Title: IRT Models for Polytomous and Continuous Item Responses
Description: pcIRT estimates the multidimensional polytomous Rasch model
(Rasch, 1961) and the Continous Rating Scale model (Mueller, 1987).
Author: Christine Hohensinn
Maintainer: Christine Hohensinn <christine.hohensinn@univie.ac.at>
Diff between pcIRT versions 0.1 dated 2014-01-12 and 0.2 dated 2015-07-17
pcIRT-0.1/pcIRT/R/MPRMl.R |only pcIRT-0.1/pcIRT/R/gamfunk.R |only pcIRT-0.1/pcIRT/R/print.LR.R |only pcIRT-0.1/pcIRT/R/summary.MPRMl.R |only pcIRT-0.1/pcIRT/data/example1.rda |only pcIRT-0.1/pcIRT/data/example2.rda |only pcIRT-0.1/pcIRT/man/CRSM.Rd |only pcIRT-0.1/pcIRT/man/LRT.Rd |only pcIRT-0.1/pcIRT/man/MPRM.Rd |only pcIRT-0.1/pcIRT/man/MPRMl.Rd |only pcIRT-0.1/pcIRT/man/dLRT.Rd |only pcIRT-0.1/pcIRT/man/example1.Rd |only pcIRT-0.1/pcIRT/man/example2.Rd |only pcIRT-0.1/pcIRT/man/person_par.Rd |only pcIRT-0.1/pcIRT/man/weight_test.Rd |only pcIRT-0.2/pcIRT/DESCRIPTION | 20 - pcIRT-0.2/pcIRT/MD5 | 99 ++++--- pcIRT-0.2/pcIRT/NAMESPACE | 52 ++- pcIRT-0.2/pcIRT/R/CRSM.R | 121 +++++++-- pcIRT-0.2/pcIRT/R/DRM.R |only pcIRT-0.2/pcIRT/R/LRT.DRM.R |only pcIRT-0.2/pcIRT/R/LRT.MPRM.R |only pcIRT-0.2/pcIRT/R/LRT.R | 75 +++-- pcIRT-0.2/pcIRT/R/MPRM.R | 461 +++++++++++++++++++++++++---------- pcIRT-0.2/pcIRT/R/RcppExports.R |only pcIRT-0.2/pcIRT/R/dLRT.R | 35 ++ pcIRT-0.2/pcIRT/R/gmc.CRSM.R | 26 + pcIRT-0.2/pcIRT/R/gmc.R | 45 +++ pcIRT-0.2/pcIRT/R/gmc.aLR.R | 24 + pcIRT-0.2/pcIRT/R/iccplot.CRSM.R |only pcIRT-0.2/pcIRT/R/iccplot.DRM.R |only pcIRT-0.2/pcIRT/R/iccplot.MPRM.R |only pcIRT-0.2/pcIRT/R/iccplot.R |only pcIRT-0.2/pcIRT/R/pcIRT-package.R |only pcIRT-0.2/pcIRT/R/person_par.CRSM.R | 22 - pcIRT-0.2/pcIRT/R/person_par.MPRM.R | 55 ++-- pcIRT-0.2/pcIRT/R/person_par.R | 40 +++ pcIRT-0.2/pcIRT/R/print.CRSM.R | 22 + pcIRT-0.2/pcIRT/R/print.DRM.R |only pcIRT-0.2/pcIRT/R/print.MPRM.R | 8 pcIRT-0.2/pcIRT/R/print.aLR.R | 10 pcIRT-0.2/pcIRT/R/print.dLR.R | 8 pcIRT-0.2/pcIRT/R/print.wt.R | 9 pcIRT-0.2/pcIRT/R/simCRSM.R | 65 ++++ pcIRT-0.2/pcIRT/R/simMPRM.R | 42 +++ pcIRT-0.2/pcIRT/R/summary.CRSM.R | 28 +- pcIRT-0.2/pcIRT/R/summary.DRM.R |only pcIRT-0.2/pcIRT/R/summary.MPRM.R | 10 pcIRT-0.2/pcIRT/R/summary.aLR.R | 8 pcIRT-0.2/pcIRT/R/summary.dLR.R | 9 pcIRT-0.2/pcIRT/R/summary.wt.R | 9 pcIRT-0.2/pcIRT/R/weight_test.R | 52 +++ pcIRT-0.2/pcIRT/README.md |only pcIRT-0.2/pcIRT/data/analog.rda |only pcIRT-0.2/pcIRT/data/reason.rda |only pcIRT-0.2/pcIRT/man/crsm.Rd |only pcIRT-0.2/pcIRT/man/dLR.Rd |only pcIRT-0.2/pcIRT/man/drm.Rd |only pcIRT-0.2/pcIRT/man/extraversion.Rd |only pcIRT-0.2/pcIRT/man/gmc.Rd | 87 +++--- pcIRT-0.2/pcIRT/man/iccplot.Rd |only pcIRT-0.2/pcIRT/man/lrt.Rd |only pcIRT-0.2/pcIRT/man/mprm.Rd |only pcIRT-0.2/pcIRT/man/pcIRT-package.Rd | 101 ++++--- pcIRT-0.2/pcIRT/man/perspar.Rd |only pcIRT-0.2/pcIRT/man/reason.test.Rd |only pcIRT-0.2/pcIRT/man/simCRSM.Rd | 95 +++---- pcIRT-0.2/pcIRT/man/simMPRM.Rd | 82 +++--- pcIRT-0.2/pcIRT/man/wt.Rd |only pcIRT-0.2/pcIRT/src |only 70 files changed, 1224 insertions(+), 496 deletions(-)
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: There lacks an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. To meet this need, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for semantic similarity calculation between ontology terms (and genes), and network affinity calculation using Random Walk with Restart; both can be done via high-performance parallel computing. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.0.6 dated 2014-09-17 and 1.0.7 dated 2015-07-17
