Title: Randomization for Clinical Trials
Description: This tool enables the user to choose a randomization procedure
based on sound scientific criteria. It comprises the generation of
randomization sequences as well the assessment of randomization procedures
based on carefully selected criteria. Furthermore, randomizeR provides a
function for the comparison of randomization procedures.
Author: Thi Mui Pham [ctb],
David Schindler [aut],
Diane Uschner [aut, cre]
Maintainer: Diane Uschner <duschner@ukaachen.de>
Diff between randomizeR versions 1.0 dated 2015-09-09 and 1.1.0 dated 2016-01-19
DESCRIPTION | 33 - MD5 | 203 +++++----- NAMESPACE | 21 - R/abcdPar.R |only R/abcdSeq.R |only R/assess.R | 54 ++ R/bbcdPar.R |only R/bbcdSeq.R |only R/bsdPar.R | 9 R/chenPar.R |only R/chenSeq.R |only R/chronBias.R | 23 - R/combinedBias.R |only R/compare.R | 15 R/corGuess.R | 2 R/doublyT.R | 4 R/gbcdPar.R |only R/gbcdSeq.R |only R/mpPar.R | 5 R/randPar.R | 64 +++ R/randSeq.R | 50 ++ R/randomizeROverview.R | 15 R/randomizeRPackage.R | 1 R/rpbrPar.R | 12 R/rpbrSeq.R | 9 R/rtbdPar.R | 50 +- R/rtbdSeq.R | 8 R/saveAssess.R | 6 R/saveRand.R | 32 + R/testDec.R | 2 R/util.R | 3 build/vignette.rds |binary inst/doc/comparison-example.pdf |binary inst/doc/randomizeR-refCard.Rnw |only inst/doc/randomizeR-refCard.pdf |only man/K.Rd | 2 man/N.Rd | 2 man/a.Rd |only man/abcdPar.Rd |only man/abcdRand.Rd |only man/assess.Rd | 43 +- man/bbcdPar.Rd |only man/bbcdRand.Rd |only man/blocks.Rd | 2 man/bsdPar.Rd | 16 man/bsdRand.Rd | 4 man/cash-assessment-method.Rd | 2 man/cash-comparison-method.Rd | 2 man/cash-endpoint-method.Rd | 2 man/cash-issue-method.Rd | 2 man/cash-randPar-method.Rd | 2 man/cash-randSeq-method.Rd | 2 man/chenPar.Rd |only man/chenRand.Rd |only man/chronBias.Rd | 45 +- man/coin.Rd | 2 man/combineBias.Rd |only man/compare.Rd | 24 - man/corGuess.Rd | 17 man/crPar.Rd | 16 man/createParam.Rd | 18 man/createSeq.Rd | 2 man/doublyT.Rd | 2 man/doublyTValues.Rd | 5 man/ebcPar.Rd | 16 man/gbcdPar.Rd |only man/gbcdRand.Rd |only man/genNcps.Rd | 3 man/generateAllSequences.Rd | 53 ++ man/generateRandomSequences.Rd | 115 ++++- man/getCorGuesses.Rd | 3 man/getDesign.Rd | 46 +- man/getExpectation.Rd | 26 - man/getProbabilities.Rd | 25 - man/getRandomizationList.Rd | 3 man/hadaPar.Rd | 18 man/imbal.Rd | 18 man/issue.Rd | 25 - man/method.Rd | 2 man/mpPar.Rd | 16 man/mti.Rd | 2 man/mu.Rd | 2 man/normEndp.Rd | 8 man/overview.Rd | 33 + man/pbrPar.Rd | 20 man/plot.Rd | 3 man/plotSeq.Rd |only man/randBlocks.Rd | 2 man/randPar-class.Rd | 2 man/randPar.Rd | 14 man/randSeq-class.Rd | 4 man/randomizeR-package.Rd | 22 - man/rarPar.Rd | 16 man/ratio.Rd | 2 man/rho.Rd |only man/rpbrPar.Rd | 16 man/rtbdPar.Rd | 16 man/saveAssess.Rd | 7 man/saveRand.Rd | 7 man/seed.Rd | 2 man/selBias.Rd | 38 - man/setPower.Rd | 22 - man/sigma.Rd | 2 man/summary.Rd | 7 man/tbdPar.Rd | 18 man/type.Rd | 4 man/udPar.Rd | 16 tests/testthat/OnlyOnce/test_empiricalVsTheoreticalFrequency.R | 55 ++ tests/testthat/test_combineBias.R |only tests/testthat/test_lengthOfSequences.R | 24 - tests/testthat/test_mti.R | 6 tests/testthat/test_nrOfSequences.R | 32 + tests/testthat/test_seedGenSeq.R | 17 tests/testthat/test_sequenceProbability.R | 11 vignettes/randomizeR-refCard.Rnw |only 115 files changed, 1121 insertions(+), 511 deletions(-)
Title: Benchmarking and Rescaling R2 using Noise Percentile Analysis
Description: Provides the tools needed to benchmark the R2 value corresponding to a certain acceptable noise level while also providing a rescaling function based on that noise level yielding a new value of R2 we refer to as R2k which is independent of both the number of degrees of freedom and the noise distribution function.
Author: Joseph G Kreke, PhD; Harris, Inc.
Sangeet Khemlani, PhD; Naval Research Laboratory.
Greg Trafton, PhD; Naval Research Laboratory.
Maintainer: Joseph G Kreke <jkreke2@gmail.com>
Diff between pAnalysis versions 1.0 dated 2015-11-18 and 2.0 dated 2016-01-19
pAnalysis-1.0/pAnalysis/R/Percentile_Analysis_Functions.R |only pAnalysis-2.0/pAnalysis/DESCRIPTION | 8 ++++---- pAnalysis-2.0/pAnalysis/MD5 | 6 +++--- pAnalysis-2.0/pAnalysis/R/Percentile_Analysis_Functions_v2.R |only pAnalysis-2.0/pAnalysis/build/partial.rdb |binary 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-123 dated 2016-01-17 and 3.1-124 dated 2016-01-19
ChangeLog | 19 DESCRIPTION | 10 MD5 | 44 - NAMESPACE | 6 R/VarCorr.R | 29 - R/gls.R | 30 - R/gnls.R | 69 +- R/lme.R | 1203 ++++++++++++++++++++++++------------------------ R/newFunc.R | 42 - R/nlme.R | 576 +++++++++++----------- man/VarCorr.Rd | 9 man/glsControl.Rd | 4 man/gnlsControl.Rd | 4 man/lmeControl.Rd | 4 man/nlmeControl.Rd | 4 src/corStruct.c | 2 src/gnls.c | 4 src/nlme.c | 4 src/nlmefit.c | 2 src/nls.c | 2 tests/anova.gls.R | 7 tests/nlme.R | 5 tests/sigma-fixed-etc.R | 10 23 files changed, 1055 insertions(+), 1034 deletions(-)
Title: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic
Trees from Human Microbiome Data
Description: Tools to model, compare, and visualize populations of taxonomic tree objects.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMPTrees versions 1.2 dated 2013-09-16 and 1.3 dated 2016-01-19
