil-2.2.10/emil/R/pamr.r | 4 ++ emil-2.2.10/emil/R/qda.r | 5 ++ emil-2.2.10/emil/R/randomForest.r | 2 + emil-2.2.10/emil/R/rpart.r | 2 + emil-2.2.10/emil/R/survival.r | 18 ++++++++-- emil-2.2.10/emil/inst/CITATION | 35 +++++++++----------- emil-2.2.10/emil/man/evaluate.Rd | 11 ++++++ emil-2.2.10/emil/man/fit_caret.Rd | 6 +++ emil-2.2.10/emil/man/fit_cforest.Rd | 15 ++++++++ emil-2.2.10/emil/man/fit_glmnet.Rd | 5 ++ emil-2.2.10/emil/man/fit_lda.Rd | 7 ++++ emil-2.2.10/emil/man/fit_qda.Rd | 7 ++++ emil-2.2.10/emil/man/fit_randomForest.Rd | 4 ++ emil-2.2.10/emil/man/fit_rpart.Rd | 4 ++ emil-2.2.10/emil/man/plot_Surv.Rd |only emil-2.2.10/emil/man/pre_pamr.Rd | 6 +++ emil-2.2.10/emil/man/pvalue.coxph.Rd | 8 ++++ emil-2.2.10/emil/src/RcppExports.cpp | 6 +-- emil-2.2.10/emil/src/init.c | 12 +++--- emil-2.2.8/emil/man/plot.Surv.Rd |only 29 files changed, 201 insertions(+), 72 deletions(-)
Title: Stan-Based Fit to Gastric Emptying Curves
Description: Stan-based curve-fitting function
for use with package 'breathtestcore' by the same author.
Stan functions are refactored here for easier testing.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathteststan versions 0.4.1 dated 2018-04-26 and 0.4.3 dated 2018-07-30
breathteststan-0.4.1/breathteststan/R/breathteststan-internal.R |only breathteststan-0.4.1/breathteststan/R/breathteststan.R |only breathteststan-0.4.1/breathteststan/exec |only breathteststan-0.4.1/breathteststan/inst/chunks |only breathteststan-0.4.1/breathteststan/src/Modules.cpp |only breathteststan-0.4.1/breathteststan/src/RcppExports.cpp |only breathteststan-0.4.1/breathteststan/src/include |only breathteststan-0.4.1/breathteststan/tools/make_cpp.R |only breathteststan-0.4.3/breathteststan/DESCRIPTION | 23 ++++--- breathteststan-0.4.3/breathteststan/MD5 | 32 ++++------ breathteststan-0.4.3/breathteststan/NAMESPACE | 5 - breathteststan-0.4.3/breathteststan/R/breathteststan-package.R |only breathteststan-0.4.3/breathteststan/R/stan_fit.R | 8 +- breathteststan-0.4.3/breathteststan/R/stanmodels.R | 31 ++++----- breathteststan-0.4.3/breathteststan/inst/include |only breathteststan-0.4.3/breathteststan/src/Makevars | 20 +++++- breathteststan-0.4.3/breathteststan/src/Makevars.win | 19 +++++ breathteststan-0.4.3/breathteststan/src/init.cpp | 2 breathteststan-0.4.3/breathteststan/src/stan_files |only breathteststan-0.4.3/breathteststan/tests/testthat/test_coef_by_group.R | 2 breathteststan-0.4.3/breathteststan/tools/make_cc.R |only 21 files changed, 83 insertions(+), 59 deletions(-)
More information about breathteststan at CRAN
Permanent link
Title: Random Effects for the Identification of Differential Splicing
Description: Contains the REIDS
model presented in Van Moerbeke et al
(2017) <doi:10.1186/s12859-017-1687-8> for the detection of alternative splicing. The method is extended by incorporating junction information for the
assessment of alternative splicing. The vignette introduces the model and shows an example work flow.
Author: Marijke Van Moerbeke
Maintainer: Marijke Van Moerbeke <marijke.vanmoerbeke@uhasselt.be>
Diff between REIDS versions 0.0.2 dated 2018-04-13 and 0.1.0 dated 2018-07-30
REIDS-0.0.2/REIDS/inst/doc/ASExons.R |only REIDS-0.0.2/REIDS/inst/doc/CreateOutput.R |only REIDS-0.0.2/REIDS/inst/doc/DataProcessing.R |only REIDS-0.0.2/REIDS/inst/doc/FIRMAScores.R |only REIDS-0.0.2/REIDS/inst/doc/HTA-2_0_ExonAndTranscriptAnnotations.py |only REIDS-0.0.2/REIDS/inst/doc/HTA-2_0_JunAssociations.py |only REIDS-0.0.2/REIDS/inst/doc/Line_Indexer_Pivot.pbs |only REIDS-0.0.2/REIDS/inst/doc/REIDSFunction_ClusterVersion.R |only REIDS-0.0.2/REIDS/inst/doc/REIDSFunction_ClusterVersion.pbs |only REIDS-0.0.2/REIDS/inst/doc/SpliceIndex.R |only