Title: Deprecated 'classic' Rcpp API
Diff between RcppClassic versions 0.9.4 dated 2013-07-27 and 0.9.5 dated 2014-01-25
Description: The RcppClassic package provides a deprecated C++ library which
facilitates the integration of R and C++.
New projects should use the new Rcpp API in the Rcpp package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss,
and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel
ChangeLog | 16 ++++
DESCRIPTION | 16 ++--
MD5 | 28 ++++---
NAMESPACE | 3
R/inline.R | 4 -
README.md |only
build |only
cleanup | 2
inst/doc/RcppClassic-intro.R | 2
inst/doc/RcppClassic-intro.Rnw | 60 +++++++++++------
inst/doc/RcppClassic-intro.pdf |binary
inst/doc/RcppClassic-unitTests.pdf |binary
src/RcppResultSet.cpp | 4 -
vignettes/RcppClassic-intro.Rnw | 60 +++++++++++------
vignettes/unitTests-results/RcppClassic-unitTests.html | 18 ++---
vignettes/unitTests-results/RcppClassic-unitTests.txt | 30 ++++----
16 files changed, 157 insertions(+), 86 deletions(-)
Title: Wiener process distribution functions
Diff between RWiener versions 1.1-0 dated 2013-08-07 and 1.2-0 dated 2014-01-25
Description: This package provides Wiener process distribution functions,
namely the Wiener first passage time density, CDF, quantile and random
functions.
Author: Dominik Wabersich
Maintainer: Dominik Wabersich
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/wienerdist.R | 27 +++++++++++++++++++++++----
man/wiener_likelihood.Rd | 20 ++++++++++++++++++--
man/wienerdist.Rd | 2 +-
5 files changed, 50 insertions(+), 15 deletions(-)
Title: Recursive Partitioning and Regression Trees
Diff between rpart versions 4.1-4 dated 2013-12-10 and 4.1-5 dated 2014-01-25
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of R port)
Maintainer: Brian Ripley
ChangeLog | 5 ++++-
DESCRIPTION | 14 ++++++++------
MD5 | 12 ++++++------
inst/doc/longintro.pdf |binary
inst/doc/usercode.pdf |binary
tests/treble.R | 5 +++--
tests/treble.Rout.save | 12 ++++++------
7 files changed, 27 insertions(+), 21 deletions(-)
Title: Apache OpenNLP Tools Interface
Diff between openNLP versions 0.2-1 dated 2013-08-20 and 0.2-2 dated 2014-01-25
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/chunk.R | 8 ++++----
R/ner.R | 16 ++++++++--------
R/parse.R | 9 +++++----
R/pos.R | 8 ++++----
R/sentdetect.R | 4 ++--
R/tokenize.R | 8 ++++----
man/Maxent_Chunk_Annotator.Rd | 2 +-
man/Maxent_Entity_Annotator.Rd | 2 +-
man/Maxent_POS_Tag_Annotator.Rd | 2 +-
man/Maxent_Sent_Token_Annotator.Rd | 2 +-
man/Maxent_Word_Token_Annotator.Rd | 2 +-
man/Parse_Annotator.Rd | 12 ++++++++----
14 files changed, 57 insertions(+), 52 deletions(-)
Title: Natural Language Processing Infrastructure
Diff between NLP versions 0.1-0 dated 2013-08-17 and 0.1-1 dated 2014-01-25
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++--
MD5 | 43 +++++++++++++++--------
NAMESPACE | 54 ++++++++++++++++++++++++++++-
R/annotate.R | 2 -
R/annotation.R | 10 ++++-
R/annotators.R | 69 ++++++++++++++++++++++++++++++++++++++
R/aptd.R |only
R/conll.R |only
R/span.R | 9 ++++
R/string.R | 7 +--
R/sysdata.rda |only
R/tagged.R |only
R/tree.R |only
R/viewers.R |only
R/wordlist.R |only
inst |only
man/AnnotatedPlainTextDocument.Rd |only
man/Annotation.Rd | 12 +++---
man/Annotator.Rd | 5 +-
man/CoNLLTextDocument.Rd |only
man/Span.Rd | 9 ++--
man/String.Rd | 14 +++----
man/TaggedTextDocument.Rd |only
man/Tree.Rd |only
man/WordListDocument.Rd |only
man/annotate.Rd | 2 -
man/annotations_in_spans.Rd | 2 -
man/annotators.Rd | 31 +++++++++++++++--
man/tagsets.Rd |only
man/viewers.Rd |only
30 files changed, 225 insertions(+), 52 deletions(-)
Title: Generalized Non-negative Matrix Factorization Based on Renyi
Divergence
Diff between gnmf versions 0.6 dated 2014-01-09 and 0.7 dated 2014-01-25
Description: This package performs generalized non-negative matrix factorization based on Renyi divergence.
