Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization and EM clustering. Furthermore, there are specialized
distance measures, plotting functions and some helper functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.1 dated 2015-10-15 and 1.0.2 dated 2015-10-16
svs-1.0.1/svs/inst/extdata/Ctxt_Dut.csv |only svs-1.0.1/svs/inst/extdata/Ctxt_Eng.csv |only svs-1.0.1/svs/inst/extdata/Ctxt_Fra.csv |only svs-1.0.1/svs/inst/extdata/InvT_Eng.csv |only svs-1.0.1/svs/inst/extdata/InvT_Fra.csv |only svs-1.0.1/svs/inst/extdata/SndT_Eng.csv |only svs-1.0.1/svs/inst/extdata/SndT_Fra.csv |only svs-1.0.1/svs/man/Ctxt_Dut.csv.Rd |only svs-1.0.1/svs/man/Ctxt_Eng.csv.Rd |only svs-1.0.1/svs/man/Ctxt_Fra.csv.Rd |only svs-1.0.1/svs/man/InvT_Eng.csv.Rd |only svs-1.0.1/svs/man/InvT_Fra.csv.Rd |only svs-1.0.1/svs/man/SndT_Eng.csv.Rd |only svs-1.0.1/svs/man/SndT_Fra.csv.Rd |only svs-1.0.2/svs/DESCRIPTION | 8 +-- svs-1.0.2/svs/MD5 | 48 ++++++++++---------- svs-1.0.2/svs/R/svs.r | 74 +++++++++++++++++++------------- svs-1.0.2/svs/inst/extdata/Ctxt_Dut.txt |only svs-1.0.2/svs/inst/extdata/Ctxt_Eng.txt |only svs-1.0.2/svs/inst/extdata/Ctxt_Fra.txt |only svs-1.0.2/svs/inst/extdata/InvT_Eng.txt |only svs-1.0.2/svs/inst/extdata/InvT_Fra.txt |only svs-1.0.2/svs/inst/extdata/SndT_Eng.txt |only svs-1.0.2/svs/inst/extdata/SndT_Fra.txt |only svs-1.0.2/svs/man/Ctxt_Dut.txt.Rd |only svs-1.0.2/svs/man/Ctxt_Eng.txt.Rd |only svs-1.0.2/svs/man/Ctxt_Fra.txt.Rd |only svs-1.0.2/svs/man/InvT_Eng.txt.Rd |only svs-1.0.2/svs/man/InvT_Fra.txt.Rd |only svs-1.0.2/svs/man/SndT_Eng.txt.Rd |only svs-1.0.2/svs/man/SndT_Fra.txt.Rd |only svs-1.0.2/svs/man/fast_E_M.Rd | 3 - svs-1.0.2/svs/man/fast_dca.Rd | 3 - svs-1.0.2/svs/man/fast_lsa.Rd | 3 - svs-1.0.2/svs/man/fast_mca.Rd | 3 - svs-1.0.2/svs/man/fast_nmf.Rd | 3 - svs-1.0.2/svs/man/fast_psa.Rd | 3 - svs-1.0.2/svs/man/fast_sca.Rd | 3 - svs-1.0.2/svs/man/svs-package.Rd | 18 ++++--- 39 files changed, 97 insertions(+), 72 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.0.1 dated 2015-09-22 and 2.1.0 dated 2015-10-16
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS | 9 +++++++++ R/xform.R | 34 ++++++++++++++++++++++++++++------ man/xform.Rd | 26 ++++++++++++++++++++------ src/DeformationField.cpp | 2 +- src/main.cpp | 35 +++++++++++++++++++++++++++++++++++ src/reg-lib/_reg_aladin.h | 22 +++++++++++----------- tests/testthat/test-10-xform.R | 7 +++++++ tests/testthat/test-20-niftyreg.R | 4 ++-- tests/testthat/test-25-transform.R | 3 +++ 12 files changed, 134 insertions(+), 42 deletions(-)
Title: Interactive Dendrograms
Description: Interactive dendrogram that enables the user to select and
color clusters, to zoom and pan the dendrogram, and to visualize
the clustered data not only in a built-in heat map, but also in
'GGobi' interactive plots and user-supplied plots.
