Title: Linearized Bregman Algorithms for Generalized Linear Models
Description: Efficient procedures for fitting the regularization path
for linear, binomial, multinomial, Ising and Potts models with lasso,
group lasso or column lasso(only for multinomial) penalty.
The package uses Linearized Bregman Algorithm to solve the
regularization path through iterations. Bregman Inverse Scale Space Differential
Inclusion solver is also provided for linear model with lasso penalty.
Author: Feng Ruan, Jiechao Xiong and Yuan Yao
Maintainer: Jiechao Xiong <xiongjiechao@pku.edu.cn>
Diff between Libra versions 1.3-2 dated 2015-11-09 and 1.4 dated 2015-11-18
DESCRIPTION | 18 ++- MD5 | 44 +++++---- NAMESPACE | 2 R/cv.iss.R | 2 R/cv.lb.R | 41 ++++---- R/ising.R |only R/iss.R | 31 +----- R/lb.R | 239 ++++++++++++++++++++++++++++---------------------- R/plot.lb.R | 31 +++--- R/potts.R |only R/predict.lb.R | 34 +++---- man/cv.iss.Rd | 11 +- man/cv.lb.Rd | 42 +++++--- man/ising.Rd |only man/iss.Rd | 39 ++------ man/lb.Rd | 96 ++++++++++---------- man/plot.lb.Rd | 11 +- man/potts.Rd |only man/predict.lb.Rd | 10 +- src/LBLasso.c | 166 +++++++++++++++++++++++----------- src/LBheader.c | 157 +++++++++++++++++++++++--------- src/LBheader.h | 9 + src/LBlogistic.c | 163 ++++++++++++++++++++++------------ src/LBmultilogistic.c | 210 +++++++++++++++++++++++++++++++++---------- src/ising.c |only src/potts.c |only 26 files changed, 838 insertions(+), 518 deletions(-)
Title: R Interface to the EcoData Retriever
Description: Provides an R interface to the EcoData Retriever
(http://ecodataretriever.org/) via the EcoData Retriever's
command line interface. The EcoData Retriever automates the
tasks of finding, downloading, and cleaning ecological datasets,
and then stores them in a local database.
Author: Daniel McGlinn [aut, cre],
Ethan White [aut]
Maintainer: Daniel McGlinn <danmcglinn@gmail.com>
Diff between ecoretriever versions 0.2 dated 2015-11-13 and 0.2.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ecoretriever.R | 15 ++++++++++----- 3 files changed, 16 insertions(+), 11 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.23 dated 2015-09-30 and 2.24 dated 2015-11-18
BDgraph-2.23/BDgraph/R/log_Ig.R |only BDgraph-2.23/BDgraph/R/phat.R |only BDgraph-2.23/BDgraph/R/prob.R |only BDgraph-2.23/BDgraph/man/log_Ig.Rd |only BDgraph-2.23/BDgraph/man/phat.Rd |only BDgraph-2.23/BDgraph/man/prob.Rd |only BDgraph-2.24/BDgraph/DESCRIPTION | 10 BDgraph-2.24/BDgraph/MD5 | 96 ++--- BDgraph-2.24/BDgraph/NAMESPACE | 8 BDgraph-2.24/BDgraph/NEWS | 4 BDgraph-2.24/BDgraph/R/bdgraph.R | 334 ++++++++++-------- BDgraph-2.24/BDgraph/R/bdgraph.sim.R | 10 BDgraph-2.24/BDgraph/R/compare.R | 43 +- BDgraph-2.24/BDgraph/R/gnorm.R |only BDgraph-2.24/BDgraph/R/pgraph.R |only BDgraph-2.24/BDgraph/R/plinks.R |only BDgraph-2.24/BDgraph/R/plotcoda.R | 26 - BDgraph-2.24/BDgraph/R/plotroc.R | 96 ++++- BDgraph-2.24/BDgraph/R/rgwish.R | 6 BDgraph-2.24/BDgraph/R/select.R | 41 +- BDgraph-2.24/BDgraph/R/traceplot.R | 44 +- BDgraph-2.24/BDgraph/build/vignette.rds |binary BDgraph-2.24/BDgraph/inst/doc/BDgraph.pdf |binary BDgraph-2.24/BDgraph/inst/doc/vignette.pdf |binary BDgraph-2.24/BDgraph/man/BDgraph-package.Rd | 4 BDgraph-2.24/BDgraph/man/bdgraph.Rd | 63 ++- BDgraph-2.24/BDgraph/man/bdgraph.npn.Rd | 18 - BDgraph-2.24/BDgraph/man/bdgraph.sim.Rd | 10 BDgraph-2.24/BDgraph/man/compare.Rd | 37 +- BDgraph-2.24/BDgraph/man/gnorm.Rd |only BDgraph-2.24/BDgraph/man/pgraph.Rd |only BDgraph-2.24/BDgraph/man/plinks.Rd |only BDgraph-2.24/BDgraph/man/plot.bdgraph.Rd | 12 BDgraph-2.24/BDgraph/man/plot.sim.Rd | 2 BDgraph-2.24/BDgraph/man/plotcoda.Rd | 12 BDgraph-2.24/BDgraph/man/plotroc.Rd | 40 +- BDgraph-2.24/BDgraph/man/print.bdgraph.Rd | 12 BDgraph-2.24/BDgraph/man/rgwish.Rd | 14 BDgraph-2.24/BDgraph/man/select.Rd | 16 BDgraph-2.24/BDgraph/man/summary.bdgraph.Rd | 18 - BDgraph-2.24/BDgraph/man/surveyData.Rd | 2 BDgraph-2.24/BDgraph/man/traceplot.Rd | 18 - BDgraph-2.24/BDgraph/src/Ig.cpp | 4 BDgraph-2.24/BDgraph/src/copula.cpp | 100 ++--- BDgraph-2.24/BDgraph/src/copula.h | 12 BDgraph-2.24/BDgraph/src/gcgm_bd.cpp | 383 +++++++++++++-------- BDgraph-2.24/BDgraph/src/gcgm_bd_multi_update.cpp |only BDgraph-2.24/BDgraph/src/gcgm_rj.cpp | 301 +++++++++------- BDgraph-2.24/BDgraph/src/ggm_bd.cpp | 390 +++++++++++++--------- BDgraph-2.24/BDgraph/src/ggm_bd_multi_update.cpp |only BDgraph-2.24/BDgraph/src/ggm_rj.cpp | 309 +++++++++-------- BDgraph-2.24/BDgraph/src/matrix.cpp | 162 +++++++-- BDgraph-2.24/BDgraph/src/matrix.h | 21 - BDgraph-2.24/BDgraph/src/rgwish.cpp | 142 +++----- BDgraph-2.24/BDgraph/src/rgwish.h | 4 BDgraph-2.24/BDgraph/vignettes/BDgraph.pdf |binary 56 files changed, 1661 insertions(+), 1163 deletions(-)
Title: Software for Analysis of Weighted, Two-Mode, and Longitudinal
Networks
Description: R package for analyzing weighted, two-mode, and longitudinal networks.