Author: Jose M. Maisog, Guoli Wang, Karthik Devarajan
Maintainer: Jose M. Maisog
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
man/gnmf-package.Rd | 4 ++--
man/gnmf.Rd | 4 ++--
4 files changed, 14 insertions(+), 14 deletions(-)
Title: Fast partial SVD by implicitly-restarted Lanczos
bidiagonalization
Diff between irlba versions 1.0.2 dated 2012-11-05 and 1.0.3 dated 2014-01-25
Description: A fast and memory-efficient method for computing a few approximate singular values and singular vectors of large matrices.
Author: Jim Baglama and Lothar Reichel
Maintainer: Bryan W. Lewis
DESCRIPTION | 16 ++++++++--------
MD5 | 15 +++++++++------
NAMESPACE | 2 +-
R/irlba.R | 8 ++++----
inst/doc/irlba.R |only
inst/doc/irlba.Rnw | 26 +++++++++++++-------------
inst/doc/irlba.pdf |binary
man/irlba.Rd | 4 +++-
tests |only
vignettes |only
10 files changed, 38 insertions(+), 33 deletions(-)
Title: Semantic packaging tools for standard analytics
Diff between RJSONLD versions 1.0.1 dated 2014-01-15 and 1.0.2 dated 2014-01-25
Description: Package the results of standard statistical functions into
JSON-LD. Semantics can be explored at
https://standardanalytics.io/stats, and discussed at
https://github.com/standard-analytics/terms
Author: Joseph Dureau
Maintainer: Joseph Dureau
DESCRIPTION | 8 +--
MD5 | 6 +-
R/RJSONLD.export.R | 90 +++++++++++++++++++++++++++++++++++-------
man/RJSONLD.export-methods.Rd | 7 +++
4 files changed, 91 insertions(+), 20 deletions(-)
Title: Classical Test Theory Functions
Diff between CTT versions 1.0 dated 2008-09-03 and 2.0 dated 2014-01-25
Description: Contains common CTT functions
Author: John T. Willse
Maintainer: John T. Willse
DESCRIPTION | 23 ++++----
MD5 |only
NAMESPACE | 2
R/disattenuated.cor.R | 2
R/distractor.analysis.R | 29 +++++++---
R/polyserial.R |only
R/reliability.R | 9 +--
R/score.R | 10 ++-
man/CTT-package.Rd | 5 +
man/disattenuated.cor.Rd | 100 ++++++++++++++++++-------------------
man/distractor.analysis.Rd | 2
man/polyserial.Rd |only
man/reliability.Rd | 15 ++---
man/score.Rd | 2
man/spearman.brown.Rd | 66 ++++++++++++------------
man/subscales.Rd | 121 ++++++++++++++++++++++-----------------------
16 files changed, 204 insertions(+), 182 deletions(-)
Title: Protein Sequence Descriptor Calculation and Similarity
Computation with R
Diff between protr versions 0.2-0 dated 2013-12-19 and 0.2-1 dated 2014-01-25
Description: The protr package focus on offering a unique and comprehensive
toolkit for protein sequence descriptor calculation and similarity
computation. The descriptors included in the protr package are extensively
utilized in Bioinformatics and Chemogenomics research. The qualitative
descriptors listed in protr include Amino Acid Composition (Amino Acid
Composition/Dipeptide Composition/Tripeptide Composition) descriptor,
