Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-51 dated 2015-10-17 and 0.9-52 dated 2015-11-15
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 +++---
MD5 | 14 +++++------
NEWS | 5 +++-
R/MVA.biplot.R | 34 ++++++++++++---------------
R/MVA.cor.R | 53 ++++++++++++++++++++++++-------------------
R/zzz.R | 2 -
man/MVA.biplot.Rd | 4 +--
man/RVAideMemoire-package.Rd | 4 +--
8 files changed, 66 insertions(+), 58 deletions(-)
Title: Package Allowing R to Call Python
Description: Run Python code, make function calls, assign and retrieve variables, etc. from R.
Author: Carlos J. Gil Bellosta
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>
Diff between rPython versions 0.0-5 dated 2014-08-03 and 0.0-6 dated 2015-11-15
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/python.assign.R | 47 +++++++++++++++++++++++------------------------ R/python.method.call.R | 2 +- man/python.assign.Rd | 5 +++-- 5 files changed, 37 insertions(+), 37 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.6 dated 2015-05-03 and 0.0.7 dated 2015-11-15
ChangeLog | 18 ++ DESCRIPTION | 8 - MD5 | 11 - README.md | 2 inst/include/annoylib.h | 347 +++++++++++++++++++++------------------------- inst/include/kissrandom.h |only src/annoy.cpp | 135 ++++++++++++----- 7 files changed, 281 insertions(+), 240 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.1 dated 2015-09-10 and 0.12.2 dated 2015-11-15
ChangeLog | 95 ++++ DESCRIPTION | 8 MD5 | 73 +-- build/Rcpp.pdf |binary inst/NEWS.Rd | 119 +++-- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 22 - inst/include/Rcpp/Dimension.h | 2 inst/include/Rcpp/Nullable.h | 9 inst/include/Rcpp/String.h | 566 +++++++++++++------------- inst/include/Rcpp/api/meat/is.h | 5 inst/include/Rcpp/complex.h | 25 - inst/include/Rcpp/config.h | 4 inst/include/Rcpp/sugar/functions/cummax.h |only inst/include/Rcpp/sugar/functions/cummin.h |only inst/include/Rcpp/sugar/functions/cumprod.h |only inst/include/Rcpp/sugar/functions/functions.h | 5 inst/include/Rcpp/vector/Matrix.h | 51 ++ inst/include/Rcpp/vector/MatrixColumn.h | 8 inst/include/Rcpp/vector/Subsetter.h | 28 + inst/unitTests/cpp/Matrix.cpp | 16 inst/unitTests/cpp/Subset.cpp | 7 inst/unitTests/cpp/misc.cpp | 22 + inst/unitTests/cpp/sugar.cpp | 46 ++ inst/unitTests/runit.Matrix.R | 27 + inst/unitTests/runit.misc.R | 17 inst/unitTests/runit.subset.R | 4 inst/unitTests/runit.sugar.R | 62 ++ src/attributes.cpp | 8 src/barrier.cpp | 4 vignettes/Rcpp.bib | 22 - 39 files changed, 844 insertions(+), 411 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.2 dated 2015-11-04 and 0.4.3 dated 2015-11-15
DESCRIPTION | 10 +++-- MD5 | 14 ++++---- R/MIIVsem-data.R | 2 - R/miivs.R | 44 ++++++++++++++++++++------ man/MIIVsem.Rd | 6 +-- man/bollen1989a.Rd | 10 ++--- man/miive.Rd | 89 +++++++++++++++++++++++++++-------------------------- man/miivs.Rd | 31 +++++++++--------- 8 files changed, 118 insertions(+), 88 deletions(-)
Title: Hierarchical Latent Space Network Model (HLSM)
Description: Hierarchical latent space network model for fitting ensemble of networks.