dnet-1.0.6/dnet/data/org.Hs.string900.RData |only dnet-1.0.6/dnet/man/org.Hs.string900.Rd |only dnet-1.0.7/dnet/DESCRIPTION | 39 +- dnet-1.0.7/dnet/MD5 | 192 ++++++------- dnet-1.0.7/dnet/NAMESPACE | 6 dnet-1.0.7/dnet/R/dBUMfit.r | 36 +- dnet-1.0.7/dnet/R/dBUMscore.r | 12 dnet-1.0.7/dnet/R/dCheckParallel.r | 29 +- dnet-1.0.7/dnet/R/dCommSignif.r | 4 dnet-1.0.7/dnet/R/dDAGancestor.r | 5 dnet-1.0.7/dnet/R/dDAGannotate.r | 4 dnet-1.0.7/dnet/R/dDAGgeneSim.r | 33 +- dnet-1.0.7/dnet/R/dDAGinduce.r | 4 dnet-1.0.7/dnet/R/dDAGlevel.r | 2 dnet-1.0.7/dnet/R/dDAGreverse.r | 2 dnet-1.0.7/dnet/R/dDAGroot.r | 4 dnet-1.0.7/dnet/R/dDAGtermSim.r | 31 +- dnet-1.0.7/dnet/R/dDAGtip.r | 4 dnet-1.0.7/dnet/R/dEnricher.r | 250 ++++-------------- dnet-1.0.7/dnet/R/dEnricherView.r | 16 - dnet-1.0.7/dnet/R/dFDRscore.r | 8 dnet-1.0.7/dnet/R/dFunArgs.r |only dnet-1.0.7/dnet/R/dGSEA.r | 146 +--------- dnet-1.0.7/dnet/R/dGSEAwrite.r | 2 dnet-1.0.7/dnet/R/dPvalAggregate.r | 4 dnet-1.0.7/dnet/R/dRDataLoader.r | 126 +++++---- dnet-1.0.7/dnet/R/dRWR.r | 137 +++++---- dnet-1.0.7/dnet/R/dRWRcontact.r | 23 - dnet-1.0.7/dnet/R/dRWRpipeline.r | 26 + dnet-1.0.7/dnet/R/dSVDsignif.r | 2 dnet-1.0.7/dnet/R/visBoxplotAdv.r | 74 ++--- dnet-1.0.7/dnet/R/visDAG.r | 28 +- dnet-1.0.7/dnet/R/visGSEA.r | 78 ++--- dnet-1.0.7/dnet/R/visNet.r | 16 - dnet-1.0.7/dnet/R/visNetAnimate.r |only dnet-1.0.7/dnet/R/visNetArc.r | 14 - dnet-1.0.7/dnet/R/visNetCircle.r | 4 dnet-1.0.7/dnet/R/visNetMul.r | 26 - dnet-1.0.7/dnet/R/visNetReorder.r | 28 +- dnet-1.0.7/dnet/data/TCGA_mutations.RData |binary dnet-1.0.7/dnet/data/datalist | 1 dnet-1.0.7/dnet/data/ig.HPPA.RData |binary dnet-1.0.7/dnet/data/org.Hs.egHPPA.RData |binary dnet-1.0.7/dnet/inst/CITATION | 4 dnet-1.0.7/dnet/inst/NEWS | 12 dnet-1.0.7/dnet/inst/staticdocs/CITATIONs.md | 2 dnet-1.0.7/dnet/inst/staticdocs/INSTALLATIONs.md | 35 +- dnet-1.0.7/dnet/inst/staticdocs/RData.md | 6 dnet-1.0.7/dnet/inst/staticdocs/demo/CLL.r | 2 dnet-1.0.7/dnet/inst/staticdocs/demo/Fang.r | 18 - dnet-1.0.7/dnet/inst/staticdocs/demo/Hiratani.r | 4 dnet-1.0.7/dnet/inst/staticdocs/demo/TCGA.r | 6 dnet-1.0.7/dnet/inst/staticdocs/docs.r | 19 - dnet-1.0.7/dnet/inst/staticdocs/faq/FAQ1.r | 5 dnet-1.0.7/dnet/inst/staticdocs/faq/FAQ2.r | 4 dnet-1.0.7/dnet/inst/staticdocs/faq/FAQ6.r | 30 +- dnet-1.0.7/dnet/inst/staticdocs/templates/footer.html | 2 dnet-1.0.7/dnet/man/dBUMfit.Rd | 3 dnet-1.0.7/dnet/man/dBUMscore.Rd | 3 dnet-1.0.7/dnet/man/dCheckParallel.Rd | 3 dnet-1.0.7/dnet/man/dCommSignif.Rd | 5 dnet-1.0.7/dnet/man/dContrast.Rd | 3 dnet-1.0.7/dnet/man/dDAGancestor.Rd | 5 dnet-1.0.7/dnet/man/dDAGannotate.Rd | 7 dnet-1.0.7/dnet/man/dDAGgeneSim.Rd | 11 dnet-1.0.7/dnet/man/dDAGinduce.Rd | 7 dnet-1.0.7/dnet/man/dDAGlevel.Rd | 5 dnet-1.0.7/dnet/man/dDAGreverse.Rd | 5 dnet-1.0.7/dnet/man/dDAGroot.Rd | 7 dnet-1.0.7/dnet/man/dDAGtermSim.Rd | 9 dnet-1.0.7/dnet/man/dDAGtip.Rd | 7 dnet-1.0.7/dnet/man/dEnricher.Rd | 87 +++--- dnet-1.0.7/dnet/man/dEnricherView.Rd | 8 dnet-1.0.7/dnet/man/dFDRscore.Rd | 3 dnet-1.0.7/dnet/man/dFunArgs.Rd |only dnet-1.0.7/dnet/man/dGSEA.Rd | 92 +++--- dnet-1.0.7/dnet/man/dGSEAview.Rd | 3 dnet-1.0.7/dnet/man/dGSEAwrite.Rd | 3 dnet-1.0.7/dnet/man/dNetConfidence.Rd | 3 dnet-1.0.7/dnet/man/dNetFind.Rd | 3 dnet-1.0.7/dnet/man/dNetInduce.Rd | 3 dnet-1.0.7/dnet/man/dNetPipeline.Rd | 3 dnet-1.0.7/dnet/man/dNetReorder.Rd | 3 dnet-1.0.7/dnet/man/dPvalAggregate.Rd | 3 dnet-1.0.7/dnet/man/dRDataLoader.Rd | 181 +++++++------ dnet-1.0.7/dnet/man/dRWR.Rd | 3 dnet-1.0.7/dnet/man/dRWRcontact.Rd | 3 dnet-1.0.7/dnet/man/dRWRpipeline.Rd | 3 dnet-1.0.7/dnet/man/dSVDsignif.Rd | 3 dnet-1.0.7/dnet/man/ig.HPPA.Rd | 3 dnet-1.0.7/dnet/man/org.Hs.egHPPA.Rd | 8 dnet-1.0.7/dnet/man/visBoxplotAdv.Rd | 10 dnet-1.0.7/dnet/man/visDAG.Rd | 5 dnet-1.0.7/dnet/man/visGSEA.Rd | 3 dnet-1.0.7/dnet/man/visNet.Rd | 5 dnet-1.0.7/dnet/man/visNetAnimate.Rd |only dnet-1.0.7/dnet/man/visNetArc.Rd | 3 dnet-1.0.7/dnet/man/visNetCircle.Rd | 3 dnet-1.0.7/dnet/man/visNetMul.Rd | 7 dnet-1.0.7/dnet/man/visNetReorder.Rd | 11 100 files changed, 1026 insertions(+), 1084 deletions(-)
Title: Linear Mixed Effects Models with Non-Stationary Stochastic
Processes
Description: Contains functions to estimate model parameters and filter, smooth and forecast random effects coefficients for mixed models with stationary and non-stationary stochastic processes under multivariate normal and t response distributions, diagnostic checks, bootstrap standard error calculation, etc.