This is a backport of Qt-based 'idendro'
(https://github.com/tsieger/idendro) to base R graphics and Tcl/Tk GUI.
Author: Tomas Sieger
Maintainer: Tomas Sieger <tomas.sieger@seznam.cz>
Diff between idendr0 versions 1.5.1 dated 2015-10-14 and 1.5.2 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/idendro.R | 9 +++++---- man/hca5000.Rd | 8 ++++---- man/idendr0-package.Rd | 4 ++-- man/idendro.Rd | 8 ++++---- 7 files changed, 31 insertions(+), 24 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-3 dated 2015-10-05 and 0.1-4 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/gimme.R | 12 ++++++------ man/gimmeSEM.Rd | 2 +- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.1 dated 2015-10-12 and 6.1.1 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 7 ++++--- NEWS | 4 ++++ R/FormatNests.R | 2 +- R/STSRE_TSD.R | 8 ++++---- R/TRN_MHmcmc_p.R | 4 ++-- R/embryogrowth-package.R | 4 ++-- R/hist.NestsResult.R | 4 ++-- R/info.nests.R | 18 +++++++++--------- R/likelihoodR.R | 10 +++++----- R/nest.R | 2 +- R/plot.NestsResult.R | 10 +++++----- R/plotR.R | 8 ++++---- R/plotR_hist.R | 2 +- R/searchR.R | 10 +++++----- R/tsd_MHmcmc_p.R | 2 +- R/weightmaxentropy.R | 2 +- man/STSRE_TSD.Rd | 8 ++++---- man/embryogrowth-package.Rd | 4 ++-- man/nest.Rd | 2 +- 21 files changed, 82 insertions(+), 77 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between coda versions 0.17-1 dated 2015-03-03 and 0.18-1 dated 2015-10-16
CHANGELOG | 15 ++++++++++ DESCRIPTION | 16 ++++++----- MD5 | 20 +++++++------- NAMESPACE | 17 ++++++++--- R/codamenu.R | 16 ----------- R/mcextractor.R | 8 ++++- R/mcmclist.R | 80 +++++++++++++++++++++++++++++++++++--------------------- R/util.R | 3 -- data/line.rda |binary inst/AUTHORS | 15 +++++++++- man/cumuplot.Rd | 4 -- 11 files changed, 118 insertions(+), 76 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks.
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between survsim versions 1.1.3 dated 2015-03-26 and 1.1.4 dated 2015-10-16
survsim-1.1.3/survsim/R/survsim-internal.R |only survsim-1.1.3/survsim/README.md |only survsim-1.1.4/survsim/DESCRIPTION | 11 +-- survsim-1.1.4/survsim/MD5 | 16 ++--- survsim-1.1.4/survsim/NAMESPACE | 8 +- survsim-1.1.4/survsim/R/crisk.ncens.sim.R | 85 +++++++++++++++++---------- survsim-1.1.4/survsim/man/crisk.sim.Rd | 4 - survsim-1.1.4/survsim/man/mult.ev.sim.Rd | 2 survsim-1.1.4/survsim/man/rec.ev.sim.Rd | 2 survsim-1.1.4/survsim/man/simple.surv.sim.Rd | 4 - 10 files changed, 79 insertions(+), 53 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.3 dated 2015-09-12 and 1.2.4 dated 2015-10-16
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/likelihood.R | 5 +++-- R/mnlogit.R | 2 ++ 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The HistData package provides a collection of small data sets
that are interesting and important in the history of statistics and data visualization.
The goal of the package is to make these available, both for instructional use
and for historical research. Some of these present interesting challenges for graphics
or analysis in R.