Autocorrelation (Normalized Moreau-Broto Autocorrelation/Moran
Autocorrelation/Geary Autocorrelation) descriptor, CTD
(Composition/Transition/Distribution) descriptor, Conjoint Traid
descriptor, Quasi-sequence Order (Sequence Order Coupling
Number/Quasi-sequence Order Descriptors) descriptor and Pseudo Amino Acid
Composition (Pseudo Amino Acid Composition/Amphiphilic Pseudo Amino Acid
Composition) descriptor. The quantitative descriptors, for
Proteochemometric (PCM) Modeling, includes the Generalized Scales-Based
Descriptors derived by Principal Components Analysis, Generalized
Scales-Based Descriptors derived by AA-Properties (AAindex), Generalized
Scales-Based Descriptors derived by 20+ classes of 2D and 3D Molecular
Descriptors (Topological, WHIM, VHSE, etc.), Generalized Scales-Based
Descriptors derived by Factor Analysis, Generalized Scales-Based
Descriptors derived by Multidimensional Scaling, and Generalized BLOSUM/PAM
Matrix-Derived Descriptors. The protr package also integrates the
functionality of parallellized similarity computation derived by protein
sequence alignment and Gene Ontology (GO) semantic similarity measures
between a list of protein sequences / GO terms / Entrez Gene IDs. ProtrWeb,
the web service built on protr, is located at:
http://cbdd.csu.edu.cn:8080/protrweb/ . The protr package is developed by
Computational Biology and Drug Design (CBDD) Group, Central South
University.
Author: Nan Xiao
Maintainer: Nan Xiao
protr-0.2-0/protr/vignettes/fig/Thumbs.db |only
protr-0.2-1/protr/DESCRIPTION | 10 +++++-----
protr-0.2-1/protr/LICENSE |only
protr-0.2-1/protr/MD5 | 8 ++++----
protr-0.2-1/protr/NEWS | 5 +++++
protr-0.2-1/protr/inst/doc/protr.pdf |binary
6 files changed, 14 insertions(+), 9 deletions(-)
Title: Some further GIS capabilities for R
Diff between GISTools versions 0.7-1 dated 2012-07-03 and 0.7-2 dated 2014-01-25
Description: Some mapping and spatial data manipulation tools - in particular
drawing choropleth maps with nice looking legends, and aggregation of point
data to polygons.
Author: Chris Brunsdon and Hongyan Chen
Maintainer: Chris Brunsdon
DESCRIPTION | 17 +++++++++--------
MD5 | 14 +++++++-------
NAMESPACE | 1 +
man/GISTools-package.Rd | 8 ++------
man/auto.shading.Rd | 11 ++++-------
man/choro.legend.Rd | 8 ++------
man/choropleth.Rd | 7 ++-----
man/shading.Rd | 7 ++-----
8 files changed, 29 insertions(+), 44 deletions(-)
Title: a problem solving environment for fitting separable nonlinear
models in physics and chemistry applications
Diff between TIMP versions 1.10.3 dated 2013-09-30 and 1.11.0 dated 2014-01-25
Description: TIMP is a problem solving environment for fitting
separable nonlinear models to measurements arising in physics
and chemistry experiments, and has been extensively applied to