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Samrachana Adhikari <asam.cmu@gmail.com>
Diff between HLSM versions 0.4 dated 2014-08-23 and 0.5 dated 2015-11-15
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 8 ++++++++ R/HLSM_run.R | 16 +++++++++++----- R/HLSM_run_fixedEF.R | 19 ++++++++++++------- R/covFunction.R | 7 +++++-- demo/HLSM.school.advice.R | 4 ++++ man/plots.Rd | 23 +++++++++++++++++++++++ src/HLSM.cpp | 14 ++++++-------- 9 files changed, 84 insertions(+), 37 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 NIST curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES block
cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key)
encryption. 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 [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.4 dated 2015-05-11 and 0.5 dated 2015-11-15
openssl-0.4/openssl/R/onload.R |only openssl-0.4/openssl/R/rand_bytes.R |only openssl-0.4/openssl/src/Makevars |only openssl-0.4/openssl/src/digest.c |only openssl-0.4/openssl/src/rand_bytes.c |only openssl-0.5/openssl/DESCRIPTION | 31 - openssl-0.5/openssl/MD5 | 141 ++++- openssl-0.5/openssl/NAMESPACE | 94 +++ openssl-0.5/openssl/NEWS | 4 openssl-0.5/openssl/R/aes.R |only openssl-0.5/openssl/R/base64.R | 8 openssl-0.5/openssl/R/bignum.R |only openssl-0.5/openssl/R/cert.R |only openssl-0.5/openssl/R/encrypt.R |only openssl-0.5/openssl/R/envelope.R |only openssl-0.5/openssl/R/hash.R | 86 ++- openssl-0.5/openssl/R/keygen.R |only openssl-0.5/openssl/R/list.R |only openssl-0.5/openssl/R/mykey.R |only openssl-0.5/openssl/R/openssh.R |only openssl-0.5/openssl/R/openssl.R | 20 openssl-0.5/openssl/R/rand.R |only openssl-0.5/openssl/R/read.R |only openssl-0.5/openssl/R/signing.R |only openssl-0.5/openssl/R/ssh2.R |only openssl-0.5/openssl/R/stream.R | 4 openssl-0.5/openssl/R/write.R |only openssl-0.5/openssl/build/vignette.rds |binary openssl-0.5/openssl/configure | 94 +++ openssl-0.5/openssl/inst/cacert.pem |only openssl-0.5/openssl/inst/doc/crypto_hashing.html | 326 ++++++++---- openssl-0.5/openssl/inst/doc/secure_rng.html | 308 ++++++++--- openssl-0.5/openssl/man/aes_cbc.Rd |only openssl-0.5/openssl/man/base64.Rd | 8 openssl-0.5/openssl/man/bignum.Rd |only openssl-0.5/openssl/man/certs.Rd |only openssl-0.5/openssl/man/encrypt.Rd |only openssl-0.5/openssl/man/encrypt_envelope.Rd |only openssl-0.5/openssl/man/hash.Rd | 26 openssl-0.5/openssl/man/keygen.Rd |only openssl-0.5/openssl/man/my_key.Rd |only openssl-0.5/openssl/man/openssl.Rd | 18 openssl-0.5/openssl/man/rand_bytes.Rd | 2 openssl-0.5/openssl/man/read_key.Rd |only openssl-0.5/openssl/man/signatures.Rd |only openssl-0.5/openssl/man/write_pem.Rd |only openssl-0.5/openssl/src/Makevars.in |only openssl-0.5/openssl/src/Makevars.win | 4 openssl-0.5/openssl/src/aes.c |only openssl-0.5/openssl/src/base64.c | 11 openssl-0.5/openssl/src/bignum.c |only openssl-0.5/openssl/src/cert.c |only openssl-0.5/openssl/src/encrypt.c |only openssl-0.5/openssl/src/envelope.c |only openssl-0.5/openssl/src/error.c |only openssl-0.5/openssl/src/hash.c |only openssl-0.5/openssl/src/keygen.c |only openssl-0.5/openssl/src/onload.c | 21 openssl-0.5/openssl/src/openssh.c |only openssl-0.5/openssl/src/rand.c |only openssl-0.5/openssl/src/read.c |only openssl-0.5/openssl/src/signing.c |only openssl-0.5/openssl/src/ssl.c |only openssl-0.5/openssl/src/stream.c | 1 openssl-0.5/openssl/src/utils.h |only openssl-0.5/openssl/src/write.c |only openssl-0.5/openssl/tests/keys |only openssl-0.5/openssl/tests/testthat/test_bignum.R |only openssl-0.5/openssl/tests/testthat/test_encrypt.R |only openssl-0.5/openssl/tests/testthat/test_hash.R |only openssl-0.5/openssl/tests/testthat/test_hash_output_value.R | 12 openssl-0.5/openssl/tests/testthat/test_keys_dsa.R |only openssl-0.5/openssl/tests/testthat/test_keys_ecdsa.R |only openssl-0.5/openssl/tests/testthat/test_keys_ecdsa384.R |only openssl-0.5/openssl/tests/testthat/test_keys_ecdsa521.R |only openssl-0.5/openssl/tests/testthat/test_keys_rsa.R |only openssl-0.5/openssl/tools/winlibs.R | 6 77 files changed, 920 insertions(+), 305 deletions(-)
Title: Non-Parametric Survival Analysis
Description: Contains functions for non-parametric survival analysis of
exact and interval-censored observations.