Author: Michael Friendly [aut, cre],
Stephane Dray [ctb],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.7-5 dated 2014-04-26 and 0.7-6 dated 2015-10-16
DESCRIPTION | 16 ++++---- MD5 | 92 +++++++++++++++++++++++----------------------- NEWS | 4 ++ data/Arbuthnot.RData |binary data/Armada.RData |only data/Bowley.RData |binary data/Cavendish.RData |binary data/ChestSizes.RData |binary data/CushnyPeebles.RData |binary data/CushnyPeeblesN.RData |binary data/Dactyl.RData |binary data/DrinksWages.RData |binary data/Fingerprints.RData |binary data/Galton.RData |binary data/GaltonFamilies.RData |binary data/Guerry.RData |binary data/Jevons.RData |binary data/Langren.all.RData |binary data/Langren1644.RData |binary data/Macdonell.RData |binary data/MacdonellDF.RData |binary data/Michelson.RData |binary data/MichelsonSets.RData |binary data/Minard.cities.RData |binary data/Minard.temp.RData |binary data/Minard.troops.RData |binary data/Nightingale.RData |binary data/OldMaps.RData |binary data/PearsonLee.RData |binary data/PolioTrials.RData |binary data/Prostitutes.RData |binary data/Pyx.RData |binary data/Quarrels.RData |binary data/Snow.deaths.RData |binary data/Snow.polygons.RData |binary data/Snow.pumps.RData |binary data/Snow.streets.RData |binary data/Wheat.RData |binary data/Wheat.monarchs.RData |binary data/Yeast.RData |binary data/YeastD.mat.RData |binary data/ZeaMays.RData |binary man/Armada.Rd |only man/Cavendish.Rd | 2 - man/HistData-package.Rd | 9 ++-- man/Michelson.Rd | 2 - man/PolioTrials.Rd | 2 - man/Snow.Rd | 7 ++- 48 files changed, 71 insertions(+), 63 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel hydraulics.
Provides functions for computing normal and critical depths, steady-state
water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 1.0 dated 2015-10-11 and 1.1 dated 2015-10-16
DESCRIPTION | 8 +-- MD5 | 26 +++++----- NAMESPACE | 2 R/graduallyvariedflow_v2.r | 7 ++ R/route_wave_v4.r | 1 inst/doc/quickstart.R | 2 inst/doc/quickstart.Rmd | 6 +- inst/doc/quickstart.html | 91 ++++++-------------------------------- inst/doc/technical-vignette.Rmd | 6 ++ inst/doc/technical-vignette.html | 6 ++ man/compute_profile.Rd | 4 + src/rivmech_characteristic_v7.cpp | 21 ++++++-- vignettes/quickstart.Rmd | 6 +- vignettes/technical-vignette.Rmd | 6 ++ 14 files changed, 83 insertions(+), 109 deletions(-)
Title: CAlibrating Penalities Using Slope HEuristics
Description: Calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.
Author: Sylvain Arlot, Vincent Brault, Jean-Patrick Baudry, Cathy Maugis and Bertrand Michel
Maintainer: Vincent Brault <vincent.brault@agroparistech.fr>
Diff between capushe versions 1.0 dated 2012-02-17 and 1.1 dated 2015-10-16
capushe-1.0/capushe/main.R |only capushe-1.0/capushe/testsDev |only capushe-1.1/capushe/DESCRIPTION | 20 ++--- capushe-1.1/capushe/MD5 | 29 +++---- capushe-1.1/capushe/NAMESPACE | 43 ++++++----- capushe-1.1/capushe/R/DDSE.R | 6 - capushe-1.1/capushe/R/Djump.R | 109 ++++++++++++++++++++++++----- capushe-1.1/capushe/R/capushe.R | 99 ++++++++++++++++++++++---- capushe-1.1/capushe/R/prog.R | 4 - capushe-1.1/capushe/man/BICAICcapushe.Rd | 2 capushe-1.1/capushe/man/DDSE.Rd | 2 capushe-1.1/capushe/man/Djump.Rd | 32 +++++++- capushe-1.1/capushe/man/capushe-package.Rd | 4 - capushe-1.1/capushe/man/capushe.Rd | 15 +++ capushe-1.1/capushe/man/validation.Rd | 2 15 files changed, 276 insertions(+), 91 deletions(-)
Title: R Wrapper for the Bit.ly, Ow.ly and Goo.gl API
Description: Allows users accessing 'Bit.ly API' http://dev.bitly.com/ and retrieve many useful statistics. Additionally provides an experimental support of 'Ow.ly' http://ow.ly/api-docs and 'Goo.gl' http://goo.gl.