REIDS-0.0.2/REIDS/inst/doc/TC12000010_LineIndex.csv |only REIDS-0.0.2/REIDS/inst/doc/TC12000010_Pivot.csv |only REIDS-0.0.2/REIDS/man/FilterInformativeGenes.Rd |only REIDS-0.0.2/REIDS/man/REIDSFunction_ClusterVersion.Rd |only REIDS-0.0.2/REIDS/man/Search.Rd |only REIDS-0.0.2/REIDS/vignettes/Biblio.bib |only REIDS-0.0.2/REIDS/vignettes/DataProcessing_Folders.png |only REIDS-0.1.0/REIDS/DESCRIPTION | 8 REIDS-0.1.0/REIDS/MD5 | 83 REIDS-0.1.0/REIDS/NAMESPACE | 23 REIDS-0.1.0/REIDS/R/Functions.R | 3794 ++++++++-- REIDS-0.1.0/REIDS/R/data.R | 17 REIDS-0.1.0/REIDS/data/TC1500264.RData |only REIDS-0.1.0/REIDS/data/datalist |only REIDS-0.1.0/REIDS/inst/doc/ExonAndTranscriptAnnotations.py |only REIDS-0.1.0/REIDS/inst/doc/ID_Name_TC.py | 62 REIDS-0.1.0/REIDS/inst/doc/JunctionAssociations.py |only REIDS-0.1.0/REIDS/inst/doc/Line_Indexer_PivotFile.pbs |only REIDS-0.1.0/REIDS/inst/doc/README.txt | 69 REIDS-0.1.0/REIDS/inst/doc/REIDSFunction_HPCVersion.R |only REIDS-0.1.0/REIDS/inst/doc/REIDSFunction_HPCVersion.pbs |only REIDS-0.1.0/REIDS/inst/doc/REIDSJunctionAssesment_HPCVersion.R |only REIDS-0.1.0/REIDS/inst/doc/REIDSJunctionAssesment_HPCVersion.pbs |only REIDS-0.1.0/REIDS/inst/doc/REIDS_Vignette.R | 194 REIDS-0.1.0/REIDS/inst/doc/REIDS_Vignette.Rnw | 745 - REIDS-0.1.0/REIDS/inst/doc/REIDS_Vignette.pdf |binary REIDS-0.1.0/REIDS/inst/doc/REMAP_ExtractInfo.pbs |only REIDS-0.1.0/REIDS/inst/doc/REMAP_ExtractInfo.py |only REIDS-0.1.0/REIDS/inst/doc/TC1500264_LineIndex.csv |only REIDS-0.1.0/REIDS/inst/doc/TC1500264_Pivot.csv |only REIDS-0.1.0/REIDS/inst/doc/TC1500264_REMAP.txt |only REIDS-0.1.0/REIDS/inst/doc/TC1500264_REMAP_Indices.txt |only REIDS-0.1.0/REIDS/inst/doc/TC1500264_TC_Gene_SplitFile.txt |only REIDS-0.1.0/REIDS/man/ASExons.Rd | 35 REIDS-0.1.0/REIDS/man/CreateOutput.Rd | 12 REIDS-0.1.0/REIDS/man/DataProcessing.Rd | 15 REIDS-0.1.0/REIDS/man/ExonTesting.Rd | 19 REIDS-0.1.0/REIDS/man/ExpressionLevelPlot.Rd | 2 REIDS-0.1.0/REIDS/man/JunInfo.Rd | 35 REIDS-0.1.0/REIDS/man/PivotTransformData.Rd | 22 REIDS-0.1.0/REIDS/man/REIDSFunction.Rd | 33 REIDS-0.1.0/REIDS/man/REIDSFunction_HPCVersion.Rd |only REIDS-0.1.0/REIDS/man/REIDSJunctionAssessment_HPCVersion.Rd |only REIDS-0.1.0/REIDS/man/REIDS_Analysis.Rd |only REIDS-0.1.0/REIDS/man/REIDS_IsoformAssesment.Rd |only REIDS-0.1.0/REIDS/man/REIDS_JunctionAssesment.Rd | 62 REIDS-0.1.0/REIDS/man/REIDSmodel_intern.Rd | 7 REIDS-0.1.0/REIDS/man/REMAP_SplitProbeSets.Rd |only REIDS-0.1.0/REIDS/man/TC1500264.Rd |only REIDS-0.1.0/REIDS/man/reidsfunction_genebygene.Rd | 15 REIDS-0.1.0/REIDS/vignettes/FolderStructure.png |only REIDS-0.1.0/REIDS/vignettes/REIDS_Biblio.bib |only REIDS-0.1.0/REIDS/vignettes/REIDS_Vignette.Rnw | 745 - 63 files changed, 4175 insertions(+), 1822 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>
Diff between frailtypack versions 2.12.6 dated 2017-10-06 and 2.12.7 dated 2018-07-30
DESCRIPTION | 8 ++-- MD5 | 38 ++++++++++----------- NEWS | 9 +++++ R/additivePenal.R | 2 - R/epoce.R | 20 +++++------ R/frailtyPenal.R | 78 ++++++++++++++++++++++++++++++++++++++++++--- R/longiPenal.R | 15 ++++++++ R/multivPenal.R | 13 ++++++- R/prediction.R | 2 - R/print.jointNestedPenal.R | 7 ++-- R/trivPenal.R | 40 +++++++++++++++++++---- R/trivPenalNL.R | 26 ++++++++++++++- man/additivePenal.Rd | 1 man/frailtyPenal.Rd | 16 ++++++++- man/longiPenal.Rd | 12 ++++-- man/trivPenal.Rd | 17 ++++++++- man/trivPenalNL.Rd | 20 +++++++++-- src/aresidusMartingale.f90 | 6 ++- src/funcpasweib_log.f90 | 4 +- src/joint.f90 | 14 +++++--- 20 files changed, 274 insertions(+), 74 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-28 1.6.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-12 1.4.1
2017-04-25 1.4
2016-04-22 1.3
2015-06-18 1.2
2015-06-03 1.1
2015-01-15 1.0