HMPTrees-1.2/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.R |only HMPTrees-1.3/HMPTrees/DESCRIPTION | 23 +++--- HMPTrees-1.3/HMPTrees/MD5 | 32 ++++----- HMPTrees-1.3/HMPTrees/NAMESPACE | 4 + HMPTrees-1.3/HMPTrees/NEWS | 11 ++- HMPTrees-1.3/HMPTrees/R/checkTreeValidHelp.R | 7 -- HMPTrees-1.3/HMPTrees/R/compareTwoDataSets.R | 35 ++++------ HMPTrees-1.3/HMPTrees/R/generateTree.R | 7 -- HMPTrees-1.3/HMPTrees/R/getMLEandLoglike.R | 2 HMPTrees-1.3/HMPTrees/R/pairedCompareTwoDataSets.R |only HMPTrees-1.3/HMPTrees/R/plotTree.R | 2 HMPTrees-1.3/HMPTrees/R/transformHMPTreetoHMP.R | 12 +-- HMPTrees-1.3/HMPTrees/R/traverseTree.R | 11 +-- HMPTrees-1.3/HMPTrees/build |only HMPTrees-1.3/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.Rnw | 2 HMPTrees-1.3/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.pdf |binary HMPTrees-1.3/HMPTrees/man/HMPTrees-package.Rd | 7 -- HMPTrees-1.3/HMPTrees/man/pairedCompareTwoDataSets.Rd |only HMPTrees-1.3/HMPTrees/vignettes/Creating-Data-From-RDP-Tutorial.Rnw | 2 19 files changed, 81 insertions(+), 76 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.2.6 dated 2015-07-02 and 1.3.0 dated 2016-01-19
DESCRIPTION | 10 - MD5 | 24 +-- NEWS | 8 - R/bpcp2sample.R | 138 ++++++++++++----- R/kmciFunctions.R | 355 ++++++++++++++++++++++------------------------ build |only inst/CITATION | 2 inst/doc/discreteBPCP.R |only inst/doc/discreteBPCP.Rnw |only inst/doc/discreteBPCP.pdf |only man/bpcp-package.Rd | 4 man/bpcpControl.Rd | 6 man/kmciALL.Rd | 6 man/plot.kmciLR.Rd | 2 tests |only vignettes |only 16 files changed, 310 insertions(+), 245 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap standard errors on various network estimation routines, such as EBICglasso() from the 'qgraph' package and IsingFit() from the 'IsingFit' package.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 0.1 dated 2015-03-02 and 0.2 dated 2016-01-19
DESCRIPTION | 14 - MD5 | 23 +- NAMESPACE | 19 +- R/bootTable.R | 117 ++++++++---- R/bootnet.R | 307 +++++++++++++++++++++++++++++---- R/bootstrapIncreasesEdges.R |only R/comparePlot.R |only R/estimateNetwork.R | 1 R/evenMoreTests.R |only R/plotMethod.R | 405 ++++++++++++++++++++++++++++++++++++++++---- R/summaryMethod.R | 159 ++++++++++++++--- man/bootnet.Rd | 78 ++++++-- man/plot.bootnet.Rd | 49 ++++- man/summary.bootnet.Rd | 13 + 14 files changed, 999 insertions(+), 186 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export and Engage API. The R functions allow for event and profile data export as well as for segmentation, retention and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner
Maintainer: Meinhard Ploner <meinhard.ploner@prosiebensat1digital.de>
Diff between RMixpanel versions 0.1-3 dated 2016-01-14 and 0.2-1 dated 2016-01-19
