Sun, 15 Nov 2015

Package RVAideMemoire updated to version 0.9-52 with previous version 0.9-51 dated 2015-10-17

Title: Diverse Basic Statistical and Graphical Functions
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

Diff between RVAideMemoire versions 0.9-51 dated 2015-10-17 and 0.9-52 dated 2015-11-15

 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(-)

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Package rPython updated to version 0.0-6 with previous version 0.0-5 dated 2014-08-03

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(-)

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Package RcppAnnoy updated to version 0.0.7 with previous version 0.0.6 dated 2015-05-03

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(-)

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Package Rcpp updated to version 0.12.2 with previous version 0.12.1 dated 2015-09-10

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 
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 build/Rcpp.pdf                                |binary
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 src/attributes.cpp                            |    8 
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Package MIIVsem updated to version 0.4.3 with previous version 0.4.2 dated 2015-11-04

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 ++++----
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Package HLSM updated to version 0.5 with previous version 0.4 dated 2014-08-23

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 +++++++-------
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 NAMESPACE                 |    8 ++++++++
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 R/covFunction.R           |    7 +++++--
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New package CALF with initial version 0.1
Package: CALF
Type: Package
Title: Coarse Approximation Linear Function
Version: 0.1
Date: 2015-11-15
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Description: Contains a greedy algorithm for coarse approximation linear function.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.0
NeedsCompilation: no
Packaged: 2015-11-15 18:01:45 UTC; stlane
Repository: CRAN
Date/Publication: 2015-11-15 22:26:53

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New package calACS with initial version 0.2
Package: calACS
Type: Package
Title: Count All Common Subsequences
Version: 0.2
Date: 2015-11-14
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Description: Count all common subsequences between 2 string sequences, with items separated by the same delimiter. The first string input is a length- one vector, the second string input can be a vector or list containing multiple strings. Algorithm from Wang, H. All common subsequences (2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.
License: GPL
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-11-15 19:47:43 UTC; alano
Repository: CRAN
Date/Publication: 2015-11-15 22:27:06

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Package openssl updated to version 0.5 with previous version 0.4 dated 2015-05-11

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

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 77 files changed, 920 insertions(+), 305 deletions(-)

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Package npsurv updated to version 0.3-4 with previous version 0.3-3 dated 2015-11-12

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(-)

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New package SocialMediaLab with initial version 0.18.0
Package: SocialMediaLab
Version: 0.18.0
Date: 2015-11-15
Title: Tools for Collecting Social Media Data and Generating Networks for Analysis
Description: A suite of tools for collecting and constructing networks from social media data. Provides easy-to-use functions for collecting data across popular platforms (Instagram, Facebook, Twitter, and YouTube) and generating different types of networks for analysis.
Type: Package
Imports: tm,stringr,twitteR,RCurl,bitops,rjson,plyr,igraph,Rfacebook,Hmisc,data.table,httpuv,instaR,methods,httr
Author: Timothy Graham & Robert Ackland
Maintainer: Timothy Graham <timothy.graham3@uq.net.au>
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-11-14 23:19:19 UTC; Tim
Repository: CRAN
Date/Publication: 2015-11-15 10:08:52

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Package sms updated to version 2.3.1 with previous version 2.3 dated 2014-07-08

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 +
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New package simmer with initial version 3.0.0
Package: simmer
Type: Package
Version: 3.0.0
Title: Just Let it Simmer
Description: Discrete-Event Simulation (DES) package for R.
Encoding: UTF-8
Authors@R: c( person("Bart", "Smeets", email="bartsmeets86@gmail.com", role="aut"), person("Iñaki", "Ucar", email="i.ucar86@gmail.com", role=c("aut", "cre")))
URL: https://github.com/Bart6114/simmer
BugReports: https://github.com/Bart6114/simmer/issues
Depends: R (>= 3.1.2)
Imports: Rcpp, R6, magrittr
Suggests: dplyr, tidyr, ggplot2, scales, testthat, knitr, rmarkdown
LinkingTo: Rcpp (>= 0.12.0)
License: MIT + file LICENSE
RoxygenNote: 5.0.0
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2015-11-14 16:30:49 UTC; inaki
Author: Bart Smeets [aut], Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Repository: CRAN
Date/Publication: 2015-11-15 10:09:09

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Package ShapeChange updated to version 1.1 with previous version 1.0 dated 2015-10-07

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 
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 8 files changed, 931 insertions(+), 669 deletions(-)

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Package rnrfa updated to version 0.2.1 with previous version 0.2.0 dated 2015-07-02

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

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Package rcbalance updated to version 1.7.4 with previous version 1.7.3 dated 2015-11-05

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 +++---
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 4 files changed, 14 insertions(+), 13 deletions(-)

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Package PharmacoGx updated to version 1.1.2 with previous version 1.0.6 dated 2015-07-24

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

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 PharmacoGx-1.1.2/PharmacoGx/R/callingWaterfall.R                          |    8 
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 PharmacoGx-1.1.2/PharmacoGx/R/rankGeneDrugPerturbation.R                  |   22 
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More information about PharmacoGx at CRAN
Permanent link

New package landest with initial version 1.0
Package: landest
Type: Package
Title: Landmark Estimation of Survival and Treatment Effect
Version: 1.0
Date: 2015-11-08
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>
Description: Provides functions to estimate survival and a treatment effect using a landmark estimation approach.
License: GPL
Imports: stats, survival
Packaged: 2015-11-14 16:43:05 UTC; parast
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-11-15 10:09:05

More information about landest at CRAN
Permanent link

Package growcurves updated to version 0.2.4.0 with previous version 0.2.3.9 dated 2014-02-23

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 
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 growcurves-0.2.4.0/growcurves/NAMESPACE                         |   16 
 growcurves-0.2.4.0/growcurves/NEWS                              |   12 
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 growcurves-0.2.4.0/growcurves/R/ddpMCMCplots.R                  |   28 
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 growcurves-0.2.4.0/growcurves/src/mmCchol.cpp                   |    2 
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 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(-)

More information about growcurves at CRAN
Permanent link

Package ggRandomForests updated to version 1.2.0 with previous version 1.1.4 dated 2015-03-29

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 -
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 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
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 man/calc_auc.Rd                                      |   10 
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 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
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Package dtwclust updated to version 1.2.0 with previous version 1.1.0 dated 2015-09-12

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(-)

More information about dtwclust at CRAN
Permanent link


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