Author: Yong Wang
Maintainer: Yong Wang <yongwang@auckland.ac.nz>
Diff between npsurv versions 0.3-3 dated 2015-11-12 and 0.3-4 dated 2015-11-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Uhaz.R | 34 +++++++++++++++++++++++++--------- man/gastric.Rd | 19 ++++++++++++++----- 4 files changed, 46 insertions(+), 21 deletions(-)
More information about SocialMediaLab at CRAN
Permanent link
Title: Spatial Microsimulation
Description: Produce small area population estimates by fitting census data to
survey data.
Author: Dimitris Kavroudakis <dimitris123@gmail.com>
Maintainer: Dimitris Kavroudakis <dimitris123@gmail.com>
Diff between sms versions 2.3 dated 2014-07-08 and 2.3.1 dated 2015-11-15
sms-2.3.1/sms/DESCRIPTION | 11 +-- sms-2.3.1/sms/MD5 | 56 +++++++-------- sms-2.3.1/sms/NAMESPACE | 12 ++- sms-2.3.1/sms/NEWS | 4 + sms-2.3.1/sms/R/sms.R | 72 +++++++++++++++----- sms-2.3.1/sms/inst/CITATION |only sms-2.3.1/sms/man/addDataAssociation.Rd | 7 + sms-2.3.1/sms/man/calculate_error.Rd | 9 +- sms-2.3.1/sms/man/census.Rd | 9 +- sms-2.3.1/sms/man/checkIfNamesInDataColumns.Rd | 7 + sms-2.3.1/sms/man/check_lexicon.Rd | 7 + sms-2.3.1/sms/man/createLexicon.Rd | 3 sms-2.3.1/sms/man/find_best_selection.Rd | 9 +- sms-2.3.1/sms/man/find_best_selection_SA.Rd | 11 +-- sms-2.3.1/sms/man/getInfo-microsimulation-method.Rd | 3 sms-2.3.1/sms/man/getInfo.Rd | 3 sms-2.3.1/sms/man/getTAEs-microsimulation-method.Rd | 5 - sms-2.3.1/sms/man/getTAEs.Rd | 3 sms-2.3.1/sms/man/microsimulation-class.Rd | 9 +- sms-2.3.1/sms/man/mysetSeed.Rd |only sms-2.3.1/sms/man/plotTries.Rd | 5 - sms-2.3.1/sms/man/random_panel_selection.Rd | 5 - sms-2.3.1/sms/man/run_parallel_HC.Rd | 12 ++- sms-2.3.1/sms/man/run_parallel_SA.Rd | 11 +-- sms-2.3.1/sms/man/run_serial.Rd | 5 - sms-2.3.1/sms/man/selection_for_area.Rd | 9 +- sms-2.3.1/sms/man/sms-package.Rd | 14 ++- sms-2.3.1/sms/man/survey.Rd | 13 +-- sms-2.3/sms/inst/doc |only 29 files changed, 196 insertions(+), 118 deletions(-)
Title: Change-Point Estimation using Shape-Restricted Splines
Description: In a scatterplot where the response variable is Gaussian, Poisson or binomial, we consider the case in which the mean function is smooth with a change-point, which is a mode, an inflection point or a jump point. The main routine estimates the mean curve and the change-point as well using shape-restricted B-splines. An optional subroutine delivering a bootstrapping confidence interval for the change-point is incorporated in the main routine.
Author: Xiyue Liao and Mary C Meyer
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeChange versions 1.0 dated 2015-10-07 and 1.1 dated 2015-11-15
DESCRIPTION | 8 MD5 | 14 R/ShapeChange.R | 1481 ++++++++++++++++++++++++++------------------- man/ShapeChange-package.Rd | 4 man/changept.Rd | 65 + man/ip.Rd | 3 man/jp.Rd | 18 man/tp.Rd | 7 8 files changed, 931 insertions(+), 669 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive. The package contains R wrappers to the UK NRFA data temporary-API.