Author: John Malc [aut, cre] (@dmpe)
Maintainer: John Malc <cincenko@outlook.com>
Diff between RBitly versions 0.6.1 dated 2015-07-04 and 0.7.3 dated 2015-10-16
DESCRIPTION | 20 - MD5 | 92 ++++---- NAMESPACE | 9 NEWS | 20 + R/ApiKey.R | 113 ++++++++-- R/Domains.R | 4 R/Links.R | 210 +++++++++++++++++-- R/LinksMetrics.R | 67 ++++-- R/UserInfo.R | 22 -- R/UserMetrics.R | 24 +- README.md | 97 ++++----- build/vignette.rds |binary inst/doc/Tutorial.R | 53 +++- inst/doc/Tutorial.Rmd | 64 +++-- inst/doc/Tutorial.html | 134 ++++++++---- man/bitly_pro_domain.Rd | 2 man/link_Metrics_Clicks.Rd | 4 man/link_Metrics_Countries.Rd | 2 man/link_Metrics_Encoders.Rd | 2 man/link_Metrics_EncodersByCount.Rd | 2 man/link_Metrics_EncodersCount.Rd | 2 man/link_Metrics_Owly.Rd |only man/link_Metrics_Referrers.Rd | 2 man/link_Metrics_ReferrersByDomain.Rd | 2 man/link_Metrics_ReferringDomains.Rd | 2 man/links_Expand.Rd | 2 man/links_ExpandGoogl.Rd |only man/links_ExpandOwly.Rd |only man/links_Info.Rd | 2 man/links_InfoOwly.Rd |only man/links_Lookup.Rd | 2 man/links_Shorten.Rd | 9 man/links_ShortenGoogl.Rd |only man/links_ShortenOwly.Rd |only man/rbitlyApi.Rd | 24 +- man/rbitlyApi_up.Rd | 2 man/user_Info.Rd | 2 man/user_LinkHistory.Rd | 2 man/user_Metrics_Clicks.Rd | 2 man/user_Metrics_Countries.Rd | 2 man/user_Metrics_PopularLinks.Rd | 2 man/user_Metrics_Referrers.Rd | 2 man/user_Metrics_ReferringDomains.Rd | 2 man/user_Metrics_ShortenCounts.Rd | 2 man/user_TrackingDomains.Rd | 2 tests/testthat/test-Domains.R | 2 tests/testthat/test-Links.R | 39 +++ tests/testthat/test-UserInfo_LinkMetrics.R | 7 tests/testthat/test-UserMetrics.R | 4 vignettes/Tutorial.Rmd | 312 +++++++++++++++-------------- 50 files changed, 918 insertions(+), 454 deletions(-)
Title: Preprocessing of Aligned Sequences from HTS Analyses
Description: Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil@mssm.edu>
Diff between Pasha versions 0.99.16 dated 2015-08-01 and 0.99.18 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pipelineChipSeq.R | 30 ++++++++++++++---------------- inst/doc/Pasha.pdf |binary src/MultireadCSEMBcTree.h | 2 +- tests/test_Pasha.Rout.save | 25 ++++++++++++++++--------- 6 files changed, 40 insertions(+), 35 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.4 dated 2015-09-02 and 1.4.1 dated 2015-10-16
DESCRIPTION | 14 ++++--- MD5 | 42 +++++++++++++-------- R/Fst.R | 24 +++++++++--- R/GenDist.R |only R/MCreml.R | 59 +++++++++++++++++++++++++++++- R/RcppExports.R | 4 ++ R/gibbs.R | 26 +++++++++++++ R/gwas.R | 49 ++++++++++++++++--------- R/gwas2.R | 57 ++++++++++++++--------------- R/manhattan.R | 4 +- R/reml.R | 100 ++++++++++++++++++++++++++-------------------------- R/wgr.R |only build |only inst/doc |only man/Internals.Rd | 28 +++++++++++++- man/NAM-package.Rd | 6 +-- man/gibbs.Rd | 1 man/reference.Rd | 66 +++++++++++++++++----------------- man/reml.Rd | 9 ++++ man/snpQC.Rd | 2 - man/tpod.Rd | 41 ++++++++++----------- man/wgr.Rd |only src/KMUP.cpp |only src/RcppExports.cpp | 18 +++++++++ vignettes |only 25 files changed, 360 insertions(+), 190 deletions(-)