Author: Tore Opsahl
Maintainer: Tore Opsahl <tore@opsahl.co.uk>
Diff between tnet versions 3.0.11 dated 2012-11-20 and 3.0.14 dated 2015-11-18
tnet-3.0.11/tnet/LICENSE |only tnet-3.0.14/tnet/ChangeLog | 4 + tnet-3.0.14/tnet/DESCRIPTION | 18 ++-- tnet-3.0.14/tnet/MD5 | 25 +++--- tnet-3.0.14/tnet/R/clustering_w.R | 4 - tnet-3.0.14/tnet/R/growth_l.R | 2 tnet-3.0.14/tnet/R/rg_reshuffling_w.R | 110 ++++++++++++++-------------- tnet-3.0.14/tnet/R/rg_tm.R | 2 tnet-3.0.14/tnet/R/rg_w.R | 2 tnet-3.0.14/tnet/R/tnet_ucinet.R | 2 tnet-3.0.14/tnet/data/tnet.RData |binary tnet-3.0.14/tnet/man/growth_l.Rd | 3 tnet-3.0.14/tnet/man/tnet-package.Rd | 4 - tnet-3.0.14/tnet/man/weighted_richclub_w.Rd | 3 14 files changed, 93 insertions(+), 86 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 0.5 dated 2015-11-15 and 0.6 dated 2015-11-18
openssl-0.5/openssl/R/encrypt.R |only openssl-0.5/openssl/man/base64.Rd |only openssl-0.5/openssl/man/certs.Rd |only openssl-0.5/openssl/man/encrypt.Rd |only openssl-0.5/openssl/src/encrypt.c |only openssl-0.6/openssl/DESCRIPTION | 6 openssl-0.6/openssl/MD5 | 52 +-- openssl-0.6/openssl/NAMESPACE | 1 openssl-0.6/openssl/NEWS | 6 openssl-0.6/openssl/R/base64.R | 5 openssl-0.6/openssl/R/bignum.R | 22 + openssl-0.6/openssl/R/cert.R | 12 openssl-0.6/openssl/R/hash.R | 5 openssl-0.6/openssl/R/openssl.R | 2 openssl-0.6/openssl/R/read.R | 4 openssl-0.6/openssl/R/rsa.R |only openssl-0.6/openssl/configure | 2 openssl-0.6/openssl/inst/doc/crypto_hashing.html | 325 ++++++----------------- openssl-0.6/openssl/inst/doc/secure_rng.html | 308 +++++---------------- openssl-0.6/openssl/man/base64_encode.Rd |only openssl-0.6/openssl/man/certificates.Rd |only openssl-0.6/openssl/man/hash.Rd | 2 openssl-0.6/openssl/man/openssl.Rd | 2 openssl-0.6/openssl/man/read_key.Rd | 3 openssl-0.6/openssl/man/rsa_encrypt.Rd |only openssl-0.6/openssl/src/aes.c | 26 - openssl-0.6/openssl/src/base64.c | 2 openssl-0.6/openssl/src/bignum.c | 16 + openssl-0.6/openssl/src/envelope.c | 4 openssl-0.6/openssl/src/rand.c | 2 openssl-0.6/openssl/src/rsa.c |only openssl-0.6/openssl/src/ssl.c | 63 +++- 32 files changed, 337 insertions(+), 533 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.13 dated 2015-09-16 and 1.14 dated 2015-11-18
DESCRIPTION | 10 ++++---- MD5 | 30 ++++++++++++------------ NAMESPACE | 1 NEWS | 24 +++++++++++++++++++ R/Deprecated.R | 11 -------- R/as.matrix-functions.R | 3 +- R/averageMassSpectra-functions.R | 2 - R/constructor-functions.R | 9 ++++--- R/determineWarpingFunctions-functions.R | 2 - build/vignette.rds |binary inst/doc/MALDIquant-intro.pdf |binary man/MALDIquant-defunct.Rd | 1 man/createMassPeaks-functions.Rd | 2 - man/estimateBaseline-methods.Rd | 3 +- tests/testthat/test_as.matrix-functions.R | 10 ++++---- tests/testthat/test_intensityMatrix-functions.R | 2 - 16 files changed, 63 insertions(+), 47 deletions(-)
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data
manipulation and the creation of new data, structured from basic forest
inventory data. The purpose of this package is provide functions to support
these activities.
Author: Clayton Vieira Fraga,
Ana Paula Simiqueli,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga <altoe.wagner@gmail.com>
Diff between Fgmutils versions 0.3 dated 2015-11-03 and 0.4 dated 2015-11-18
DESCRIPTION | 20 ++++++++++++-------- MD5 | 42 ++++++++++++++++++++++++++++++++++++++---- NAMESPACE | 27 +++++++++++++++++++++++++++ NEWS | 8 ++++++-- R/R21a.R |only R/R29a.R |only R/atualizaCampoBase.R | 8 ++++++++ R/avaliaAjuste.R |only R/bias.R |only R/calculaA.R |only R/calculaPerc.R |only R/ce.R |only R/fator_bias.R |only R/isfinitedataframe.R |only R/mae.R |only R/mse.R |only R/mspr.R |only R/residuoPerc.R |only R/rmse.R |only R/rrmse.R |only R/syx.R |only R/syxPerc.R |only man/R21a.Rd |only man/R29a.Rd |only man/avaliaAjuste.Rd |only man/bias.Rd |only man/calculaA.Rd |only man/calculaPerc.Rd |only man/ce.Rd |only man/fator_bias.Rd |only man/isfinitedataframe.Rd |only man/mae.Rd |only man/mse.Rd |only man/mspr.Rd |only man/residuoPerc.Rd |only man/rmse.Rd |only man/rrmse.Rd |only man/syx.Rd |only man/syxPerc.Rd |only 39 files changed, 91 insertions(+), 14 deletions(-)
Title: Fits a Catenary to Given Points
Description: Gives methods to create a catenary object and then plot it and get
properties of it. Can construct from parameters or endpoints. Also can get
catenary fitted to data.
Author: Jonathan Tuke [aut, cre],
Matthew Roughan [aut]
Maintainer: Jonathan Tuke <simon.tuke@adelaide.edu.au>
Diff between catenary versions 1.1 dated 2013-02-17 and 1.1.1 dated 2015-11-18
catenary-1.1.1/catenary/DESCRIPTION | 32 +++--- catenary-1.1.1/catenary/MD5 | 58 +++++------ catenary-1.1.1/catenary/NAMESPACE | 23 +++- catenary-1.1.1/catenary/NEWS | 5 catenary-1.1.1/catenary/R/catenary.R | 88 +++++++++-------- catenary-1.1.1/catenary/R/fittedCatenary.R | 44 +++++--- catenary-1.1.1/catenary/R/getFunctionEnvelopeCat.R | 2 catenary-1.1.1/catenary/R/getFunctionEnvelopePara.R | 2 catenary-1.1.1/catenary/R/package.R | 9 + catenary-1.1.1/catenary/inst/shiny/dataCat |only catenary-1.1.1/catenary/man/L.Rd |only catenary-1.1.1/catenary/man/Summary.Rd | 27 ++--- catenary-1.1.1/catenary/man/catenary-class.Rd | 23 +++- catenary-1.1.1/catenary/man/catenary.Rd | 39 +++---- catenary-1.1.1/catenary/man/ctesiphon.Rd | 16 +-- catenary-1.1.1/catenary/man/f.Rd | 21 ++-- catenary-1.1.1/catenary/man/fitCat.Rd | 20 ++- catenary-1.1.1/catenary/man/fitCatEndPts.Rd | 20 ++- catenary-1.1.1/catenary/man/fitMaxCat.Rd | 18 +-- catenary-1.1.1/catenary/man/fitNaturalCat.Rd | 18 +-- catenary-1.1.1/catenary/man/fittedCatenary-class.Rd | 26 +++-- catenary-1.1.1/catenary/man/fittedCatenary.Rd | 19 +-- catenary-1.1.1/catenary/man/getCatLength.Rd | 21 ++-- catenary-1.1.1/catenary/man/getFunctionEnvelopeCat.Rd | 18 +-- catenary-1.1.1/catenary/man/getFunctionEnvelopePara.Rd | 16 +-- catenary-1.1.1/catenary/man/getPoints.Rd | 6 - catenary-1.1.1/catenary/man/minmax.Rd | 9 + catenary-1.1.1/catenary/man/minmaxLength.Rd | 16 +-- catenary-1.1.1/catenary/man/plot.Rd | 31 ++++- catenary-1.1.1/catenary/man/vertex.Rd | 9 + catenary-1.1/catenary/man/accessor-methods.Rd |only 31 files changed, 370 insertions(+), 266 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows
various cartographic representations: proportional symbols, chroropleth,
typology, flows, discontinuities... It also proposes some additional useful
features: cartographic palettes, layout (scale, north arrow, title...), labels,
legends, access to cartographic API...