There are functions to retrieve stations falling in a bounding box,
to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 0.2.0 dated 2015-07-02 and 0.2.1 dated 2015-11-15
rnrfa-0.2.0/rnrfa/R/NRFA_TS.R |only rnrfa-0.2.0/rnrfa/man/NRFA_TS.Rd |only rnrfa-0.2.1/rnrfa/DESCRIPTION | 7 ++- rnrfa-0.2.1/rnrfa/MD5 | 34 +++++++++--------- rnrfa-0.2.1/rnrfa/NAMESPACE | 3 + rnrfa-0.2.1/rnrfa/R/FindTS.R | 31 ++++++++++------- rnrfa-0.2.1/rnrfa/R/NRFA_Catalogue.R | 18 +++++---- rnrfa-0.2.1/rnrfa/R/NRFA_TSdata.R |only rnrfa-0.2.1/rnrfa/R/NRFA_TSmetadata.R |only rnrfa-0.2.1/rnrfa/R/OSG2LatLon.R | 48 ++++++++++++-------------- rnrfa-0.2.1/rnrfa/R/OSGParse.R | 56 ++++++++++++++----------------- rnrfa-0.2.1/rnrfa/R/ToJSONarray.R | 22 +++++------- rnrfa-0.2.1/rnrfa/R/zzz.R | 4 +- rnrfa-0.2.1/rnrfa/man/FindInfo.Rd | 2 - rnrfa-0.2.1/rnrfa/man/FindTS.Rd | 2 - rnrfa-0.2.1/rnrfa/man/NRFA_Catalogue.Rd | 7 ++- rnrfa-0.2.1/rnrfa/man/NRFA_TSdata.Rd |only rnrfa-0.2.1/rnrfa/man/NRFA_TSmetadata.Rd |only rnrfa-0.2.1/rnrfa/man/OSG2LatLon.Rd | 2 - rnrfa-0.2.1/rnrfa/man/OSGParse.Rd | 3 + rnrfa-0.2.1/rnrfa/man/ToJSONarray.Rd | 3 + 21 files changed, 127 insertions(+), 115 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.3 dated 2015-11-05 and 1.7.4 dated 2015-11-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/build.dist.struct.R | 13 +++++++------ R/rcbalance.R | 2 +- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Analysis of Large-Scale Pharmacogenomic Data
Description: Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
Author: Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Diff between PharmacoGx versions 1.0.6 dated 2015-07-24 and 1.1.2 dated 2015-11-15
PharmacoGx-1.0.6/PharmacoGx/R/geneIdMap.R |only PharmacoGx-1.0.6/PharmacoGx/R/probeGeneMapping.R |only PharmacoGx-1.0.6/PharmacoGx/R/summarizeGeneExpression.R |only PharmacoGx-1.0.6/PharmacoGx/R/summarizeSensitivityPhenotype.R |only PharmacoGx-1.0.6/PharmacoGx/data/CGPsmall.rda |only PharmacoGx-1.0.6/PharmacoGx/man/CGPsmall.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/downloadSignatures.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/drugPertubrationSig.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/geneInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/geneInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/geneNames.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/probeGeneMapping.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/sensitivityData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/sensitivityData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/summarizeGeneExpression.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/summarizeSensitivityPhenotype.Rd |only PharmacoGx-1.1.2/PharmacoGx/DESCRIPTION | 12 PharmacoGx-1.1.2/PharmacoGx/MD5 | 158 -- PharmacoGx-1.1.2/PharmacoGx/NAMESPACE | 54 PharmacoGx-1.1.2/PharmacoGx/R/GWC.R | 49 PharmacoGx-1.1.2/PharmacoGx/R/LogLogisticRegression.R | 40 PharmacoGx-1.1.2/PharmacoGx/R/PharmacoSetClass.R | 779 ++++------ PharmacoGx-1.1.2/PharmacoGx/R/callingWaterfall.R | 8 PharmacoGx-1.1.2/PharmacoGx/R/computeAUC.R | 42 PharmacoGx-1.1.2/PharmacoGx/R/computeDrugSensitivity.R | 188 +- PharmacoGx-1.1.2/PharmacoGx/R/computeIC50.R | 28 PharmacoGx-1.1.2/PharmacoGx/R/connectivityScore.R | 11 PharmacoGx-1.1.2/PharmacoGx/R/corWeighted.R | 20 PharmacoGx-1.1.2/PharmacoGx/R/datasets.R | 12 PharmacoGx-1.1.2/PharmacoGx/R/distancePointLine.R | 6 PharmacoGx-1.1.2/PharmacoGx/R/distancePointSegment.R | 6 PharmacoGx-1.1.2/PharmacoGx/R/downloadPSet.R | 89 - PharmacoGx-1.1.2/PharmacoGx/R/downloadSignatures.R | 87 - PharmacoGx-1.1.2/PharmacoGx/R/drugDoseResponseCurve.R | 195 +- PharmacoGx-1.1.2/PharmacoGx/R/drugPerturbationSig.R | 107 - PharmacoGx-1.1.2/PharmacoGx/R/drugSensitivitySig.R | 222 +- PharmacoGx-1.1.2/PharmacoGx/R/geneDrugSensitivity.R | 90 - PharmacoGx-1.1.2/PharmacoGx/R/getRawSensitivityMatrix.R |only