time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg
DESCRIPTION | 13 +++++----
MD5 | 53 +++++++++++++++++++------------------
NAMESPACE | 2 -
R/addPrel.R | 5 ++-
R/addPrelCl.R | 11 +++++--
R/calcCirf.R | 60 +++++++++++++++++++++++++++++++------------
R/convGausExp.R |only
R/doClpConstr.R | 2 -
R/fullKF.R | 1
R/getFixed.R | 6 ++--
R/getModel.R | 2 -
R/getResults.R | 4 ++
R/getSpecList.R | 50 +++++++++++++++++++++++++++--------
R/getSpecToPlot.R | 2 +
R/init.dat.R | 4 +-
R/init.theta.R | 4 +-
R/initOneModel.R | 2 -
R/multiLin.R | 23 +++++++---------
R/set_initModelClass_kin.R | 8 +++--
data/denS4.rda |binary
data/denS5.rda |binary
data/donorAcceptorTagged.rda |binary
data/donorTagged.rda |binary
data/mea_IRF.rda |binary
data/target.rda |binary
man/dat-class.Rd | 3 +-
man/internals.Rd | 1
man/theta-class.Rd | 3 +-
28 files changed, 167 insertions(+), 92 deletions(-)
Title: Disentangles the effects of geographic and ecological isolation
on genetic differentiation
Diff between BEDASSLE versions 1.2 dated 2013-10-01 and 1.3 dated 2014-01-25
Description: This package provides functions that allow users to quantify the relative
contributions of geographic and ecological distances to empirical patterns of genetic
differentiation on a landscape. Specifically, the package contains a function that
calls a custom Markov chain Monte Carlo (MCMC) algorithm, which is used to estimate
the parameters of the inference model, as well as functions for performing MCMC
diagnosis and assessing model adequacy.
Author: Gideon Bradburd
Maintainer: Gideon Bradburd
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
R/Covariance.R | 10 +++++-----
R/MCMC.R | 4 ++--
R/plot_acceptance_rate.R | 3 ++-
man/MCMC.Rd | 17 ++++++++++-------
man/MCMC_BB.Rd | 17 ++++++++++-------
7 files changed, 38 insertions(+), 31 deletions(-)
Title: An R interface to SciDB
Diff between scidb versions 1.1-0 dated 2013-04-13 and 1.1-1 dated 2014-01-25
Description: SciDB is an open-source array database (http://scidb.org). The scidb package provides an R interface to SciDB.
Author: Paradigm4, B. W. Lewis
Maintainer: B. W. Lewis
scidb-1.1-0/scidb/R/libsock.R |only
scidb-1.1-0/scidb/R/scidb-class.R |only
scidb-1.1-0/scidb/R/scidbdf-class.R |only
scidb-1.1-0/scidb/inst/doc/p4logo.jpg |only
scidb-1.1-0/scidb/inst/doc/sine.tex |only
scidb-1.1-0/scidb/man/scidbmultiply.Rd |only
scidb-1.1-0/scidb/src/libsock.c |only
scidb-1.1-0/scidb/src/libsock.h |only
scidb-1.1-1/scidb/DESCRIPTION | 14
scidb-1.1-1/scidb/MD5 | 95 -
scidb-1.1-1/scidb/NAMESPACE | 112 +
scidb-1.1-1/scidb/NEWS | 50
scidb-1.1-1/scidb/R/aggregate.R |only
scidb-1.1-1/scidb/R/classes.R |only
scidb-1.1-1/scidb/R/dbops.R |only
scidb-1.1-1/scidb/R/glm.R |only
scidb-1.1-1/scidb/R/pkg.R | 30
scidb-1.1-1/scidb/R/scidb-arithmetic.R | 329 +++-
scidb-1.1-1/scidb/R/scidb-functions.R | 292 +---