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between cartography versions 1.0 dated 2015-10-06 and 1.1 dated 2015-11-18
DESCRIPTION | 15 ++- MD5 | 117 ++++++++++++----------- NAMESPACE | 3 NEWS |only R/choroLayer.R | 2 R/gradLinkTypoLayer.R |only R/layoutLayer.R | 17 +-- R/legends.R | 214 +++++++++++++++++++++++++++++++------------ R/palettes.R | 1 README.md | 2 build/vignette.rds |binary inst/doc/cartography.Rmd | 2 inst/doc/cartography.html | 33 +++--- man/carto.pal.Rd | 18 +-- man/cartography.Rd | 16 +-- man/cartography.colors.Rd | 2 man/choroLayer.Rd | 28 ++--- man/coasts.spdf.Rd | 2 man/countries.spdf.Rd | 2 man/discLayer.Rd | 26 ++--- man/discretization.Rd | 8 - man/display.carto.all.Rd | 2 man/display.carto.pal.Rd | 2 man/dotDensityLayer.Rd | 22 ++-- man/frame.spdf.Rd | 2 man/getBorders.Rd | 10 +- man/getGridData.Rd | 16 +-- man/getGridLayer.Rd | 12 +- man/getLinkLayer.Rd | 18 +-- man/getTiles.Rd | 20 ++-- man/gradLinkLayer.Rd | 14 +- man/gradLinkTypoLayer.Rd |only man/graticule.spdf.Rd | 2 man/labelLayer.Rd | 14 +- man/layoutLayer.Rd | 15 +-- man/legendBarsSymbols.Rd | 12 +- man/legendChoro.Rd | 10 +- man/legendCirclesSymbols.Rd | 14 +- man/legendGradLines.Rd | 12 +- man/legendPropLines.Rd | 8 - man/legendPropTriangles.Rd | 12 +- man/legendSquaresSymbols.Rd | 15 +-- man/legendTypo.Rd | 12 +- man/nuts0.df.Rd | 12 +- man/nuts0.spdf.Rd | 2 man/nuts1.df.Rd | 12 +- man/nuts1.spdf.Rd | 2 man/nuts2.df.Rd | 12 +- man/nuts2.spdf.Rd | 2 man/nuts3.df.Rd | 8 - man/nuts3.spdf.Rd | 2 man/propLinkLayer.Rd | 16 +-- man/propSymbolsChoroLayer.Rd | 56 +++++------ man/propSymbolsLayer.Rd | 62 ++++++------ man/propSymbolsTypoLayer.Rd | 26 ++--- man/propTrianglesLayer.Rd | 28 ++--- man/tilesLayer.Rd | 10 +- man/twincities.Rd | 10 +- man/typoLayer.Rd | 20 ++-- man/world.spdf.Rd | 2 vignettes/cartography.Rmd | 2 61 files changed, 575 insertions(+), 461 deletions(-)
Title: Generate APA Tables for MS Word
Description: Most psychological journals require that tables in a manuscript comply to APA (American Association of Psychology) standards. Creating APA tables manually is often time consuming and prone to transcription errors. This package generates tables for MS Word ('.docx' extension) in APA format automatically with just a few lines of code.
Author: Jort de Vreeze [aut, cre]
Maintainer: Jort de Vreeze <j.devreeze@iwm-tuebingen.de>
Diff between apaStyle versions 0.1 dated 2015-10-23 and 0.2 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS |only R/apaTable.R | 2 +- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical workflow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and reweighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 5.0-7 dated 2015-11-10 and 5.0-8 dated 2015-11-18
Zelig-5.0-7/Zelig/tests/test-all.R |only Zelig-5.0-8/Zelig/DESCRIPTION | 14 +-- Zelig-5.0-8/Zelig/MD5 | 54 +++++++----- Zelig-5.0-8/Zelig/NAMESPACE | 6 - Zelig-5.0-8/Zelig/R/model-lognorm.R | 2 Zelig-5.0-8/Zelig/R/model-ls.R | 2 Zelig-5.0-8/Zelig/R/model-relogit.R | 3 Zelig-5.0-8/Zelig/R/model-zelig.R | 101 +++++++++++++++++------- Zelig-5.0-8/Zelig/R/plots.R | 14 +-- Zelig-5.0-8/Zelig/R/utils.R | 6 - Zelig-5.0-8/Zelig/man/cluster.formula.Rd | 12 +- Zelig-5.0-8/Zelig/man/coef-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/fitted-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/plot-Zelig-ANY-method.Rd |only Zelig-5.0-8/Zelig/man/predict-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/reduce.Rd | 14 +-- Zelig-5.0-8/Zelig/man/relogit.Rd | 4 Zelig-5.0-8/Zelig/man/setfactor.Rd | 10 +- Zelig-5.0-8/Zelig/man/setval.Rd | 10 +- Zelig-5.0-8/Zelig/man/stat.Rd | 10 +- Zelig-5.0-8/Zelig/man/statlevel.Rd | 10 +- Zelig-5.0-8/Zelig/man/statmat.Rd | 8 - Zelig-5.0-8/Zelig/man/summary-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/table.levels.Rd | 22 +++-- Zelig-5.0-8/Zelig/man/vcov-Zelig-method.Rd |only Zelig-5.0-8/Zelig/tests/testthat.R |only Zelig-5.0-8/Zelig/tests/testthat/test-logit.R | 79 ------------------ Zelig-5.0-8/Zelig/tests/testthat/test-lognom.R | 40 --------- Zelig-5.0-8/Zelig/tests/testthat/test-ls.R | 87 -------------------- Zelig-5.0-8/Zelig/tests/testthat/test-negbin.R | 16 --- Zelig-5.0-8/Zelig/tests/testthat/test-poisson.R | 16 --- Zelig-5.0-8/Zelig/tests/testthat/test-probit.R | 18 ---- 32 files changed, 202 insertions(+), 356 deletions(-)
Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently
scatter plots, histograms, parallel coordinate plots and choropleth maps are
supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.1.1 dated 2015-06-07 and 0.2.0 dated 2015-11-18
DESCRIPTION | 8 +- MD5 | 30 ++++----- NAMESPACE | 3 R/misc.R | 2 R/vcmap.R | 1 R/vhist.R | 2 R/vlaunch.R | 42 +++++++++--- R/vpcp.R | 1 R/vscat.R | 10 ++- build/vignette.rds |binary exec/vdmr_cmap.js | 99 ++++++++++++++++++++++++++++- exec/vdmr_hist.js | 134 +++++++++++++++++++++++++++++++++------- exec/vdmr_main.js | 120 +++++++++++++++++++++++++++--------- exec/vdmr_pcp.js | 175 +++++++++++++++++++++++++++++++++++++++++++++-------- exec/vdmr_scat.js | 167 ++++++++++++++++++++++++++++++++++++++++++++------ man/vlaunch.Rd | 4 - 16 files changed, 665 insertions(+), 133 deletions(-)
Title: A Predictive Model for Trait Based Community Assembly of Plant
Species
Description: Implements a predictive model of community assembly called 'Traitspace' (Laughlin et al. 2012, Ecology Letters). Traitspace is a hierarchical Bayesian model that translates the theory of trait-based environmental filtering into a statistical model that incorporates intraspecific trait variation to predict the relative abundances and the distributions of species.