RMixpanel-0.1-3/RMixpanel/R/mixpanelGetPeople.R |only RMixpanel-0.1-3/RMixpanel/R/mixpanelGetPeopleCount.R |only RMixpanel-0.2-1/RMixpanel/DESCRIPTION | 12 ++--- RMixpanel-0.2-1/RMixpanel/MD5 | 18 ++++---- RMixpanel-0.2-1/RMixpanel/NAMESPACE | 1 RMixpanel-0.2-1/RMixpanel/R/mixpanelGetProfiles.R |only RMixpanel-0.2-1/RMixpanel/R/mixpanelGetProfilesCount.R |only RMixpanel-0.2-1/RMixpanel/R/mixpanelUpdateProfile.R |only RMixpanel-0.2-1/RMixpanel/README.md | 33 ++++++++++++--- RMixpanel-0.2-1/RMixpanel/build/partial.rdb |binary RMixpanel-0.2-1/RMixpanel/man/RMixpanel-package.Rd | 6 -- RMixpanel-0.2-1/RMixpanel/man/mixpanelGetSegmentation.Rd | 2 RMixpanel-0.2-1/RMixpanel/man/mixpanelUpdateProfile.Rd |only 13 files changed, 48 insertions(+), 24 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.6.0 dated 2015-11-04 and 3.6.1 dated 2016-01-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ R/Deriv.R | 9 +++++---- man/Deriv-package.Rd | 4 ++-- tests/testthat/test_Deriv.R | 9 +++++++++ 6 files changed, 32 insertions(+), 15 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.3.1 dated 2015-03-10 and 1.3.2 dated 2016-01-19
qgraph-1.3.1/qgraph/R/Jaccard.R |only qgraph-1.3.2/qgraph/DESCRIPTION | 13 - qgraph-1.3.2/qgraph/MD5 | 30 ++-- qgraph-1.3.2/qgraph/NAMESPACE | 19 ++ qgraph-1.3.2/qgraph/NEWS | 10 + qgraph-1.3.2/qgraph/R/PLOT.R | 19 ++ qgraph-1.3.2/qgraph/R/centrality.R | 233 +++++++++++++++++++------------- qgraph-1.3.2/qgraph/R/centralityTable.R | 2 qgraph-1.3.2/qgraph/R/clusteringTable.R | 2 qgraph-1.3.2/qgraph/R/cor_auto.R | 6 qgraph-1.3.2/qgraph/R/drawNode.R | 37 ++++- qgraph-1.3.2/qgraph/R/makeBW.R |only qgraph-1.3.2/qgraph/R/qgraph.R | 9 - qgraph-1.3.2/qgraph/R/qgraphAnnotate.R | 3 qgraph-1.3.2/qgraph/R/qgraphBoot.R |only qgraph-1.3.2/qgraph/R/qgraphGUI.R | 2 qgraph-1.3.2/qgraph/man/centrality.Rd | 8 - qgraph-1.3.2/qgraph/man/makeBW.Rd |only 18 files changed, 259 insertions(+), 134 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb],
Martin Maechler [ctb],
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.0-3 dated 2015-07-22 and 1.0-4 dated 2016-01-19
DESCRIPTION | 8 - MD5 | 49 +++--- NAMESPACE | 2 R/mvt.R | 173 ++++++++++++---------- R/noisy-root.R |only R/tvpack.R | 38 ++-- build/vignette.rds |binary inst/NEWS | 12 + inst/doc/MVT_Rnews.pdf |binary inst/include/mvtnorm.h | 6 man/algorithms.Rd | 17 +- man/pmvnorm.Rd | 6 man/pmvt.Rd | 31 ++-- man/qmvnorm.Rd | 18 +- man/qmvt.Rd | 18 +- src/C_FORTRAN_interface.c | 10 - src/miwa.c | 242 +++++++++++++++---------------- src/mvtnorm-init.c | 2 src/mvtnorm.h | 6 src/tvpack.f | 8 - tests/Examples/mvtnorma-Ex.Rout.save | 267 +++++++++++++++++++---------------- tests/bugfix-tests.R | 5 tests/bugfix-tests.Rout.save | 47 +++--- tests/regtest-TVPACK.R | 10 - tests/regtest-TVPACK.Rout.save | 22 +- tests/test-noisy-root.R |only tests/test-noisy-root.Rout.save |only 27 files changed, 538 insertions(+), 459 deletions(-)
Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The cmsaf R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators (cdo). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The cmsaf R-package is tested for CM SAF netcdf data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided `levbox_mergetime`
function. The cmsaf R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
A Windows binary file and scripts for an easy application of the functions are
provided at the CM SAF homepage (http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.5 dated 2015-07-30 and 1.6 dated 2016-01-19
DESCRIPTION | 8 +-- MD5 | 94 ++++++++++++++++++++++++-------------------- NAMESPACE | 8 +++ R/box_mergetime.R | 31 ++++++++------ R/change_att.R | 4 - R/cmsaf.add.R | 4 - R/cmsaf.addc.R |only R/cmsaf.div.R | 108 ++++++++++++++++++++++++--------------------------- R/cmsaf.divc.R |only R/cmsaf.mul.R | 100 ++++++++++++++++++++++------------------------- R/cmsaf.mulc.R |only R/cmsaf.sub.R | 92 ++++++++++++++++++++----------------------- R/cmsaf.subc.R |only R/dayrange.R | 28 +++++-------- R/divdpm.R | 28 +++++-------- R/extract.period.R | 28 +++++-------- R/fldmax.R | 4 - R/fldmean.R | 31 +++++--------- R/fldmin.R | 31 +++++--------- R/get_time.R | 55 ++++++++++++++++++------- R/levbox_mergetime.R | 25 +++++++---- R/mon.anomaly.R | 44 +++++++++----------- R/monmean.R | 26 +++++------- R/monsum.R | 28 +++++-------- R/muldpm.R | 4 - R/multimonmean.R | 26 +++++------- R/multimonsum.R | 28 +++++-------- R/ncinfo.R | 20 +++------ R/read_nc.R |only R/seas.anomaly.R | 24 ++++------- R/seasmean.R | 28 +++++-------- R/sellonlatbox.R | 15 +------ R/selmon.R | 10 +--- R/selperiod.R | 10 +--- R/selpoint.R | 49 +++++++++++++---------- R/seltime.R | 12 +---- R/selyear.R | 10 +--- R/timmean.R | 4 - R/trend.R | 10 +--- R/wfldmean.R | 15 +------ R/year.anomaly.R | 10 +--- R/yearmean.R | 10 +--- R/yearsum.R | 10 +--- R/ymonmean.R | 10 +--- R/ymonsum.R | 12 +---- R/yseasmean.R | 10 +--- man/cmsaf.addc.Rd |only man/cmsaf.divc.Rd |only man/cmsaf.mulc.Rd |only man/cmsaf.subc.Rd |only man/muldpm.Rd | 2 man/read_nc.Rd |only man/selpoint.Rd | 16 +++++-- 53 files changed, 519 insertions(+), 603 deletions(-)
Title: Covariance Matrix Adaptation Evolution Strategy
Description: Pure R implementation of the Covariance Matrix Adaptation -
Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between cmaesr versions 1.0 dated 2016-01-19 and 1.0.1 dated 2016-01-19
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- NEWS |only R/cmaes.R | 16 +++++++++------- man/cmaes.Rd | 4 ++-- 5 files changed, 20 insertions(+), 17 deletions(-)
Title: Binary Logic
Description: Convert to binary numbers (Base2). Shift, rotate, summary. Based on logical vector.