PharmacoGx-1.1.2/PharmacoGx/R/intersectList.R | 5 PharmacoGx-1.1.2/PharmacoGx/R/intersectPSets.R | 269 +-- PharmacoGx-1.1.2/PharmacoGx/R/rankGeneDrugPerturbation.R | 22 PharmacoGx-1.1.2/PharmacoGx/R/rankGeneDrugSensitivity.R | 22 PharmacoGx-1.1.2/PharmacoGx/R/signatureClass.R | 9 PharmacoGx-1.1.2/PharmacoGx/R/stripWhiteSpace.R | 10 PharmacoGx-1.1.2/PharmacoGx/R/summarizeMolecularProfiles.R |only PharmacoGx-1.1.2/PharmacoGx/R/summarizeSensitivityProfiles.R |only PharmacoGx-1.1.2/PharmacoGx/R/unionList.R | 13 PharmacoGx-1.1.2/PharmacoGx/build/vignette.rds |binary PharmacoGx-1.1.2/PharmacoGx/data/CCLEsmall.rda |binary PharmacoGx-1.1.2/PharmacoGx/data/CMAPsmall.rda |binary PharmacoGx-1.1.2/PharmacoGx/data/GDSCsmall.rda |only PharmacoGx-1.1.2/PharmacoGx/data/HDAC_genes.rda |binary PharmacoGx-1.1.2/PharmacoGx/data/datalist |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/CreatingPharmacoSet.R |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/CreatingPharmacoSet.Rnw |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/CreatingPharmacoSet.pdf |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/PharmacoGx.R | 183 +- PharmacoGx-1.1.2/PharmacoGx/inst/doc/PharmacoGx.Rnw | 241 ++- PharmacoGx-1.1.2/PharmacoGx/inst/doc/PharmacoGx.pdf |binary PharmacoGx-1.1.2/PharmacoGx/man/GDSCsmall.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/LogLogisticRegression.Rd | 8 PharmacoGx-1.1.2/PharmacoGx/man/PharmacoSet-class.Rd | 127 - PharmacoGx-1.1.2/PharmacoGx/man/PharmacoSet.Rd | 22 PharmacoGx-1.1.2/PharmacoGx/man/availablePSets.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/checkPSetStructure.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/computeAUC.Rd | 7 PharmacoGx-1.1.2/PharmacoGx/man/computeIC50.Rd | 11 PharmacoGx-1.1.2/PharmacoGx/man/connectivityScore.Rd | 4 PharmacoGx-1.1.2/PharmacoGx/man/downloadPSet.Rd | 8 PharmacoGx-1.1.2/PharmacoGx/man/downloadPertSig.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/drugDoseResponseCurve.Rd | 7 PharmacoGx-1.1.2/PharmacoGx/man/drugPerturbationSig.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/drugSensitivitySig.Rd | 59 PharmacoGx-1.1.2/PharmacoGx/man/featureInfo-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/featureInfo.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/featureNames.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/intersectPSet.Rd | 54 PharmacoGx-1.1.2/PharmacoGx/man/molecularProfiles-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/molecularProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/phenoInfo-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/phenoInfo.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/sensitivityInfo-set.Rd | 4 PharmacoGx-1.1.2/PharmacoGx/man/sensitivityInfo.Rd | 4 PharmacoGx-1.1.2/PharmacoGx/man/sensitivityMeasures.Rd | 6 PharmacoGx-1.1.2/PharmacoGx/man/sensitivityProfiles-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/sensitivityProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/subsetTo.Rd | 13 PharmacoGx-1.1.2/PharmacoGx/man/summarizeMolecularProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/summarizeSensitivityProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/vignettes/CreatingPharmacoSet-concordance.tex |only PharmacoGx-1.1.2/PharmacoGx/vignettes/CreatingPharmacoSet.Rnw |only PharmacoGx-1.1.2/PharmacoGx/vignettes/CreatingPharmacoSet.tex |only PharmacoGx-1.1.2/PharmacoGx/vignettes/PharmacoGx.Rnw | 241 ++- PharmacoGx-1.1.2/PharmacoGx/vignettes/pharmacogx.bib |only 110 files changed, 1876 insertions(+), 1676 deletions(-)
Title: Bayesian Semi and Nonparametric Growth Curve Models that
Additionally Include Multiple Membership Random Effects
Description: Employs a non-parametric formulation for by-subject random effect
parameters to borrow strength over a constrained number of repeated
measurement waves in a fashion that permits multiple effects per subject.