Author: Ozgur Asar, Peter J. Diggle
Maintainer: Ozgur Asar <o.asar@lancaster.ac.uk>
Diff between lmenssp versions 1.0 dated 2014-10-22 and 1.1 dated 2015-07-17
lmenssp-1.0/lmenssp/data/data.sim.ibm.short.rda |only lmenssp-1.0/lmenssp/man/data.sim.ibm.short.Rd |only lmenssp-1.1/lmenssp/DESCRIPTION | 14 lmenssp-1.1/lmenssp/MD5 | 40 lmenssp-1.1/lmenssp/NAMESPACE | 21 lmenssp-1.1/lmenssp/R/boot.nm.R |only lmenssp-1.1/lmenssp/R/filtered.R | 125 ++ lmenssp-1.1/lmenssp/R/lmenssp.R | 1451 +++++++++++++++++++++--- lmenssp-1.1/lmenssp/R/lmenssp.heavy.R |only lmenssp-1.1/lmenssp/R/qqplot.t.R |only lmenssp-1.1/lmenssp/R/smoothed.R | 133 ++ lmenssp-1.1/lmenssp/R/smoothed.heavy.R |only lmenssp-1.1/lmenssp/R/var.inspect.R |only lmenssp-1.1/lmenssp/R/variogram.R | 66 - lmenssp-1.1/lmenssp/data/data.sim.ibm.heavy.rda |only lmenssp-1.1/lmenssp/data/data.sim.ibm.rda |binary lmenssp-1.1/lmenssp/man/boot.nm.Rd |only lmenssp-1.1/lmenssp/man/data.sim.ibm.Rd | 10 lmenssp-1.1/lmenssp/man/data.sim.ibm.heavy.Rd |only lmenssp-1.1/lmenssp/man/filtered.Rd | 42 lmenssp-1.1/lmenssp/man/lmenssp-package.Rd | 29 lmenssp-1.1/lmenssp/man/lmenssp.Rd | 91 + lmenssp-1.1/lmenssp/man/lmenssp.heavy.Rd |only lmenssp-1.1/lmenssp/man/qqplot.t.Rd |only lmenssp-1.1/lmenssp/man/smoothed.Rd | 46 lmenssp-1.1/lmenssp/man/smoothed.heavy.Rd |only lmenssp-1.1/lmenssp/man/var.inspect.Rd |only lmenssp-1.1/lmenssp/man/variogram.Rd | 52 28 files changed, 1850 insertions(+), 270 deletions(-)
Title: Aster Models
Description: Aster models are exponential family regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical
parameterization (aster transform of usual parameterization).
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between aster versions 0.8-30 dated 2014-06-01 and 0.8-31 dated 2015-07-17
CHANGES | 2 ++ DESCRIPTION | 24 +++++++++++++++++------- LICENSE | 2 +- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 12 ++++++++++++ build/vignette.rds |binary inst/doc/design.pdf |binary inst/doc/ktp.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary man/aster.Rd | 2 +- man/chamae.Rd | 2 +- man/chamae2.Rd | 2 +- man/chamae3.Rd | 4 ++-- man/echin2.Rd | 2 +- man/echinacea.Rd | 2 +- man/reaster.Rd | 6 +++--- man/summary.reaster.Rd | 2 +- src/asttrans7.c | 3 +-- src/validtrips.c |only 20 files changed, 63 insertions(+), 39 deletions(-)
Title: Processes Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also includes functions to plot and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>
Diff between acc versions 1.1.1 dated 2015-06-22 and 1.1.7 dated 2015-07-17
acc-1.1.1/acc/R/accsummary.R |only acc-1.1.1/acc/man/accsummary.Rd |only acc-1.1.7/acc/DESCRIPTION | 12 ++++++------ acc-1.1.7/acc/MD5 | 36 ++++++++++++++++++------------------ acc-1.1.7/acc/NAMESPACE | 32 +++++++++++++++++++++++++++----- acc-1.1.7/acc/R/acc.R | 8 +++++++- acc-1.1.7/acc/R/accBatch.R | 7 ++++++- acc-1.1.7/acc/R/accSummary.R |only acc-1.1.7/acc/R/aggAcc.R | 11 ++++++++++- acc-1.1.7/acc/R/plotAcc.R | 12 +++++++++--- acc-1.1.7/acc/R/readRaw.R | 16 ++++++++++------ acc-1.1.7/acc/R/readRawBatch.R | 20 ++++++++++++++++---- acc-1.1.7/acc/R/simAcc.R | 9 +++++++-- acc-1.1.7/acc/man/acc.Rd | 6 +++--- acc-1.1.7/acc/man/accBatch.Rd | 4 ++-- acc-1.1.7/acc/man/accSummary.Rd |only acc-1.1.7/acc/man/aggAcc.Rd | 2 +- acc-1.1.7/acc/man/plotAcc.Rd | 34 +++++++++++++++++++++------------- acc-1.1.7/acc/man/readRaw.Rd | 11 +++++++---- acc-1.1.7/acc/man/readRawBatch.Rd | 9 +++++---- acc-1.1.7/acc/man/simAcc.Rd | 2 +- 21 files changed, 156 insertions(+), 75 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.1.0 dated 2015-02-26 and 1.2.0 dated 2015-07-17
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 10 +++++++++- NEWS | 15 +++++++++++++++ R/dict.R | 11 +++++++---- R/match.R | 38 ++++++++++++++++++++++++-------------- R/ore.R | 25 ++++++++++++++++--------- README.md | 23 +++++++++++++++++++++++ man/es.Rd | 2 +- man/matches.Rd | 2 +- man/ore.Rd | 21 ++++++++++++++------- man/ore.dict.Rd | 8 ++++++-- man/ore.ismatch.Rd | 3 ++- man/ore.lastmatch.Rd | 10 ++++++++-- man/ore.search.Rd | 4 +++- man/ore.split.Rd | 5 +++-- man/ore.subst.Rd | 3 ++- src/compile.c | 26 +++++++++++++++++++------- src/compile.h | 4 ++-- tests/testthat/test-05-ore.R | 6 ++++++ tests/testthat/test-10-match.R | 3 +++ 21 files changed, 188 insertions(+), 79 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.2.4 dated 2015-05-28 and 2.2.6 dated 2015-07-17