scidb-1.1-1/scidb/R/scidb-indexing-functions.R | 543 ++-----
scidb-1.1-1/scidb/R/scidb-methods.R |only
scidb-1.1-1/scidb/R/scidbdf-functions.R | 96 +
scidb-1.1-1/scidb/R/scidbdf-methods.R |only
scidb-1.1-1/scidb/R/utility.R | 810 ++++++++---
scidb-1.1-1/scidb/README | 7
scidb-1.1-1/scidb/README.md |only
scidb-1.1-1/scidb/inst/doc/scidb.Rnw | 1737 +++++++++++++------------
scidb-1.1-1/scidb/inst/doc/scidb.pdf |binary
scidb-1.1-1/scidb/inst/misc |only
scidb-1.1-1/scidb/man/aggregate-methods.Rd |only
scidb-1.1-1/scidb/man/as.scidb.Rd | 26
scidb-1.1-1/scidb/man/attribute_rename.Rd |only
scidb-1.1-1/scidb/man/between.Rd | 15
scidb-1.1-1/scidb/man/bind.Rd |only
scidb-1.1-1/scidb/man/build.Rd |only
scidb-1.1-1/scidb/man/cast.Rd |only
scidb-1.1-1/scidb/man/cumulate.Rd |only
scidb-1.1-1/scidb/man/df2scidb.Rd | 7
scidb-1.1-1/scidb/man/diff.scidb.Rd |only
scidb-1.1-1/scidb/man/dimnames.scidb.Rd | 30
scidb-1.1-1/scidb/man/glm.fit.Rd |only
scidb-1.1-1/scidb/man/index_lookup.Rd |only
scidb-1.1-1/scidb/man/iquery.Rd | 4
scidb-1.1-1/scidb/man/lag.Rd |only
scidb-1.1-1/scidb/man/merge-methods.Rd |only
scidb-1.1-1/scidb/man/misc-methods.Rd |only
scidb-1.1-1/scidb/man/project.Rd |only
scidb-1.1-1/scidb/man/redimension.Rd |only
scidb-1.1-1/scidb/man/rename.Rd |only
scidb-1.1-1/scidb/man/repart.Rd |only
scidb-1.1-1/scidb/man/reshape-method.Rd |only
scidb-1.1-1/scidb/man/scidb-class.Rd | 93 -
scidb-1.1-1/scidb/man/scidb.Rd | 195 +-
scidb-1.1-1/scidb/man/scidbconnect.Rd | 24
scidb-1.1-1/scidb/man/scidbdf-class.Rd | 30
scidb-1.1-1/scidb/man/scidbeval.Rd |only
scidb-1.1-1/scidb/man/scidblist.Rd | 4
scidb-1.1-1/scidb/man/scidbremove.Rd | 3
scidb-1.1-1/scidb/man/slice.Rd |only
scidb-1.1-1/scidb/man/sort-methods.Rd |only
scidb-1.1-1/scidb/man/subset-methods.Rd |only
scidb-1.1-1/scidb/man/svd.Rd |only
scidb-1.1-1/scidb/src/Makevars.win | 1
scidb-1.1-1/scidb/src/scidb.c | 440 +-----
scidb-1.1-1/scidb/tests/scidb.R | 106 +
scidb-1.1-1/scidb/tests/scidbdf.R |only
scidb-1.1-1/scidb/vignettes |only
67 files changed, 2854 insertions(+), 2239 deletions(-)
Title: Multivariate GARCH models
Diff between rmgarch versions 1.2-5 dated 2014-01-24 and 1.2-6 dated 2014-01-25
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos
Maintainer: Alexios Ghalanos
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
R/copula-main.R | 2 +-
R/gogarch-main.R | 2 +-
R/rmgarch-functions.R | 2 --
R/rmgarch-mmean.R | 10 +++++-----
inst/COPYRIGHTS | 2 +-
inst/doc/The_rmgarch_models.Rnw | 2 +-
inst/doc/The_rmgarch_models.pdf |binary
inst/rmgarch.tests/rmgarch.test3.R | 2 +-
man/rmgarch-package.Rd | 8 ++++----
src/gogarch.cpp | 1 +
vignettes/The_rmgarch_models.Rnw | 2 +-
vignettes/The_rmgarch_models.tex | 2 +-
vignettes/rmgarch1.tex | 4 ++--
16 files changed, 43 insertions(+), 39 deletions(-)