One class of models employs a Dirichlet process (DP) prior for the subject
random effects and includes an additional set of random effects that
utilize a different grouping factor and are mapped back to clients through
a multiple membership weight matrix; e.g. treatment(s) exposure or dosage.
A second class of models employs a dependent DP (DDP) prior for the subject
random effects that directly incorporates the multiple membership pattern.
Author: Terrance Savitsky
Maintainer: Terrance Savitsky <tds151@gmail.com>
Diff between growcurves versions 0.2.3.9 dated 2014-02-23 and 0.2.4.0 dated 2015-11-15
growcurves-0.2.3.9/growcurves/tests/run-all.R |only growcurves-0.2.4.0/growcurves/DESCRIPTION | 26 growcurves-0.2.4.0/growcurves/MD5 | 154 +-- growcurves-0.2.4.0/growcurves/NAMESPACE | 16 growcurves-0.2.4.0/growcurves/NEWS | 12 growcurves-0.2.4.0/growcurves/R/XZcov.R | 8 growcurves-0.2.4.0/growcurves/R/ddpMCMCplots.R | 28 growcurves-0.2.4.0/growcurves/R/ddpeffectsplot.R | 82 +- growcurves-0.2.4.0/growcurves/R/ddpgrow.R | 9 growcurves-0.2.4.0/growcurves/R/dpgrow.R | 197 +++- growcurves-0.2.4.0/growcurves/R/dpgrowmm.R | 9 growcurves-0.2.4.0/growcurves/R/dpgrowmult.R | 9 growcurves-0.2.4.0/growcurves/R/getmf.R | 7 growcurves-0.2.4.0/growcurves/R/growplot.R | 184 ++-- growcurves-0.2.4.0/growcurves/R/growthCurve.R | 8 growcurves-0.2.4.0/growcurves/R/help.R | 7 growcurves-0.2.4.0/growcurves/R/mcmcPlots.R | 2 growcurves-0.2.4.0/growcurves/man/XZcov.Rd | 82 -- growcurves-0.2.4.0/growcurves/man/datbrghtmodterms.Rd | 190 +--- growcurves-0.2.4.0/growcurves/man/datbrghtterms.Rd | 152 +-- growcurves-0.2.4.0/growcurves/man/dateduc.Rd | 65 - growcurves-0.2.4.0/growcurves/man/datsim.Rd | 70 - growcurves-0.2.4.0/growcurves/man/datsimcov.Rd | 81 -- growcurves-0.2.4.0/growcurves/man/datsimmult.Rd | 134 +-- growcurves-0.2.4.0/growcurves/man/ddpEffectsplot.Rd | 142 +-- growcurves-0.2.4.0/growcurves/man/ddpMCMCplots.Rd | 166 +--- growcurves-0.2.4.0/growcurves/man/ddpPost.Rd | 66 - growcurves-0.2.4.0/growcurves/man/ddp_quantiles.Rd | 102 -- growcurves-0.2.4.0/growcurves/man/ddpgrow.Rd | 324 +++----- growcurves-0.2.4.0/growcurves/man/dpPost.Rd | 33 growcurves-0.2.4.0/growcurves/man/dpgrow.Rd | 331 +++----- growcurves-0.2.4.0/growcurves/man/dpgrowmm.Rd | 395 +++------- growcurves-0.2.4.0/growcurves/man/dpgrowmult.Rd | 391 +++------ growcurves-0.2.4.0/growcurves/man/effectsplot.Rd | 120 +-- growcurves-0.2.4.0/growcurves/man/getmf.Rd | 37 growcurves-0.2.4.0/growcurves/man/growcurves-package.Rd | 296 +++---- growcurves-0.2.4.0/growcurves/man/growplot.Rd | 115 +- growcurves-0.2.4.0/growcurves/man/growthCurve.Rd | 172 +--- growcurves-0.2.4.0/growcurves/man/lgmPost.Rd | 25 growcurves-0.2.4.0/growcurves/man/mcmcPlots.Rd | 152 +-- growcurves-0.2.4.0/growcurves/man/mmCmvplusDpPost.Rd | 73 - growcurves-0.2.4.0/growcurves/man/mmCplusDpPost.Rd | 58 - growcurves-0.2.4.0/growcurves/man/mmIgroupDpPost.Rd | 50 - growcurves-0.2.4.0/growcurves/man/mmIplusDpPost.Rd | 44 - growcurves-0.2.4.0/growcurves/man/mmmultPost.Rd | 99 -- growcurves-0.2.4.0/growcurves/man/plot.ddpgrow.Rd | 32 growcurves-0.2.4.0/growcurves/man/plot.dpgrow.Rd | 32 growcurves-0.2.4.0/growcurves/man/plot.dpgrowmm.Rd | 32 growcurves-0.2.4.0/growcurves/man/plot.dpgrowmult.Rd | 32 growcurves-0.2.4.0/growcurves/man/relabel.Rd | 23 