OpenMx-2.2.4/OpenMx/README |only OpenMx-2.2.4/OpenMx/man/imxFilterDefinitionVariables.Rd |only OpenMx-2.2.6/OpenMx/DESCRIPTION | 19 OpenMx-2.2.6/OpenMx/MD5 | 260 +++---- OpenMx-2.2.6/OpenMx/NAMESPACE | 4 OpenMx-2.2.6/OpenMx/R/DefinitionVars.R | 23 OpenMx-2.2.6/OpenMx/R/MxAlgebra.R | 24 OpenMx-2.2.6/OpenMx/R/MxAvailableOptimizers.R |only OpenMx-2.2.6/OpenMx/R/MxCompute.R | 43 + OpenMx-2.2.6/OpenMx/R/MxData.R | 2 OpenMx-2.2.6/OpenMx/R/MxDataWLS.R | 20 OpenMx-2.2.6/OpenMx/R/MxEval.R | 2 OpenMx-2.2.6/OpenMx/R/MxExpectation.R | 6 OpenMx-2.2.6/OpenMx/R/MxExpectationBA81.R | 6 OpenMx-2.2.6/OpenMx/R/MxExpectationGREML.R | 18 OpenMx-2.2.6/OpenMx/R/MxExpectationLISREL.R | 5 OpenMx-2.2.6/OpenMx/R/MxExpectationNormal.R | 12 OpenMx-2.2.6/OpenMx/R/MxExpectationRAM.R | 5 OpenMx-2.2.6/OpenMx/R/MxExpectationStateSpace.R | 104 ++- OpenMx-2.2.6/OpenMx/R/MxFactorScores.R |only OpenMx-2.2.6/OpenMx/R/MxFitFunction.R | 6 OpenMx-2.2.6/OpenMx/R/MxFitFunctionAlgebra.R | 2 OpenMx-2.2.6/OpenMx/R/MxFitFunctionGREML.R | 9 OpenMx-2.2.6/OpenMx/R/MxFitFunctionML.R | 12 OpenMx-2.2.6/OpenMx/R/MxFitFunctionMultigroup.R | 4 OpenMx-2.2.6/OpenMx/R/MxFitFunctionR.R | 2 OpenMx-2.2.6/OpenMx/R/MxFitFunctionRow.R | 2 OpenMx-2.2.6/OpenMx/R/MxFitFunctionWLS.R | 2 OpenMx-2.2.6/OpenMx/R/MxFlatModel.R | 10 OpenMx-2.2.6/OpenMx/R/MxLISRELModel.R | 6 OpenMx-2.2.6/OpenMx/R/MxMatrix.R | 17 OpenMx-2.2.6/OpenMx/R/MxModelFunctions.R | 41 - OpenMx-2.2.6/OpenMx/R/MxModelParameters.R | 10 OpenMx-2.2.6/OpenMx/R/MxMultiModel.R | 1 OpenMx-2.2.6/OpenMx/R/MxRAMModel.R | 6 OpenMx-2.2.6/OpenMx/R/MxRun.R | 341 ++++++---- OpenMx-2.2.6/OpenMx/R/MxSummary.R | 19 OpenMx-2.2.6/OpenMx/R/MxVersion.R | 6 OpenMx-2.2.6/OpenMx/R/MxVersion.R.in | 4 OpenMx-2.2.6/OpenMx/R/omxGetNPSOL.R | 9 OpenMx-2.2.6/OpenMx/README.md |only OpenMx-2.2.6/OpenMx/inst/CITATION | 4 OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-2pl-se.R | 8 OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-3pl-se.R | 58 + OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-cyh2011-sim1.R | 39 + OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-grm-se.R | 12 OpenMx-2.2.6/OpenMx/inst/models/enormous/lib/stderrlib.R | 88 +- OpenMx-2.2.6/OpenMx/inst/models/nightly/FactorScores.R |only OpenMx-2.2.6/OpenMx/inst/models/nightly/MultilevelStateSpaceEx5.R | 39 + OpenMx-2.2.6/OpenMx/inst/models/nightly/brooke.R |only OpenMx-2.2.6/OpenMx/inst/models/nightly/fm-example2-1.R | 4 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-bifactor.R | 4 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-cai2009.R | 2 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-drm-wide.R | 4 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-ms.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/AlgebraComputePassing.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/AlgebraDeriv.R | 55 + OpenMx-2.2.6/OpenMx/inst/models/passing/GREML--minimal_test_model.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/GREML_Error_Detection.R | 52 + OpenMx-2.2.6/OpenMx/inst/models/passing/GREML_intercept_check.R |only OpenMx-2.2.6/OpenMx/inst/models/passing/IntroSEM-OneFactorCov.R | 23 OpenMx-2.2.6/OpenMx/inst/models/passing/IntroSEM-ThreeFactorScale2Test.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/LAD--CheckCode6.R | 3 OpenMx-2.2.6/OpenMx/inst/models/passing/MultipleGroupML.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/NormalML.R | 5 OpenMx-2.2.6/OpenMx/inst/models/passing/SimpleAlgebraCIs.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/SimpleConstraint.R | 3 OpenMx-2.2.6/OpenMx/inst/models/passing/SimpleMLAlgebraCIs.R | 5 OpenMx-2.2.6/OpenMx/inst/models/passing/StateSpaceInputs.R | 12 OpenMx-2.2.6/OpenMx/inst/models/passing/StateSpaceMissingData.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/UselessConstraint.R | 6 OpenMx-2.2.6/OpenMx/inst/models/passing/ifa-drm-mg2.R | 3 OpenMx-2.2.6/OpenMx/inst/models/passing/ifa-drm1.R | 16 OpenMx-2.2.6/OpenMx/inst/models/passing/ifa-grm1.R | 7 OpenMx-2.2.6/OpenMx/inst/models/passing/oneLocusLikelihood.R | 10 OpenMx-2.2.6/OpenMx/inst/models/passing/rfitfunc.R | 6 OpenMx-2.2.6/OpenMx/inst/models/passing/startingValues.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/startingValues2.R |only OpenMx-2.2.6/OpenMx/man/MxExpectationGREML-class.Rd | 1 OpenMx-2.2.6/OpenMx/man/MxFitFunctionGREML-class.Rd | 1 OpenMx-2.2.6/OpenMx/man/MxMatrix-class.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxAlgebra.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxAlgebraFromString.Rd |only OpenMx-2.2.6/OpenMx/man/mxAvailableOptimizers.Rd |only OpenMx-2.2.6/OpenMx/man/mxComputeEM.Rd | 8 OpenMx-2.2.6/OpenMx/man/mxComputeHessianQuality.Rd | 14 OpenMx-2.2.6/OpenMx/man/mxComputeStandardError.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxEval.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxExpectationBA81.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxExpectationGREML.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxExpectationStateSpace.Rd | 3 OpenMx-2.2.6/OpenMx/man/mxExpectationStateSpaceContinuousTime.Rd | 8 OpenMx-2.2.6/OpenMx/man/mxFactorScores.Rd |only OpenMx-2.2.6/OpenMx/man/mxFitFunctionAlgebra.Rd | 9 OpenMx-2.2.6/OpenMx/man/mxFitFunctionGREML.Rd | 4 OpenMx-2.2.6/OpenMx/man/mxFitFunctionML.Rd | 17 OpenMx-2.2.6/OpenMx/man/mxFitFunctionMultigroup.Rd | 122 +++ OpenMx-2.2.6/OpenMx/man/mxMatrix.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxTryHard.Rd | 9 OpenMx-2.2.6/OpenMx/man/omxSaturatedModel.Rd | 2 OpenMx-2.2.6/OpenMx/src/AlgebraFunctions.h | 265 ------- OpenMx-2.2.6/OpenMx/src/Compute.cpp | 268 +++---- OpenMx-2.2.6/OpenMx/src/Compute.h | 1 OpenMx-2.2.6/OpenMx/src/ComputeGD.cpp | 4 OpenMx-2.2.6/OpenMx/src/ComputeNR.cpp | 57 + OpenMx-2.2.6/OpenMx/src/ba81quad.cpp | 22 OpenMx-2.2.6/OpenMx/src/fitMultigroup.cpp | 2 OpenMx-2.2.6/OpenMx/src/glue.cpp | 124 ++- OpenMx-2.2.6/OpenMx/src/glue.h | 9 OpenMx-2.2.6/OpenMx/src/multi_normal_sufficient.hpp | 35 - OpenMx-2.2.6/OpenMx/src/nloptcpp.cpp | 103 ++- OpenMx-2.2.6/OpenMx/src/omxAlgebra.cpp | 1 OpenMx-2.2.6/OpenMx/src/omxData.cpp | 63 + OpenMx-2.2.6/OpenMx/src/omxData.h | 22 OpenMx-2.2.6/OpenMx/src/omxDefines.h | 4 OpenMx-2.2.6/OpenMx/src/omxExpectation.cpp | 155 ---- OpenMx-2.2.6/OpenMx/src/omxExpectation.h | 19 OpenMx-2.2.6/OpenMx/src/omxExpectationBA81.cpp | 2 OpenMx-2.2.6/OpenMx/src/omxExportBackendState.cpp | 2 OpenMx-2.2.6/OpenMx/src/omxFIMLFitFunction.cpp | 10 OpenMx-2.2.6/OpenMx/src/omxFIMLFitFunction.h | 3 OpenMx-2.2.6/OpenMx/src/omxFIMLSingleIteration.cpp | 8 OpenMx-2.2.6/OpenMx/src/omxFitFunction.cpp | 6 OpenMx-2.2.6/OpenMx/src/omxFitFunctionBA81.cpp | 10 OpenMx-2.2.6/OpenMx/src/omxGREMLExpectation.cpp | 85 +- OpenMx-2.2.6/OpenMx/src/omxGREMLExpectation.h | 3 OpenMx-2.2.6/OpenMx/src/omxGREMLfitfunction.cpp | 54 + OpenMx-2.2.6/OpenMx/src/omxHessianCalculation.cpp | 9 OpenMx-2.2.6/OpenMx/src/omxImportFrontendState.cpp | 54 + OpenMx-2.2.6/OpenMx/src/omxImportFrontendState.h | 1 OpenMx-2.2.6/OpenMx/src/omxMLFitFunction.cpp | 22 OpenMx-2.2.6/OpenMx/src/omxRowFitFunction.cpp | 7 OpenMx-2.2.6/OpenMx/src/omxState.cpp | 31 OpenMx-2.2.6/OpenMx/src/omxState.h | 7 OpenMx-2.2.6/OpenMx/src/omxStateSpaceExpectation.cpp | 322 +++++++++ OpenMx-2.2.6/OpenMx/src/omxStateSpaceExpectation.h | 3 OpenMx-2.2.6/OpenMx/src/omxWLSFitFunction.cpp | 1 137 files changed, 2195 insertions(+), 1365 deletions(-)
Title: Mixed Tempered Stable Distribution
Description: We provide detailed functions for univariate Mixed Tempered Stable distribution.
Author: Lorenzo Mercuri, Edit Rroji
Maintainer: Lorenzo Mercuri <lorenzo.mercuri@unimi.it>
Diff between MixedTS versions 1.0.1 dated 2014-08-04 and 1.0.3 dated 2015-07-17
DESCRIPTION | 16 +++---- MD5 | 22 ++++----- NAMESPACE | 7 +-- R/MixedClasses.R | 38 ++++++++++++---- R/MixedTS.R | 101 +++++++++++++++++++++++++++++++++------------ R/dMixedTS.R | 18 ++++---- R/mle.MixedTS.aux.R | 61 ++++++++++++++++----------- R/pMixedTS.R | 21 +++++---- R/qMixedTS.R | 18 ++++---- R/rMixedTS.R | 19 ++++---- man/param.MixedTS-class.Rd | 2 man/setMixedTS.param.Rd | 13 +++++ 12 files changed, 222 insertions(+), 114 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.0.4 dated 2015-07-08 and 0.1.0 dated 2015-07-17
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS | 7 ++- R/visDocumentation.R | 3 - R/visNetwork.R | 3 - README.md | 41 +++++++++--------- build/vignette.rds |binary inst/doc/Introduction-to-visNetwork.Rmd | 2 inst/doc/Introduction-to-visNetwork.html | 68 +++++++++++++++---------------- man/visDocumentation.Rd | 2 man/visNetwork.Rd | 3 - vignettes/Introduction-to-visNetwork.Rmd | 2 12 files changed, 88 insertions(+), 75 deletions(-)
Title: Vertex Enumeration of Polytopes
Description: When given a description of a polyhedral set by a system of linear inequalities Ax <= b, produce the list of the vertices of the set.