Author: Daniel Dörrhöfer <ddo@openmailbox.org>
Maintainer: Daniel Dörrhöfer <ddo@openmailbox.org>
Diff between binaryLogic versions 0.2.6 dated 2015-12-18 and 0.3.2 dated 2016-01-19
DESCRIPTION | 6 - MD5 | 12 +- R/binOperators.R | 20 ++- README.md | 220 ++++++++++++++++++++++--------------- man/switchEndianess.Rd | 12 +- tests/testthat/test-BinaryS3.R | 17 ++ tests/testthat/test-binOperators.R | 4 7 files changed, 179 insertions(+), 112 deletions(-)
Title: European Commission Annual Macro-Economic (AMECO) Database
Description: Annual macro-economic database provided by the European Commission.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ameco versions 0.1 dated 2015-10-23 and 0.2 dated 2016-01-19
DESCRIPTION | 11 ++++++----- MD5 | 22 ++++++++++++---------- NAMESPACE | 3 ++- R/data.R | 2 +- README.md | 16 ++++++++++++++-- data/ameco.RData |binary inst/doc/ameco_dataset.R | 2 +- inst/doc/ameco_dataset.Rmd | 4 ++-- inst/doc/ameco_dataset.html | 14 +++++++------- man/ameco.Rd | 4 ++-- tests |only vignettes/ameco_dataset.Rmd | 4 ++-- 12 files changed, 49 insertions(+), 33 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits a stable isotope mixing model via JAGS in R. The package allows for any number of isotopes or sources, as well as concentration dependencies.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@ucd.ie>
Diff between simmr versions 0.2 dated 2015-08-17 and 0.3 dated 2016-01-19
DESCRIPTION | 13 MD5 | 35 + NAMESPACE | 3 R/combine_sources.R |only R/compare_groups.R | 12 R/compare_sources.R |only R/plot.simmr_input.R | 39 + R/plot.simmr_output.R | 151 ++++--- README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/simmr.R | 98 +++-- inst/doc/simmr.Rmd | 129 ++++-- inst/doc/simmr.html | 919 +++++++++++++++++------------------------------ man/combine_sources.Rd |only man/compare_groups.Rd | 2 man/compare_sources.Rd |only man/plot.simmr_input.Rd | 81 ++-- man/plot.simmr_output.Rd | 9 man/simmr_mcmc.Rd | 18 vignettes/simmr.Rmd | 129 ++++-- 21 files changed, 786 insertions(+), 852 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-1 dated 2015-07-23 and 1.4-2 dated 2016-01-19
DESCRIPTION | 8 +- MD5 | 24 +++---- build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary inst/NEWS | 4 + inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.pdf |binary tests/Examples/multcomp-Ex.Rout.save | 115 +++++++++++++++++------------------ tests/regtest-Tukey.Rout.save | 14 ++-- tests/regtest-interface.Rout.save | 16 ++-- tests/regtest-mmm.Rout.save | 14 ++-- 13 files changed, 99 insertions(+), 96 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
http://ec.europa.eu/eurostat/ together with search and manipulation
utilities.
Author: Lahti Leo [aut, cre],
Biecek Przemyslaw [aut],
Kainu Markus [aut],
Huovari Janne [aut]
Maintainer: Lahti Leo <louhos@googlegroups.com>
Diff between eurostat versions 1.0.16 dated 2015-03-27 and 1.2.13 dated 2016-01-19
eurostat-1.0.16/eurostat/inst/doc/eurostat_tutorial.html |only eurostat-1.0.16/eurostat/vignettes/NUTS_2010_60M_SH |only eurostat-1.0.16/eurostat/vignettes/NUTS_2010_60M_SH.zip |only eurostat-1.0.16/eurostat/vignettes/eurostat_tutorial.md |only eurostat-1.0.16/eurostat/vignettes/figure |only eurostat-1.2.13/eurostat/DESCRIPTION | 20 - eurostat-1.2.13/eurostat/LICENSE | 4 eurostat-1.2.13/eurostat/MD5 | 179 +++++--------- eurostat-1.2.13/eurostat/NAMESPACE | 6 eurostat-1.2.13/eurostat/R/clean_eurostat_cache.R | 13 - eurostat-1.2.13/eurostat/R/data_countries.R |only eurostat-1.2.13/eurostat/R/dic_order.R |only eurostat-1.2.13/eurostat/R/eurostat-package.R | 4 eurostat-1.2.13/eurostat/R/eurostat_url.R | 12 eurostat-1.2.13/eurostat/R/eurotime2date.R | 45 ++- eurostat-1.2.13/eurostat/R/eurotime2num.R | 42 ++- eurostat-1.2.13/eurostat/R/get_eurostat.R | 140 ++++++---- eurostat-1.2.13/eurostat/R/get_eurostat_dic.R | 44 +-- eurostat-1.2.13/eurostat/R/get_eurostat_raw.R | 20 - eurostat-1.2.13/eurostat/R/get_eurostat_toc.R | 11 eurostat-1.2.13/eurostat/R/label_eurostat.R | 79 ++++-- eurostat-1.2.13/eurostat/R/search_eurostat.R | 36 +- eurostat-1.2.13/eurostat/R/set_eurostat_toc.R | 19 - eurostat-1.2.13/eurostat/R/tidy_eurostat.R | 117 ++++++--- eurostat-1.2.13/eurostat/R/utils.R |only eurostat-1.2.13/eurostat/README.md | 7 eurostat-1.2.13/eurostat/build/vignette.rds |binary eurostat-1.2.13/eurostat/data |only eurostat-1.2.13/eurostat/inst/CITATION | 8 eurostat-1.2.13/eurostat/inst/doc/eurostat_tutorial.R | 14 + eurostat-1.2.13/eurostat/inst/doc/eurostat_tutorial.Rmd | 55 +++- eurostat-1.2.13/eurostat/inst/doc/eurostat_tutorial.pdf |only eurostat-1.2.13/eurostat/man/clean_eurostat_cache.Rd | 6 eurostat-1.2.13/eurostat/man/dic_order.Rd |only eurostat-1.2.13/eurostat/man/eu_countries.Rd |only eurostat-1.2.13/eurostat/man/eurostat-package.Rd | 6 eurostat-1.2.13/eurostat/man/eurostat_url.Rd | 10 eurostat-1.2.13/eurostat/man/eurotime2date.Rd | 19 - eurostat-1.2.13/eurostat/man/eurotime2num.Rd | 18 - eurostat-1.2.13/eurostat/man/get_eurostat.Rd | 80 ++++-- eurostat-1.2.13/eurostat/man/get_eurostat_dic.Rd | 29 +- eurostat-1.2.13/eurostat/man/get_eurostat_raw.Rd | 22 - eurostat-1.2.13/eurostat/man/get_eurostat_toc.Rd | 14 - eurostat-1.2.13/eurostat/man/label_eurostat.Rd | 46 ++- eurostat-1.2.13/eurostat/man/search_eurostat.Rd | 36 +- eurostat-1.2.13/eurostat/man/set_eurostat_toc.Rd | 12 eurostat-1.2.13/eurostat/man/tidy_eurostat.Rd | 35 +- eurostat-1.2.13/eurostat/tests/testthat/test-all.R | 73 +++++ eurostat-1.2.13/eurostat/vignettes/2015-RJournal |only eurostat-1.2.13/eurostat/vignettes/eurostat_tutorial.Rmd | 55 +++- eurostat-1.2.13/eurostat/vignettes/eurostat_tutorial.html |only eurostat-1.2.13/eurostat/vignettes/fig |only eurostat-1.2.13/eurostat/vignettes/main.R | 10 eurostat-1.2.13/eurostat/vignettes/tmp |only 54 files changed, 831 insertions(+), 515 deletions(-)
Title: Diversity-Dependent Diversification
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 3.0 dated 2015-11-13 and 3.1 dated 2016-01-19
DESCRIPTION | 10 - MD5 | 62 ++++----- NAMESPACE | 4 R/bd_ML.R | 2 R/bd_loglik.R | 78 +++++------- R/dd_KI_ML.R | 2 R/dd_KI_loglik.R | 317 ++++++++++++++++++++++++++++++++++++++++++++++++- R/dd_KI_sim.R | 4 R/dd_LR.R | 2 R/dd_ML.R | 2 R/dd_MS_ML.R | 2 R/dd_MS_loglik.R | 237 ++++++++++++++++++++++++++++++++++++ R/dd_SR_ML.R | 2 R/dd_SR_loglik.R | 298 ++++++++++++++++++++++++++++++++++++++++++++-- R/dd_loglik.R | 212 +++++++++++++++++++++++++++++++- R/dd_loglik_M.R | 310 +++++++++++++++++++++++++++++++++++++---------- R/dd_loglik_bw_rhs.R | 4 R/dd_logliknorm_rhs2.R | 2 R/dd_sim.R | 2 man/DDD-internal.Rd | 20 +++ man/DDD-package.Rd | 8 - man/bd_ML.Rd | 4 man/bd_loglik.Rd | 4 man/dd_KI_ML.Rd | 4 man/dd_KI_loglik.Rd | 8 - man/dd_LR.Rd | 4 man/dd_ML.Rd | 6 man/dd_MS_ML.Rd | 2 man/dd_MS_loglik.Rd | 8 - man/dd_SR_ML.Rd | 7 - man/dd_SR_loglik.Rd | 10 - man/dd_loglik.Rd | 12 - 32 files changed, 1439 insertions(+), 210 deletions(-)
Title: Statistical Analysis of Amplicon Data of the Same Sample to
Identify Artefacts
Description: Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.