growcurves-0.2.4.0/growcurves/man/samples.Rd | 13 growcurves-0.2.4.0/growcurves/man/samples.ddpgrow.Rd | 10 growcurves-0.2.4.0/growcurves/man/samples.dpgrow.Rd | 10 growcurves-0.2.4.0/growcurves/man/samples.dpgrowmult.Rd | 10 growcurves-0.2.4.0/growcurves/man/summary.ddpgrow.Rd | 6 growcurves-0.2.4.0/growcurves/man/summary.dpgrow.Rd | 6 growcurves-0.2.4.0/growcurves/man/summary.dpgrowmm.Rd | 10 growcurves-0.2.4.0/growcurves/man/summary.dpgrowmult.Rd | 10 growcurves-0.2.4.0/growcurves/man/summary_quantiles.Rd | 70 - growcurves-0.2.4.0/growcurves/man/trtplot.Rd | 65 - growcurves-0.2.4.0/growcurves/src/DPre.cpp | 2 growcurves-0.2.4.0/growcurves/src/ddp.cpp | 5 growcurves-0.2.4.0/growcurves/src/lgm.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmC.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCchol.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCmiar.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCmvplusDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCplusDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmI.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmIgroup.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmIgroupDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmIplusDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmmult.cpp | 2 growcurves-0.2.4.0/growcurves/tests/test-all.R |only growcurves-0.2.4.0/growcurves/tests/testthat/test-XZcov.R | 2 growcurves-0.2.4.0/growcurves/tests/testthat/test-ddpgrow.R | 2 growcurves-0.2.4.0/growcurves/tests/testthat/test-dpgrowmm-mv.R | 4 growcurves-0.2.4.0/growcurves/tests/testthat/test-dpgrowmm.R | 6 growcurves-0.2.4.0/growcurves/tests/testthat/test-dpgrowmult.R | 2 79 files changed, 2041 insertions(+), 3088 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
randomForestSRC package for survival, regression and classification forests and
ggplot2 package plotting.
Author: John Ehrlinger <john.ehrlinger@gmail.com>
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 1.1.4 dated 2015-03-29 and 1.2.0 dated 2015-11-15
DESCRIPTION | 17 MD5 | 233 ++++++----- NAMESPACE | 15 NEWS | 10 R/calc_roc.R | 36 + R/combine.gg_partial.R | 66 +-- R/gg_error.R | 19 R/gg_interaction.R | 36 - R/gg_minimal_depth.R | 26 - R/gg_minimal_vimp.R | 24 - R/gg_partial.R | 29 - R/gg_partial_coplot.R | 13 R/gg_rfsrc.R | 13 R/gg_roc.R | 4 R/gg_variable.R | 12 R/gg_vimp.R | 41 + R/help.R | 2 R/interaction_data.R | 18 R/kaplan.R | 8 R/logit_loess.R |only R/nelson.R | 6 R/partial.rfsrc.R | 8 R/partial_coplot_data.R | 12 R/partial_data.R | 16 R/partial_surface_data.R | 22 - R/plot.gg_error.R | 12 R/plot.gg_interaction.R | 16 R/plot.gg_minimal_depth.R | 62 ++ R/plot.gg_minimal_vimp.R | 44 +- R/plot.gg_partial.R | 38 - R/plot.gg_partial_list.R | 24 - R/plot.gg_rfsrc.R | 14 R/plot.gg_roc.R | 4 R/plot.gg_survival.R | 2 R/plot.gg_variable.R | 212 ++++++---- R/plot.gg_vimp.R | 22 - R/quantile_pts.R | 1 R/rfsrc_cache_datasets.R | 234 ++++++----- R/rfsrc_data.R | 18 R/varsel_data.R | 18 README.md | 5 build/vignette.rds |binary data/interaction_Boston.rda |binary data/interaction_iris.rda |binary data/interaction_pbc.rda |binary data/partial_Boston.rda |binary data/partial_coplot_Boston.rda |binary data/partial_coplot_Boston2.rda |binary data/partial_coplot_pbc.rda |binary data/partial_coplot_pbc2.rda |binary data/partial_iris.rda |binary