Author: Robert Robere
Maintainer: Robert Robere <robere@cs.toronto.edu>
Diff between vertexenum versions 1.0 dated 2015-07-14 and 1.0.1 dated 2015-07-17
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/enumerate.vertices.R | 7 +++---- man/enumerate.vertices.Rd | 2 +- src/Rvertexenum.c | 16 ++++++++++++++-- src/lrslib.c | 13 ++++++++++++- src/lrsmp.c | 32 +++++++++++++++++++++++--------- 8 files changed, 67 insertions(+), 29 deletions(-)
Title: Statistical Analysis of Fuzzy Data
Description: The aim of the package is to provide some basic functions
for doing statistics with one dimensional Fuzzy Data (in the
form of polygonal fuzzy numbers). In particular, the package
contains functions for the basic operations on the class of
fuzzy numbers (sum, scalar product, mean, median, Hukuhara difference)
as well as for calculating (Bertoluzza) distance,
sample variance, sample covariance, and the
Dempster-Shafer (levelwise) histogram. Moreover a function to
simulate fuzzy random variables, bootstrap tests for the
equality of means, and a function to do linear regression given
trapezoidal fuzzy data is included. Version 1.0 fixes some bugs
of previous versions.
Author: Wolfgang Trutschnig <wolfgang@trutschnig.net>, Asun Lubiano
<lubiano@uniovi.es>
Maintainer: Asun Lubiano <lubiano@uniovi.es>
Diff between SAFD versions 0.4 dated 2012-08-10 and 1.0 dated 2015-07-17
SAFD-0.4/SAFD/R/Bcor.R |only SAFD-0.4/SAFD/R/Fquantile.R |only SAFD-0.4/SAFD/man/Bcor.Rd |only SAFD-0.4/SAFD/man/Fquantile.Rd |only SAFD-1.0/SAFD/DESCRIPTION | 25 ++--- SAFD-1.0/SAFD/MD5 | 98 ++++++++++------------ SAFD-1.0/SAFD/NAMESPACE | 3 SAFD-1.0/SAFD/R/Bcov.R | 10 +- SAFD-1.0/SAFD/R/Bvar.R | 4 SAFD-1.0/SAFD/R/DSfrequency.R | 8 - SAFD-1.0/SAFD/R/DShistogram.R | 6 - SAFD-1.0/SAFD/R/Fmedian.R | 51 +++++++---- SAFD-1.0/SAFD/R/Mmean.R | 16 ++- SAFD-1.0/SAFD/R/Msum.R | 37 ++++++-- SAFD-1.0/SAFD/R/bertoluzza.R | 15 +-- SAFD-1.0/SAFD/R/btest.mean.R | 38 ++++---- SAFD-1.0/SAFD/R/btest2.mean.R | 32 +++---- SAFD-1.0/SAFD/R/btestk.mean.R | 30 +++--- SAFD-1.0/SAFD/R/checking.R | 66 +++++++++------ SAFD-1.0/SAFD/R/checking2.R | 48 +++++++--- SAFD-1.0/SAFD/R/defuzzify.R | 4 SAFD-1.0/SAFD/R/generator.R | 12 +- SAFD-1.0/SAFD/R/hukuhara.R | 20 ++-- SAFD-1.0/SAFD/R/lrmodel.R | 12 +- SAFD-1.0/SAFD/R/sc_mult.R | 14 ++- SAFD-1.0/SAFD/R/translator.R | 14 ++- SAFD-1.0/SAFD/data/Trees.rda |binary SAFD-1.0/SAFD/data/XX.rda |binary SAFD-1.0/SAFD/data/quality.rda |only SAFD-1.0/SAFD/man/Bcov.Rd | 81 ++++++++++++++++-- SAFD-1.0/SAFD/man/Bvar.Rd | 53 ++++++++---- SAFD-1.0/SAFD/man/DSfrequency.Rd | 111 +++++++++++++++++++++++-- SAFD-1.0/SAFD/man/DShistogram.Rd | 157 +++++++++++++++++++++++++++++++++-- SAFD-1.0/SAFD/man/Fmedian.Rd | 91 +++++++++++++++++--- SAFD-1.0/SAFD/man/Mmean.Rd | 60 ++++++++++--- SAFD-1.0/SAFD/man/Msum.Rd | 99 +++++++++++++++++++--- SAFD-1.0/SAFD/man/SAFD-package.Rd | 41 ++++----- SAFD-1.0/SAFD/man/Trees.Rd | 15 +-- SAFD-1.0/SAFD/man/XX.Rd | 6 - SAFD-1.0/SAFD/man/bertoluzza.Rd | 62 ++++++++++++-- SAFD-1.0/SAFD/man/btest.mean.Rd | 74 ++++++++++++++-- SAFD-1.0/SAFD/man/btest2.mean.Rd | 96 +++++++++++++++++++-- SAFD-1.0/SAFD/man/btestk.mean.Rd | 166 +++++++++++++++++++++++++++++++++++--- SAFD-1.0/SAFD/man/checking.Rd | 134 ++++++++++++++++++++++++++---- SAFD-1.0/SAFD/man/checking2.Rd | 86 ++++++++++++++++++- SAFD-1.0/SAFD/man/decomposer.Rd | 30 +++++- SAFD-1.0/SAFD/man/defuzzify.Rd | 47 +++++----- SAFD-1.0/SAFD/man/generator.Rd | 114 +++++++++++++++++++++++--- SAFD-1.0/SAFD/man/hukuhara.Rd | 57 ++++++++----- SAFD-1.0/SAFD/man/lrmodel.Rd | 142 +++++++++++++++++++++++++++++--- SAFD-1.0/SAFD/man/quality.Rd |only SAFD-1.0/SAFD/man/sc_mult.Rd | 68 +++++++++++++-- SAFD-1.0/SAFD/man/translator.Rd | 69 +++++++++++---- 53 files changed, 1905 insertions(+), 517 deletions(-)
Title: R Interface to the UNU.RAN Random Variate Generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform RANdom variate generators.