The package includes functions to plot the predicted and the observed values. It also includes functions to compare the predicted values against the observed values using a variety of different distance measures and to implement permutation tests to test their statistical significance.
Author: Chaitanya Joshi, Xin Li, Daniel Laughlin
Maintainer: Chaitanya Joshi <cjoshi@waikato.ac.nz>
Diff between Traitspace versions 1.0 dated 2015-07-07 and 1.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Traitspace.R | 2 +- R/TraitspaceMod.R | 2 +- R/step_2D.R | 8 ++++---- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB), pre-formatted for general analysis and genome-wide association analysis using the NAM package.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, Reka Howard, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between SoyNAM versions 1.1 dated 2015-10-15 and 1.2 dated 2015-11-18
SoyNAM-1.1/SoyNAM/R/BLUPs.R |only SoyNAM-1.1/SoyNAM/man/BLUP1.Rd |only SoyNAM-1.1/SoyNAM/man/BLUP2.Rd |only SoyNAM-1.2/SoyNAM/DESCRIPTION | 10 +++++----- SoyNAM-1.2/SoyNAM/MD5 | 17 ++++++++--------- SoyNAM-1.2/SoyNAM/R/BLUP.R |only SoyNAM-1.2/SoyNAM/data/datalist | 4 ++-- SoyNAM-1.2/SoyNAM/data/soybase.RData |binary SoyNAM-1.2/SoyNAM/data/soynam.RData |binary SoyNAM-1.2/SoyNAM/man/BLUP.Rd |only SoyNAM-1.2/SoyNAM/man/SoyNAM-package.Rd | 6 +++--- SoyNAM-1.2/SoyNAM/man/soynam.Rd | 23 ++++++----------------- 12 files changed, 24 insertions(+), 36 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis <martha.ellis@gmail.com>
Diff between rSPACE versions 1.1.1 dated 2015-04-08 and 1.2.0 dated 2015-11-18
DESCRIPTION | 11 ++++---- MD5 | 14 +++++----- NAMESPACE | 6 +++- R/Create_Landscapes.r | 47 +++++++++++++++++++++++++++++------ R/Encounter_history.R | 1 R/Test_Samples.r | 8 ++++- R/Test_file.r | 14 +++++----- inst/external/ExampleSampleFrame.tif |binary 8 files changed, 73 insertions(+), 28 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: An R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/> to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.8-1 dated 2015-10-31 and 0.9-0 dated 2015-11-18
DESCRIPTION | 8 +++--- MD5 | 8 +++--- inst/NEWS.Rd | 8 ++++++ inst/include/Spectra/GenEigsSolver.h | 46 ++++++++++++++++++++--------------- inst/include/Spectra/SymEigsSolver.h | 41 +++++++++++++++++++------------ 5 files changed, 68 insertions(+), 43 deletions(-)
Title: A Report Templating System
Description: Facilitating the creation of reproducible statistical
report templates. Once created, rapport templates can be exported to
various external formats (HTML, LaTeX, PDF, ODT etc.) with pandoc as the
converter backend.
Author: Aleksandar Blagotić <alex@rapporter.net> and Gergely Daróczi
<daroczig@rapporter.net>
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between rapport versions 0.51 dated 2013-05-08 and 1.0 dated 2015-11-18
rapport-0.51/rapport/R/graphs.R |only rapport-0.51/rapport/R/misc.R |only rapport-0.51/rapport/R/stat_helpers.R |only rapport-0.51/rapport/R/stats_univar.R |only rapport-0.51/rapport/R/tables.R |only rapport-0.51/rapport/R/utils.R |only rapport-0.51/rapport/inst/templates/anova.tpl |only rapport-0.51/rapport/inst/templates/correlations.tpl |only rapport-0.51/rapport/inst/templates/crosstable.tpl |only rapport-0.51/rapport/inst/templates/deprecated/anova.tpl |only rapport-0.51/rapport/inst/templates/deprecated/correlations.tpl |only rapport-0.51/rapport/inst/templates/deprecated/crosstable.tpl |only rapport-0.51/rapport/inst/templates/deprecated/descriptives.tpl |only rapport-0.51/rapport/inst/templates/deprecated/example.tpl |only rapport-0.51/rapport/inst/templates/deprecated/generate-beta.tpl |only rapport-0.51/rapport/inst/templates/deprecated/i18n/hu/correlations.tpl |only rapport-0.51/rapport/inst/templates/deprecated/nortest.tpl |only rapport-0.51/rapport/inst/templates/deprecated/outlier-test.tpl |only rapport-0.51/rapport/inst/templates/deprecated/t-test.tpl |only rapport-0.51/rapport/inst/templates/descriptives.tpl |only rapport-0.51/rapport/inst/templates/example.tpl |only rapport-0.51/rapport/inst/templates/generate-beta.tpl |only rapport-0.51/rapport/inst/templates/i18n/hu/correlations.tpl |only rapport-0.51/rapport/inst/templates/nortest.tpl |only rapport-0.51/rapport/inst/templates/outlier-test.tpl |only rapport-0.51/rapport/inst/templates/t-test.tpl |only rapport-0.51/rapport/inst/tests/test-inputs-deprecated.R |only rapport-0.51/rapport/inst/tests/test-rp_helpers.R |only rapport-0.51/rapport/inst/tests/test-stat_helpers.R |only rapport-0.51/rapport/man/adj.rle.Rd |only rapport-0.51/rapport/man/alike.integer.Rd |only rapport-0.51/rapport/man/as.character.rp.inputs.Rd |only rapport-0.51/rapport/man/as.character.rp.meta.Rd |only rapport-0.51/rapport/man/capitalise.Rd |only rapport-0.51/rapport/man/catn.Rd |only rapport-0.51/rapport/man/fml.Rd |only rapport-0.51/rapport/man/htest.Rd |only rapport-0.51/rapport/man/htest.short.Rd |only rapport-0.51/rapport/man/is.boolean.Rd |only rapport-0.51/rapport/man/is.empty.Rd |only rapport-0.51/rapport/man/is.heading.Rd |only rapport-0.51/rapport/man/is.number.Rd |only rapport-0.51/rapport/man/is.rp.heading.Rd |only rapport-0.51/rapport/man/is.string.Rd |only rapport-0.51/rapport/man/is.tabular.Rd |only rapport-0.51/rapport/man/is.variable.Rd |only rapport-0.51/rapport/man/kurtosis.Rd |only rapport-0.51/rapport/man/lambda.test.Rd |only rapport-0.51/rapport/man/messagef.Rd |only rapport-0.51/rapport/man/pct.Rd |only rapport-0.51/rapport/man/print.rp.info.Rd |only rapport-0.51/rapport/man/print.rp.inputs.Rd |only rapport-0.51/rapport/man/print.rp.meta.Rd |only rapport-0.51/rapport/man/purge.comments.Rd |only rapport-0.51/rapport/man/rp.barplot.Rd |only rapport-0.51/rapport/man/rp.boxplot.Rd |only rapport-0.51/rapport/man/rp.densityplot.Rd |only rapport-0.51/rapport/man/rp.desc.Rd |only rapport-0.51/rapport/man/rp.dotplot.Rd |only rapport-0.51/rapport/man/rp.freq.Rd |only rapport-0.51/rapport/man/rp.graph.check.Rd |only rapport-0.51/rapport/man/rp.hist.Rd |only rapport-0.51/rapport/man/rp.iqr.Rd |only rapport-0.51/rapport/man/rp.kurtosis.Rd |only rapport-0.51/rapport/man/rp.label-set.Rd |only rapport-0.51/rapport/man/rp.label.Rd |only rapport-0.51/rapport/man/rp.lineplot.Rd |only rapport-0.51/rapport/man/rp.max.Rd |only rapport-0.51/rapport/man/rp.mean.Rd |only rapport-0.51/rapport/man/rp.median.Rd |only rapport-0.51/rapport/man/rp.min.Rd |only rapport-0.51/rapport/man/rp.missing.Rd |only rapport-0.51/rapport/man/rp.name.Rd |only rapport-0.51/rapport/man/rp.outlier.Rd |only rapport-0.51/rapport/man/rp.percent.Rd |only rapport-0.51/rapport/man/rp.qqplot.Rd |only rapport-0.51/rapport/man/rp.range.Rd |only rapport-0.51/rapport/man/rp.scatterplot.Rd |only rapport-0.51/rapport/man/rp.sd.Rd |only rapport-0.51/rapport/man/rp.se.mean.Rd |only rapport-0.51/rapport/man/rp.skewness.Rd |only rapport-0.51/rapport/man/rp.sum.Rd |only rapport-0.51/rapport/man/rp.univar.Rd |only rapport-0.51/rapport/man/rp.valid.Rd |only rapport-0.51/rapport/man/rp.var.Rd |only rapport-0.51/rapport/man/skewness.Rd |only rapport-0.51/rapport/man/stopf.Rd |only rapport-0.51/rapport/man/tocamel.Rd |only rapport-0.51/rapport/man/tpl.body.Rd |only rapport-0.51/rapport/man/tpl.check.Rd |only rapport-0.51/rapport/man/tpl.example.Rd |only rapport-0.51/rapport/man/tpl.export.Rd |only rapport-0.51/rapport/man/tpl.find.Rd |only rapport-0.51/rapport/man/tpl.header.Rd |only rapport-0.51/rapport/man/tpl.info.Rd |only rapport-0.51/rapport/man/tpl.inputs.Rd |only rapport-0.51/rapport/man/tpl.list.Rd |only rapport-0.51/rapport/man/tpl.meta.Rd |only rapport-0.51/rapport/man/tpl.paths.Rd |only rapport-0.51/rapport/man/tpl.paths.add.Rd |only rapport-0.51/rapport/man/tpl.paths.remove.Rd |only rapport-0.51/rapport/man/tpl.paths.reset.Rd |only rapport-0.51/rapport/man/tpl.renew.Rd |only rapport-0.51/rapport/man/tpl.rerun.Rd |only rapport-0.51/rapport/man/trim.space.Rd |only rapport-0.51/rapport/man/vgsub.Rd |only rapport-0.51/rapport/man/warningf.Rd |only rapport-1.0/rapport/DESCRIPTION | 32 rapport-1.0/rapport/MD5 | 255 ++---- rapport-1.0/rapport/NAMESPACE | 139 +-- rapport-1.0/rapport/NEWS | 65 + rapport-1.0/rapport/R/deprecated.R | 58 - rapport-1.0/rapport/R/export.R | 89 +- rapport-1.0/rapport/R/init.R | 18 rapport-1.0/rapport/R/inputs.R | 42 rapport-1.0/rapport/R/print.methods.R | 32 rapport-1.0/rapport/R/rapport.R | 93 ++ rapport-1.0/rapport/R/rp_helpers.R | 302 +------ rapport-1.0/rapport/R/template.R | 425 ++++++---- rapport-1.0/rapport/R/tpl-check.R | 15 rapport-1.0/rapport/data/ius2008.rda |binary rapport-1.0/rapport/demo/rapport.R | 109 +- rapport-1.0/rapport/inst/includes/stylesheets/custom.css | 4 rapport-1.0/rapport/inst/templates/ANOVA.rapport |only rapport-1.0/rapport/inst/templates/AnalyzeWizard.rapport |only rapport-1.0/rapport/inst/templates/BartlettsTest.rapport |only rapport-1.0/rapport/inst/templates/BrownForsythTest.rapport |only rapport-1.0/rapport/inst/templates/Correlation.rapport |only rapport-1.0/rapport/inst/templates/Crosstable.rapport |only rapport-1.0/rapport/inst/templates/Descriptives.rapport |only rapport-1.0/rapport/inst/templates/Example.rapport |only rapport-1.0/rapport/inst/templates/FTest.rapport |only rapport-1.0/rapport/inst/templates/FactorAnalysis.rapport |only rapport-1.0/rapport/inst/templates/GLM.rapport |only rapport-1.0/rapport/inst/templates/GenerateBeta.rapport |only rapport-1.0/rapport/inst/templates/HierarchicalClusterAnalysis.rapport |only rapport-1.0/rapport/inst/templates/HomogeneityCrosstable.rapport |only rapport-1.0/rapport/inst/templates/KMeansCluster.rapport |only rapport-1.0/rapport/inst/templates/KolmogorovSmirnovTest.rapport |only rapport-1.0/rapport/inst/templates/KruskalWallisTest.rapport |only rapport-1.0/rapport/inst/templates/LinearRegression.rapport |only rapport-1.0/rapport/inst/templates/MDS.rapport |only rapport-1.0/rapport/inst/templates/Minimal.rapport |only rapport-1.0/rapport/inst/templates/NormalityTest.rapport |only rapport-1.0/rapport/inst/templates/OutlierTest.rapport |only rapport-1.0/rapport/inst/templates/PCA.rapport |only rapport-1.0/rapport/inst/templates/TTestOneSample.rapport |only rapport-1.0/rapport/inst/templates/TTestTwoSample.rapport |only rapport-1.0/rapport/inst/templates/WilcoxonTest.rapport |only rapport-1.0/rapport/inst/templates/deprecated/ANOVA.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Correlation.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Crosstable.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Descriptives.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Example.rapport |only rapport-1.0/rapport/inst/templates/deprecated/GenerateBeta.rapport |only rapport-1.0/rapport/inst/templates/deprecated/NormalityTest.rapport |only rapport-1.0/rapport/inst/templates/deprecated/OutlierTest.rapport |only rapport-1.0/rapport/inst/templates/deprecated/i18n/hu/correlations.rapport |only rapport-1.0/rapport/inst/templates/graphs |only rapport-1.0/rapport/inst/templates/i18n/hu/correlations.rapport |only rapport-1.0/rapport/inst/tests/test-deprecated.R |only rapport-1.0/rapport/inst/tests/test-internals.R |only rapport-1.0/rapport/inst/tests/test-rapport.R | 20 rapport-1.0/rapport/man/as.character.rapport.inputs.Rd |only rapport-1.0/rapport/man/as.character.rapport.meta.Rd |only rapport-1.0/rapport/man/as.yaml.bool.Rd | 10 rapport-1.0/rapport/man/check.input.value.Rd | 19 rapport-1.0/rapport/man/check.input.value.class.Rd | 15 rapport-1.0/rapport/man/check.report.chunks.Rd | 11 rapport-1.0/rapport/man/check.tpl.Rd |only rapport-1.0/rapport/man/extract.meta.Rd | 40 rapport-1.0/rapport/man/get.tags.Rd | 27 rapport-1.0/rapport/man/guess.input.Rd | 9 rapport-1.0/rapport/man/guess.input.description.Rd | 12 rapport-1.0/rapport/man/guess.input.label.Rd | 11 rapport-1.0/rapport/man/guess.input.name.Rd | 24 rapport-1.0/rapport/man/guess.l.Rd | 21 rapport-1.0/rapport/man/guess.old.input.length.Rd | 12 rapport-1.0/rapport/man/guess.old.input.type.Rd | 11 rapport-1.0/rapport/man/inputs-deprecated.Rd | 215 +---- rapport-1.0/rapport/man/is.rapport.Rd | 11 rapport-1.0/rapport/man/ius2008.Rd | 100 +- rapport-1.0/rapport/man/print.rapport.Rd | 11 rapport-1.0/rapport/man/print.rapport.info.Rd |only rapport-1.0/rapport/man/print.rapport.inputs.Rd |only rapport-1.0/rapport/man/print.rapport.meta.Rd |only rapport-1.0/rapport/man/rapport-helpers.Rd |only rapport-1.0/rapport/man/rapport-package.Rd | 87 -- rapport-1.0/rapport/man/rapport.Rd | 108 -- rapport-1.0/rapport/man/rapport.body.Rd |only rapport-1.0/rapport/man/rapport.check.template.Rd |only rapport-1.0/rapport/man/rapport.docx.Rd | 15 rapport-1.0/rapport/man/rapport.example.Rd |only rapport-1.0/rapport/man/rapport.export.Rd |only rapport-1.0/rapport/man/rapport.header.Rd |only rapport-1.0/rapport/man/rapport.html.Rd | 15 rapport-1.0/rapport/man/rapport.info.Rd |only rapport-1.0/rapport/man/rapport.inputs.Rd |only rapport-1.0/rapport/man/rapport.ls.Rd |only rapport-1.0/rapport/man/rapport.meta.Rd |only rapport-1.0/rapport/man/rapport.odt.Rd | 15 rapport-1.0/rapport/man/rapport.path.Rd |only rapport-1.0/rapport/man/rapport.path.add.Rd |only rapport-1.0/rapport/man/rapport.path.remove.Rd |only rapport-1.0/rapport/man/rapport.path.reset.Rd |only rapport-1.0/rapport/man/rapport.pdf.Rd | 15 rapport-1.0/rapport/man/rapport.read.Rd |only rapport-1.0/rapport/man/rapport.renew.Rd |only rapport-1.0/rapport/man/rapport.rerun.Rd |only rapport-1.0/rapport/man/rapport.tangle.Rd |only 210 files changed, 1200 insertions(+), 1312 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.50.0 dated 2015-10-15 and 0.60.0 dated 2015-11-18