Author: Anja Lange [aut, cre], Daniel Hoffmann [aut]
Maintainer: Anja Lange <anja.lange@uni-due.de>
Diff between AmpliconDuo versions 1.0 dated 2014-03-20 and 1.1 dated 2016-01-19
DESCRIPTION | 13 -- MD5 | 22 +-- R/plotORdensity.R | 275 ++++++++++++++++++++++---------------------- data/ampliconfreqs.long.rda |binary data/ampliconfreqs.rda |binary data/amplicons.rda |binary data/site.f.rda |binary man/AmpliconDuo-package.Rd | 12 - man/ampliconfreqs.Rd | 6 man/ampliconfreqs.long.Rd | 6 man/plotAmpliconduo.Rd | 2 man/plotAmpliconduo.set.Rd | 2 12 files changed, 167 insertions(+), 171 deletions(-)
Title: Thermoluminescence Glow Curve Deconvolution
Description: Deconvolving first-order and general-order thermoluminescence glow
curves using a modified Levenberg-Marquardt algorithm. It provides the
possibility of setting constraints or fixing any of parameters. It offers
an interactive way to initialize parameters by clicking with a mouse on a
plot at positions where peak maxima should be located. The optimal estimate
is obtained by "trial-and-error". It also provides routines for simulating
first-order, second-order, and general-order glow peaks (or glow curves).
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Linda R. Petzold [ctb], Alan C. Hindmarsh [ctb], R. Woodrow Setzer [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between tgcd versions 1.7 dated 2015-09-16 and 1.8 dated 2016-01-19
DESCRIPTION | 12 ++++----- MD5 | 10 +++---- R/simPeak.R | 4 +-- man/simPeak.Rd | 17 ++++++++----- src/qeOTOR.f90 | 50 ++++++++++++++++++++------------------ src/simPeak.f90 | 72 ++++++++++++++++++++++++++++---------------------------- 6 files changed, 87 insertions(+), 78 deletions(-)
More information about SubpathwayLNCE at CRAN
Permanent link
Title: Multi-States Semi-Markov Models
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol <agnieszka.krol@isped.u-bordeaux2.fr>
Diff between SemiMarkov versions 1.4.2 dated 2015-08-04 and 1.4.3 dated 2016-01-19
DESCRIPTION | 8 +- MD5 | 6 - R/SemiMarkov.r | 184 +++++++++++++++++++++++++----------------------------- man/semiMarkov.Rd | 2 4 files changed, 95 insertions(+), 105 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided.
'CCTZ' is a C++ library for translating between absolute and civil times
using the rules of a time zone.
The 'CCTZ' source code, released under the Apache 2.0 License, is included in
this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.0.2 dated 2015-12-02 and 0.0.3 dated 2016-01-19
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/include/src/cctz.h | 10 +++++----- inst/include/src/cctz_libc.h | 4 ---- src/cctz_fmt.cc | 21 +++++++++++++++++++++ src/cctz_if.cc | 4 +--- src/cctz_info.cc | 24 ++++++++++++++++++++---- src/cctz_libc.cc | 33 +++++++++++++++++++++++++-------- 9 files changed, 89 insertions(+), 36 deletions(-)