data/partial_pbc.rda |binary data/rfsrc_Boston.rda |binary data/rfsrc_iris.rda |binary data/rfsrc_pbc.rda |binary data/rfsrc_pbc_test.rda |binary data/varsel_Boston.rda |binary data/varsel_iris.rda |binary data/varsel_pbc.rda |binary inst/doc/randomForestSRC-Regression.R | 71 ++- inst/doc/randomForestSRC-Regression.Rnw | 65 +-- inst/doc/randomForestSRC-Regression.pdf |binary inst/doc/randomForestSRC-Survival.R | 280 ++++++------- inst/doc/randomForestSRC-Survival.Rnw | 393 +++++++++---------- inst/doc/randomForestSRC-Survival.pdf |binary man/calc_auc.Rd | 10 man/calc_roc.rfsrc.Rd | 11 man/combine.gg_partial.Rd | 46 +- man/ggRandomForests-package.Rd | 58 +- man/gg_error.Rd | 19 man/gg_interaction.Rd | 49 +- man/gg_minimal_depth.Rd | 35 - man/gg_minimal_vimp.Rd | 33 - man/gg_partial.Rd | 62 +- man/gg_partial_coplot.rfsrc.Rd | 24 - man/gg_rfsrc.rfsrc.Rd | 17 man/gg_roc.rfsrc.Rd | 10 man/gg_survival.Rd | 21 - man/gg_variable.rfsrc.Rd | 32 - man/gg_vimp.rfsrc.Rd | 19 man/interaction_data.Rd | 114 +++-- man/kaplan.Rd | 12 man/logit_loess.Rd |only man/nelson.Rd | 16 man/partial.rfsrc.Rd | 32 - man/partial_coplot_data.Rd | 52 +- man/partial_data.Rd | 102 ++-- man/partial_surface_data.Rd | 99 ++-- man/plot.gg_error.Rd | 19 man/plot.gg_interaction.Rd | 21 - man/plot.gg_minimal_depth.Rd | 16 man/plot.gg_minimal_vimp.Rd | 30 - man/plot.gg_partial.Rd | 41 - man/plot.gg_partial_list.Rd | 31 - man/plot.gg_rfsrc.Rd | 16 man/plot.gg_roc.Rd | 9 man/plot.gg_survival.Rd | 19 man/plot.gg_variable.Rd | 27 - man/plot.gg_vimp.Rd | 25 - man/print.gg_minimal_depth.Rd | 7 man/quantile_pts.Rd | 13 man/rfsrc_cache_datasets.Rd | 43 +- man/rfsrc_data.Rd | 95 ++-- man/shift.Rd | 8 man/surface_matrix.Rd | 12 man/varsel_data.Rd | 100 ++-- tests |only vignettes/ggRandomForests.bib | 121 ++--- vignettes/randomForestSRC-Regression-concordance.tex |only vignettes/randomForestSRC-Regression.Rnw | 65 +-- vignettes/randomForestSRC-Survival.Rnw | 393 +++++++++---------- 111 files changed, 2301 insertions(+), 1904 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Time Series Clustering with Dynamic Time Warping
Description: Time series clustering using different techniques related to the
Dynamic Time Warping distance and its corresponding lower bounds. Additionally,
an implementation of k-Shape clustering is available.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 1.1.0 dated 2015-09-12 and 1.2.0 dated 2015-11-15
DESCRIPTION | 14 - MD5 | 66 ++--- NAMESPACE | 63 ++--- R/SBD.R | 76 +++++- R/TADPole.R | 67 +++-- R/dtw-lb.R | 2 R/dtwclust-classes.R | 4 R/dtwclust-plot.R | 15 - R/dtwclust.R | 233 ++++++++++++------- R/kcca-list.R | 4 R/lb-improved.R | 4 R/lb-keogh.R | 2 R/pkg.R | 2 R/shape-extraction.R | 4 R/uciCT.R | 44 +-- R/utils.R | 571 ++++++++++++++++++++++++++---------------------- R/zscore.R | 1 README.md | 106 +++++++- inst/REFERENCES.bib | 274 +++++++++++------------ man/DBA.Rd | 124 +++++----- man/NCCc.Rd | 2 man/SBD.Rd | 114 +++++---- man/TADPole.Rd | 2 man/dtw_lb.Rd | 7 man/dtwclust-class.Rd | 3 man/dtwclust-package.Rd | 2 man/dtwclust.Rd | 114 +++++---- man/lb_improved.Rd | 148 ++++++------ man/lb_keogh.Rd | 154 ++++++------ man/plot-methods.Rd | 100 ++++---- man/reinterpolate.Rd | 2 man/shape_extraction.Rd | 6 man/uciCT.Rd | 2 man/zscore.Rd | 2 34 files changed, 1325 insertions(+), 1009 deletions(-)