PSCBS-0.50.0/PSCBS/R/PairedPSCBS.BOOT,DEFUNCT.R |only PSCBS-0.60.0/PSCBS/DESCRIPTION | 12 PSCBS-0.60.0/PSCBS/MD5 | 33 PSCBS-0.60.0/PSCBS/NAMESPACE | 3 PSCBS-0.60.0/PSCBS/NEWS | 3481 +++++------ PSCBS-0.60.0/PSCBS/R/999.DEPRECATED.R |only PSCBS-0.60.0/PSCBS/R/PairedPSCBS.BOOT.R | 17 PSCBS-0.60.0/PSCBS/R/PairedPSCBS.BOOT.sets.R | 17 PSCBS-0.60.0/PSCBS/R/PairedPSCBS.PLOT,many.R | 17 PSCBS-0.60.0/PSCBS/R/randomSeed.R |only PSCBS-0.60.0/PSCBS/R/segmentByCBS.R | 192 PSCBS-0.60.0/PSCBS/R/segmentByPairedPSCBS.R | 78 PSCBS-0.60.0/PSCBS/inst/doc/CBS.pdf |binary PSCBS-0.60.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary PSCBS-0.60.0/PSCBS/man/randomSeed.Rd |only PSCBS-0.60.0/PSCBS/tests/randomSeed.R |only PSCBS-0.60.0/PSCBS/tests/segmentByCBS,futures.R |only PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS,calls.R | 2 PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS,futures.R |only PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS,noNormalBAFs.R | 2 PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS.R | 2 21 files changed, 1921 insertions(+), 1935 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
Description: Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can in
general be programmed on. A useful OptPath object (archive) to log function
evaluations is also provided.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Karin Schork [aut]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between ParamHelpers versions 1.5 dated 2015-02-03 and 1.6 dated 2015-11-18
DESCRIPTION | 33 ++- MD5 | 245 ++++++++++++++------------- NAMESPACE | 15 + NEWS | 17 + R/LearnerParam.R | 16 + R/OptPath.R | 4 R/OptPathDF.R | 2 R/OptPathDF_getter.R | 15 - R/OptPathDF_setter.R | 5 R/OptPath_getter.R | 2 R/OptPath_plotEAF.R |only R/OptPath_plotYTraces.R |only R/OptPath_plotter.R |only R/OptPath_setter.R | 4 R/ParamSet.R | 30 +-- R/aParam.R | 22 ++ R/convertParamSetToIrace.R | 30 +-- R/convertTypesToCInts.R | 4 R/dfRowsToList.R | 8 R/dropParams.R | 2 R/filterParams.R | 51 ++++- R/generateDesign.R | 14 + R/generateGridDesign.R | 31 +-- R/generateRandomDesign.R | 8 R/getDefaults.R | 3 R/getParamIds.R | 4 R/getParamLengths.R | 4 R/getParamNr.R | 4 R/getParamTypeCounts.R | 1 R/getParamTypes.R | 15 - R/hasForbidden.R | 2 R/hasRequires.R | 4 R/hasTrafo.R | 4 R/hasType.R | 24 +- R/isFeasible.R | 24 +- R/isForbidden.R | 2 R/isMissingValue.R | 4 R/isRequiresOk.R |only R/isType.R | 14 + R/isVector.R | 2 R/makeLearnerParamFuns.R | 56 +++--- R/makeParamFuns.R | 98 ++++++++-- R/paramValueToString.R | 4 R/removeMissingValues.R | 2 R/renderOptPathPlot.R |only R/renderOptPathPlot_helpers.R |only R/renderOptPathPlot_workers.R |only R/sample.R | 6 R/utils.R | 10 - R/zzz.R | 3 man/LearnerParam.Rd | 28 +-- man/OptPath.Rd | 24 +- man/Param.Rd | 47 +++-- man/addOptPathEl.Rd | 23 +- man/as.data.frame.OptPathDF.Rd | 2 man/convertParamSetToIrace.Rd | 8 man/dfRowsToList.Rd | 9 man/discreteNameToValue.Rd | 2 man/discreteValueToName.Rd | 2 man/dropParams.Rd | 6 man/extractParamSetFromSooFunction.Rd | 2 man/filterParams.Rd | 34 ++- man/generateDesign.Rd | 9 man/generateGridDesign.Rd | 7 man/generateRandomDesign.Rd | 7 man/getDefaults.Rd | 2 man/getLower.Rd | 2 man/getOptPathBestIndex.Rd | 21 +- man/getOptPathCol.Rd | 25 +- man/getOptPathCols.Rd | 23 +- man/getOptPathDOB.Rd | 25 +- man/getOptPathEOL.Rd | 25 +- man/getOptPathEl.Rd | 25 +- man/getOptPathErrorMessages.Rd | 23 +- man/getOptPathExecTimes.Rd | 23 +- man/getOptPathLength.Rd | 23 +- man/getOptPathParetoFront.Rd | 23 +- man/getOptPathX.Rd | 23 +- man/getOptPathY.Rd | 23 +- man/getParamIds.Rd | 2 man/getParamLengths.Rd | 2 man/getParamNr.Rd | 2 man/getParamTypeCounts.Rd | 2 man/getParamTypes.Rd | 6 man/hasFiniteBoxConstraints.Rd | 2 man/hasForbidden.Rd | 2 man/hasRequires.Rd | 2 man/hasTrafo.Rd | 2 man/hasType.Rd | 5 man/isEmpty.Rd | 2 man/isFeasible.Rd | 4 man/isForbidden.Rd | 2 man/isRequiresOk.Rd |only man/isType.Rd | 5 man/makeParamSet.Rd | 4 man/paramValueToString.Rd | 2 man/plotEAF.Rd |only man/plotOptPath.Rd |only man/plotYTraces.Rd |only man/removeMissingValues.Rd | 2 man/renderOptPathPlot.Rd |only man/renderYTraces.Rd |only man/repairPoint.Rd | 2 man/sampleValue.Rd | 6 man/sampleValues.Rd | 6 man/setOptPathElDOB.Rd | 23 +- man/setOptPathElEOL.Rd | 23 +- man/setValueCNames.Rd | 2 man/trafoOptPath.Rd | 2 man/trafoValue.Rd | 2 src/c_dfRowsToList.c | 11 - tests/testthat/helper_zzz.R |only tests/testthat/test_LearnerParam.R | 40 ++-- tests/testthat/test_OptPath.R | 31 +-- tests/testthat/test_Param.R | 29 +++ tests/testthat/test_ParamSet.R | 28 ++- tests/testthat/test_convertDiscrete.R | 18 - tests/testthat/test_convertParamSetToIrace.R | 21 +- tests/testthat/test_dfRowToList.R | 20 +- tests/testthat/test_dropParams.R | 12 - tests/testthat/test_filterParams.R | 91 +++++++--- tests/testthat/test_generateDesign.R | 15 + tests/testthat/test_generateGridDesign.R | 14 + tests/testthat/test_getDefaults.R | 5 tests/testthat/test_getParamTypeCounts.R | 4 tests/testthat/test_getParamTypes.R | 28 +-- tests/testthat/test_hasIsType.R | 27 +- tests/testthat/test_paramValueToString.R | 9 tests/testthat/test_plotEAF.R |only tests/testthat/test_plotYTrace.R |only tests/testthat/test_renderOptPathPlot.R |only tests/testthat/test_sample.R | 1 132 files changed, 1168 insertions(+), 694 deletions(-)
Title: Naive Discriminative Learning
Description: Naive discriminative learning implements learning and
classification models based on the Rescorla-Wagner equations and their
equilibrium equations.
Author: Antti Arppe [aut],
Peter Hendrix [aut],
Petar Milin [aut],
R. Harald Baayen [aut],
Tino Sering [aut, cre],
Cyrus Shaoul [aut]
Maintainer: Tino Sering <konstantin.sering@uni-tuebingen.de>
Diff between ndl versions 0.2.16 dated 2014-02-27 and 0.2.17 dated 2015-11-18
DESCRIPTION | 29 +++++++++++------- MD5 | 34 ++++++++++----------- NAMESPACE | 34 +++++++++++++++++++++ NEWS | 9 +++++ R/anova.ndlClassify.R | 29 ++++++++---------- R/estimateWeights.R | 67 ++++++++++++++++++++++++------------------- R/modelStatistics.R | 6 +-- R/ndlClassify.R | 9 +++-- R/ndlCuesOutcomes.R | 3 - R/predict.ndlClassify.R | 2 - R/summary.ndlClassify.R | 6 ++- R/summary.ndlCrossvalidate.R | 2 - README.md | 24 +++++++-------- man/learnLegacy.Rd | 7 ++-- man/lexample.Rd | 2 + man/ndl.package.Rd | 4 +- man/serbianUniCyr.Rd | 2 + src/learn.module.cpp | 28 ++++++++++++++--- 18 files changed, 188 insertions(+), 109 deletions(-)
Title: Normalize NanoString miRNA and mRNA Data
Description: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
Author: Daryl M. Waggott
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between NanoStringNorm versions 1.1.19 dated 2015-03-20 and 1.1.21 dated 2015-11-18
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 16 +++++++++++++++- R/Plot.NanoStringNorm.R | 4 ++-- R/read.xls.RCC.R | 8 +++----- build/vignette.rds |binary inst/doc/NanoStringNorm_Introduction.Rnw | 2 +- inst/doc/NanoStringNorm_Introduction.pdf |binary man/Plot.NanoStringNorm.Rd | 2 +- vignettes/NanoStringNorm_Introduction.Rnw | 2 +- 10 files changed, 39 insertions(+), 27 deletions(-)
More information about NanoStringNorm at CRAN
Permanent link
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.5 dated 2015-01-06 and 1.6 dated 2015-11-18
msm-1.5/msm/TODO |only msm-1.5/msm/inst/NEWS.mine |only msm-1.5/msm/inst/NEWS.r57 |only msm-1.5/msm/inst/NEWS.r64 |only msm-1.6/msm/ChangeLog | 83 ++++ msm-1.6/msm/DESCRIPTION | 23 - msm-1.6/msm/MD5 | 71 ++-- msm-1.6/msm/NAMESPACE | 19 - msm-1.6/msm/R/hmm-dists.R | 10 msm-1.6/msm/R/hmm.R | 175 +++++++--- msm-1.6/msm/R/msm.R | 135 +++++-- msm-1.6/msm/R/optim.R | 19 - msm-1.6/msm/R/outputs.R | 12 msm-1.6/msm/R/phase.R | 3 msm-1.6/msm/R/simul.R | 7 msm-1.6/msm/build/vignette.rds |binary msm-1.6/msm/inst/NEWS | 52 ++- msm-1.6/msm/inst/doc/msm-manual.R | 78 ++-- msm-1.6/msm/inst/doc/msm-manual.pdf |binary msm-1.6/msm/man/MatrixExp.Rd | 12 msm-1.6/msm/man/draic.msm.Rd | 20 - msm-1.6/msm/man/hmmMV.Rd |only msm-1.6/msm/man/hmodel.object.Rd | 1 msm-1.6/msm/man/msm.Rd | 81 ++-- msm-1.6/msm/man/pearson.msm.Rd | 2 msm-1.6/msm/man/simmulti.msm.Rd | 7 msm-1.6/msm/man/sojourn.msm.Rd | 7 msm-1.6/msm/man/totlos.msm.Rd | 2 msm-1.6/msm/src/doc/msm-manual.Rnw | 42 +- msm-1.6/msm/src/hmm.h | 1 msm-1.6/msm/src/hmmderiv.c | 1 msm-1.6/msm/src/lik.c | 376 ++++++++++++++++------ msm-1.6/msm/src/msm.h | 2 msm-1.6/msm/src/pijt.c | 19 - msm-1.6/msm/tests/testthat/test_datasumm.r | 1 msm-1.6/msm/tests/testthat/test_models.r | 85 ++-- msm-1.6/msm/tests/testthat/test_models_hmm.r | 48 +- msm-1.6/msm/tests/testthat/test_models_hmmmulti.r |only msm-1.6/msm/tests/testthat/test_models_misc.r | 40 +- msm-1.6/msm/vignettes |only 40 files changed, 980 insertions(+), 454 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al.
(2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.7.5 dated 2015-11-16 and 0.7.7 dated 2015-11-18
DESCRIPTION | 14 MD5 | 64 +- NAMESPACE | 32 - NEWS | 178 +++---- R/Qm.R | 34 - R/af.R | 986 ++++++++++++++++++++-------------------- R/bglmnet.R | 624 ++++++++++++------------- R/glmfence.R | 252 +++++----- R/lmfence.R | 300 ++++++------ R/mplot-package.R | 792 ++++++++++++++++---------------- R/mplot.R | 560 +++++++++++----------- R/qrange.R | 118 ++-- R/sigMM.R | 50 +- R/vis.R | 1250 +++++++++++++++++++++++++-------------------------- README.md | 146 ++--- inst/CITATION | 42 - man/af.Rd | 244 ++++----- man/artificialeg.Rd | 84 +-- man/bglmnet.Rd | 102 ++-- man/bodyfat.Rd | 102 ++-- man/diabetes.Rd | 88 +-- man/fev.Rd | 100 ++-- man/mplot-package.Rd | 22 man/mplot.Rd | 73 +- man/plot.af.Rd | 150 +++--- man/plot.bglmnet.Rd | 179 +++---- man/plot.vis.Rd | 269 +++++----- man/print.af.Rd | 48 - man/print.vis.Rd | 48 - man/summary.af.Rd | 48 - man/txt.fn.Rd | 42 - man/vis.Rd | 160 +++--- man/wallabies.Rd | 116 ++-- 33 files changed, 3683 insertions(+), 3634 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-1 dated 2015-10-03 and 1.2-2 dated 2015-11-18
DESCRIPTION | 8 +++--- MD5 | 54 +++++++++++++++++++++++--------------------- R/jomo.MCMCchain.R |only R/jomo.R |only R/jomo1.MCMCchain.R | 2 - R/jomo1.R | 2 - R/jomo1cat.MCMCchain.R | 21 ++++++----------- R/jomo1cat.R | 19 +++++---------- R/jomo1con.MCMCchain.R | 4 +-- R/jomo1con.R | 4 +-- R/jomo1mix.MCMCchain.R | 23 +++++++----------- R/jomo1mix.R | 23 +++++++----------- R/jomo1ran.MCMCchain.R | 2 - R/jomo1ran.R | 2 - R/jomo1rancat.MCMCchain.R | 25 ++++++++------------ R/jomo1rancat.R | 25 ++++++++------------ R/jomo1rancathr.MCMCchain.R | 25 ++++++++------------ R/jomo1rancathr.R | 25 ++++++++------------ R/jomo1rancon.MCMCchain.R | 8 +++--- R/jomo1rancon.R | 8 +++--- R/jomo1ranconhr.MCMCchain.R | 8 +++--- R/jomo1ranconhr.R | 8 +++--- R/jomo1ranmix.MCMCchain.R | 27 ++++++++-------------- R/jomo1ranmix.R | 27 ++++++++-------------- R/jomo1ranmixhr.MCMCchain.R | 27 ++++++++-------------- R/jomo1ranmixhr.R | 27 ++++++++-------------- man/jomo-package.Rd | 1 man/jomo.MCMCchain.Rd |only man/jomo.Rd |only man/jomo1ran.MCMCchain.Rd | 2 - 30 files changed, 175 insertions(+), 232 deletions(-)
Title: Joint Generalized Estimating Equation Solver
Description: Fits two different joint generalized estimating equation models to multivariate longitudinal data.
Author: Gul Inan
Maintainer: Gul Inan <inanx002@umn.edu>
Diff between JGEE versions 1.0 dated 2015-08-18 and 1.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/JGEE-package.Rd | 2 +- man/JGee2.Rd | 40 ++++++++++++++++++++++++++++++++-------- 4 files changed, 40 insertions(+), 16 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between hypervolume versions 1.4 dated 2015-09-24 and 1.4.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/hypervolume.R | 6 +++--- R/hypervolume_inclusion_test.R | 4 ++-- R/hypervolume_plot.R | 5 ++++- R/hypervolume_set.R | 14 +++++++------- man/hypervolume_inclusion_test.Rd | 8 ++++++-- man/hypervolume_set.Rd | 12 ++++++++++-- 8 files changed, 43 insertions(+), 28 deletions(-)
Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with
administrative records easier and more consistent. Includes functions to
clean strings, identify cutpoints, and quickly combine shapefiles and
dataframes for plotting. Includes four alternative themes for ggplot2. Also
includes three example datasets of administrative education records for
learning how to process records with errors.
Author: Jason P. Becker [ctb],
Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jknowles@gmail.com>
Diff between eeptools versions 0.9.0 dated 2015-09-23 and 0.9.1 dated 2015-11-18
DESCRIPTION | 15 +++---- MD5 | 84 ++++++++++++++++++++--------------------- NAMESPACE | 4 - NEWS.md | 10 ++++ R/autoplot.lm.R | 14 +++--- R/eeptools.R | 2 R/mapfunctions.R | 22 +++++----- R/max_mis.R | 11 +++-- R/theme_dpi.R | 4 - inst/doc/intro.html | 13 +++--- man/age_calc.Rd | 14 +++--- man/autoplot.lm.Rd | 7 +-- man/cleanTex.Rd | 8 +-- man/crosstabplot.Rd | 12 ++--- man/crosstabs.Rd | 8 +-- man/cutoff.Rd | 13 +++--- man/decomma.Rd | 9 ++-- man/defac.Rd | 7 +-- man/eeptools.Rd | 10 ++-- man/gelmansim.Rd | 12 ++--- man/ggmapmerge.Rd | 8 +-- man/lag_data.Rd | 9 ++-- man/leading_zero.Rd | 14 +++--- man/makenum.Rd | 15 +++---- man/mapmerge.Rd | 10 ++-- man/max_mis.Rd | 11 ++--- man/midsch.Rd | 14 +++--- man/moves_calc.Rd | 35 ++++++++--------- man/nth_max.Rd | 6 ++ man/profpoly.Rd | 4 - man/profpoly.data.Rd | 4 - man/remove_char.Rd | 12 ++--- man/retained_calc.Rd | 16 +++---- man/statamode.Rd | 24 +++++------ man/stuatt.Rd | 10 ++-- man/stulevel.Rd | 10 ++-- man/theme_dpi.Rd | 6 +- man/theme_dpi_map.Rd | 10 ++-- man/theme_dpi_map2.Rd | 12 ++--- man/theme_dpi_mapPNG.Rd | 12 ++--- man/thresh.Rd | 12 ++--- tests/testthat/test-maptools.R | 2 tests/testthat/test-utils.R | 6 +- 43 files changed, 282 insertions(+), 259 deletions(-)
Title: Optimisation with Continuous Convex Piecewise (Linear and
Quadratic) Functions
Description: Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented with sorted breakpoints and slopes. This includes functions that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain. These functions can be very useful for a large class of optimisation problems. Efficient manipulation (such as log(N) insertion) of such data structure is obtained with map standard template library of C++ (that hides balanced trees). This package is a wrapper on such a class based on Rcpp modules.
Author: Robin Girard
Maintainer: Robin Girard <robin.girard@mines-paristech.fr>
Diff between ConConPiWiFun versions 0.4.4 dated 2014-10-02 and 0.4.6 dated 2015-11-18
ConConPiWiFun-0.4.4/ConConPiWiFun/R/test |only ConConPiWiFun-0.4.6/ConConPiWiFun/DESCRIPTION | 6 ConConPiWiFun-0.4.6/ConConPiWiFun/MD5 | 30 - ConConPiWiFun-0.4.6/ConConPiWiFun/NAMESPACE | 1 ConConPiWiFun-0.4.6/ConConPiWiFun/R/OptimStorage.R |only ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/convex_function_manip.hpp | 9 ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cplfunction.hpp | 6 ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cplfunctionvec.hpp | 151 +++++++++- ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cpqfunction.hpp | 21 + ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cpqfunctionvec.hpp | 124 ++++++++ ConConPiWiFun-0.4.6/ConConPiWiFun/man/OptimPriceStorage.Rd |only ConConPiWiFun-0.4.6/ConConPiWiFun/man/cplfunctionvec.Rd | 9 ConConPiWiFun-0.4.6/ConConPiWiFun/src/Makevars | 5 ConConPiWiFun-0.4.6/ConConPiWiFun/src/Makevars.win | 7 ConConPiWiFun-0.4.6/ConConPiWiFun/src/Modules.cc | 15 15 files changed, 331 insertions(+), 53 deletions(-)