Thus it allows to build non-uniform random number generators from quite arbitrary
distributions. In particular, it provides an algorithm for fast numerical inversion
for distribution with given density function.
In addition, the package contains densities, distribution functions and quantiles
from a couple of distributions.
Author: Josef Leydold and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Runuran versions 0.21.0 dated 2014-08-27 and 0.22.0 dated 2015-07-17
DESCRIPTION | 13 MD5 | 678 +++++++-------- NAMESPACE | 3 NEWS | 5 build/vignette.rds |binary inst/doc/Runuran.pdf |binary inst/include/unuran.h | 2 man/Runuran-package.Rd | 2 src/Makevars.in | 2 src/unuran-src/distr/cemp.c | 2 src/unuran-src/distr/cemp.h | 2 src/unuran-src/distr/condi.c | 2 src/unuran-src/distr/condi.h | 2 src/unuran-src/distr/cont.c | 2 src/unuran-src/distr/cont.h | 2 src/unuran-src/distr/corder.c | 2 src/unuran-src/distr/corder.h | 2 src/unuran-src/distr/cvec.c | 2 src/unuran-src/distr/cvec.h | 2 src/unuran-src/distr/cvemp.c | 2 src/unuran-src/distr/cvemp.h | 2 src/unuran-src/distr/cxtrans.c | 2 src/unuran-src/distr/cxtrans.h | 2 src/unuran-src/distr/deprecated_distr.h | 2 src/unuran-src/distr/discr.c | 2 src/unuran-src/distr/discr.h | 2 src/unuran-src/distr/distr.c | 2 src/unuran-src/distr/distr.h | 2 src/unuran-src/distr/distr_info.c | 2 src/unuran-src/distr/distr_source.h | 2 src/unuran-src/distr/distr_struct.h | 2 src/unuran-src/distr/matr.c | 2 src/unuran-src/distr/matr.h | 2 src/unuran-src/distributions/c_F.c | 2 src/unuran-src/distributions/c_beta.c | 2 src/unuran-src/distributions/c_beta_gen.c | 2 src/unuran-src/distributions/c_burr.c | 2 src/unuran-src/distributions/c_cauchy.c | 2 src/unuran-src/distributions/c_chi.c | 2 src/unuran-src/distributions/c_chi_gen.c | 2 src/unuran-src/distributions/c_chisquare.c | 2 src/unuran-src/distributions/c_exponential.c | 2 src/unuran-src/distributions/c_exponential_gen.c | 2 src/unuran-src/distributions/c_extremeI.c | 2 src/unuran-src/distributions/c_extremeII.c | 2 src/unuran-src/distributions/c_gamma.c | 2 src/unuran-src/distributions/c_gamma_gen.c | 2 src/unuran-src/distributions/c_ghyp.c | 2 src/unuran-src/distributions/c_gig.c | 2 src/unuran-src/distributions/c_gig2.c | 2 src/unuran-src/distributions/c_gig_gen.c | 2 src/unuran-src/distributions/c_hyperbolic.c | 2 src/unuran-src/distributions/c_ig.c | 2 src/unuran-src/distributions/c_laplace.c | 2 src/unuran-src/distributions/c_logistic.c | 2 src/unuran-src/distributions/c_lognormal.c | 2 src/unuran-src/distributions/c_lomax.c | 2 src/unuran-src/distributions/c_meixner.c | 2 src/unuran-src/distributions/c_normal.c | 2 src/unuran-src/distributions/c_normal_gen.c | 2 src/unuran-src/distributions/c_pareto.c | 2 src/unuran-src/distributions/c_powerexponential.c | 2 src/unuran-src/distributions/c_powerexponential_gen.c | 2 src/unuran-src/distributions/c_rayleigh.c | 2 src/unuran-src/distributions/c_slash.c | 2 src/unuran-src/distributions/c_slash_gen.c | 2 src/unuran-src/distributions/c_student.c | 2 src/unuran-src/distributions/c_student_gen.c | 2 src/unuran-src/distributions/c_triangular.c | 2 src/unuran-src/distributions/c_uniform.c | 2 src/unuran-src/distributions/c_vg.c | 2 src/unuran-src/distributions/c_weibull.c | 2 src/unuran-src/distributions/d_binomial.c | 2 src/unuran-src/distributions/d_binomial_gen.c | 2 src/unuran-src/distributions/d_geometric.c | 2 src/unuran-src/distributions/d_hypergeometric.c | 2 src/unuran-src/distributions/d_hypergeometric_gen.c | 2 src/unuran-src/distributions/d_logarithmic.c | 2 src/unuran-src/distributions/d_logarithmic_gen.c | 2 src/unuran-src/distributions/d_negativebinomial.c | 2 src/unuran-src/distributions/d_poisson.c | 2 src/unuran-src/distributions/d_poisson_gen.c | 2 src/unuran-src/distributions/d_zipf.c | 2 src/unuran-src/distributions/d_zipf_gen.c | 2 src/unuran-src/distributions/m_correlation.c | 2 src/unuran-src/distributions/unur_distributions.h | 2 src/unuran-src/distributions/unur_distributions_source.h | 2 src/unuran-src/distributions/unur_stddistr.h | 2 src/unuran-src/distributions/vc_copula.c | 2 src/unuran-src/distributions/vc_multicauchy.c | 2 src/unuran-src/distributions/vc_multiexponential.c | 2 src/unuran-src/distributions/vc_multinormal.c | 2 src/unuran-src/distributions/vc_multinormal_gen.c | 2 src/unuran-src/distributions/vc_multistudent.c | 2 src/unuran-src/methods/arou.c | 2 src/unuran-src/methods/arou.h | 2 src/unuran-src/methods/arou_struct.h | 2 src/unuran-src/methods/ars.c | 2 src/unuran-src/methods/ars.h | 2 src/unuran-src/methods/ars_struct.h | 2 src/unuran-src/methods/auto.c | 2 src/unuran-src/methods/auto.h | 2 src/unuran-src/methods/auto_struct.h | 2 src/unuran-src/methods/cext.c | 2 src/unuran-src/methods/cext.h | 2 src/unuran-src/methods/cext_struct.h | 2 src/unuran-src/methods/cstd.c | 2 src/unuran-src/methods/cstd.h | 2 src/unuran-src/methods/cstd_struct.h | 2 src/unuran-src/methods/dari.c | 2 src/unuran-src/methods/dari.h | 2 src/unuran-src/methods/dari_struct.h | 2 src/unuran-src/methods/dau.c | 2 src/unuran-src/methods/dau.h | 2 src/unuran-src/methods/dau_struct.h | 2 src/unuran-src/methods/deprecated_methods.h | 2 src/unuran-src/methods/deprecated_tdrgw.h | 2 src/unuran-src/methods/deprecated_vmt.h | 2 src/unuran-src/methods/deprecated_vmt_struct.h | 2 src/unuran-src/methods/dext.c | 2 src/unuran-src/methods/dext.h | 2 src/unuran-src/methods/dext_struct.h | 2 src/unuran-src/methods/dgt.c | 2 src/unuran-src/methods/dgt.h | 2 src/unuran-src/methods/dgt_struct.h | 2 src/unuran-src/methods/dsrou.c | 2 src/unuran-src/methods/dsrou.h | 2 src/unuran-src/methods/dsrou_struct.h | 2 src/unuran-src/methods/dss.c | 2 src/unuran-src/methods/dss.h | 2 src/unuran-src/methods/dss_struct.h | 2 src/unuran-src/methods/dstd.c | 2 src/unuran-src/methods/dstd.h | 2 src/unuran-src/methods/dstd_struct.h | 2 src/unuran-src/methods/empk.c | 2 src/unuran-src/methods/empk.h | 2 src/unuran-src/methods/empk_struct.h | 2 src/unuran-src/methods/empl.c | 2 src/unuran-src/methods/empl.h | 2 src/unuran-src/methods/empl_struct.h | 2 src/unuran-src/methods/gibbs.c | 2 src/unuran-src/methods/gibbs.h | 2 src/unuran-src/methods/gibbs_struct.h | 2 src/unuran-src/methods/hinv.c | 2 src/unuran-src/methods/hinv.h | 2 src/unuran-src/methods/hinv_struct.h | 2 src/unuran-src/methods/hist.c | 2 src/unuran-src/methods/hist.h | 2 src/unuran-src/methods/hist_struct.h | 2 src/unuran-src/methods/hitro.c | 2 src/unuran-src/methods/hitro.h | 2 src/unuran-src/methods/hitro_struct.h | 2 src/unuran-src/methods/hrb.c | 2 src/unuran-src/methods/hrb.h | 2 src/unuran-src/methods/hrb_struct.h | 2 src/unuran-src/methods/hrd.c | 2 src/unuran-src/methods/hrd.h | 2 src/unuran-src/methods/hrd_struct.h | 2 src/unuran-src/methods/hri.c | 2 src/unuran-src/methods/hri.h | 2 src/unuran-src/methods/hri_struct.h | 2 src/unuran-src/methods/itdr.c | 2 src/unuran-src/methods/itdr.h | 2 src/unuran-src/methods/itdr_struct.h | 2 src/unuran-src/methods/mcorr.c | 2 src/unuran-src/methods/mcorr.h | 2 src/unuran-src/methods/mcorr_struct.h | 2 src/unuran-src/methods/mixt.c | 2 src/unuran-src/methods/mixt.h | 2 src/unuran-src/methods/mixt_struct.h | 2 src/unuran-src/methods/mvstd.c | 2 src/unuran-src/methods/mvstd.h | 2 src/unuran-src/methods/mvstd_struct.h | 2 src/unuran-src/methods/mvtdr.c | 2 src/unuran-src/methods/mvtdr.h | 2 src/unuran-src/methods/mvtdr_debug.ch | 2 src/unuran-src/methods/mvtdr_info.ch | 2 src/unuran-src/methods/mvtdr_init.ch | 2 src/unuran-src/methods/mvtdr_newset.ch | 2 src/unuran-src/methods/mvtdr_sample.ch | 2 src/unuran-src/methods/mvtdr_struct.h | 2 src/unuran-src/methods/ninv.c | 2 src/unuran-src/methods/ninv.h | 2 src/unuran-src/methods/ninv_debug.ch | 2 src/unuran-src/methods/ninv_info.ch | 2 src/unuran-src/methods/ninv_init.ch | 2 src/unuran-src/methods/ninv_newset.ch | 2 src/unuran-src/methods/ninv_newton.ch | 2 src/unuran-src/methods/ninv_regula.ch | 2 src/unuran-src/methods/ninv_sample.ch | 2 src/unuran-src/methods/ninv_struct.h | 2 src/unuran-src/methods/norta.c | 2 src/unuran-src/methods/norta.h | 2 src/unuran-src/methods/norta_struct.h | 2 src/unuran-src/methods/nrou.c | 2 src/unuran-src/methods/nrou.h | 2 src/unuran-src/methods/nrou_struct.h | 2 src/unuran-src/methods/pinv.c | 2 src/unuran-src/methods/pinv.h | 2 src/unuran-src/methods/pinv_debug.ch | 2 src/unuran-src/methods/pinv_info.ch | 2 src/unuran-src/methods/pinv_init.ch | 2 src/unuran-src/methods/pinv_newset.ch | 2 src/unuran-src/methods/pinv_newton.ch | 2 src/unuran-src/methods/pinv_prep.ch | 2 src/unuran-src/methods/pinv_sample.ch | 2 src/unuran-src/methods/pinv_struct.h | 2 src/unuran-src/methods/srou.c | 2 src/unuran-src/methods/srou.h | 2 src/unuran-src/methods/srou_struct.h | 2 src/unuran-src/methods/ssr.c | 2 src/unuran-src/methods/ssr.h | 2 src/unuran-src/methods/ssr_struct.h | 2 src/unuran-src/methods/tabl.c | 2 src/unuran-src/methods/tabl.h | 2 src/unuran-src/methods/tabl_debug.ch | 2 src/unuran-src/methods/tabl_info.ch | 2 src/unuran-src/methods/tabl_init.ch | 2 src/unuran-src/methods/tabl_newset.ch | 2 src/unuran-src/methods/tabl_sample.ch | 2 src/unuran-src/methods/tabl_struct.h | 2 src/unuran-src/methods/tdr.c | 2 src/unuran-src/methods/tdr.h | 2 src/unuran-src/methods/tdr_debug.ch | 2 src/unuran-src/methods/tdr_gw_debug.ch | 2 src/unuran-src/methods/tdr_gw_init.ch | 2 src/unuran-src/methods/tdr_gw_sample.ch | 2 src/unuran-src/methods/tdr_ia_sample.ch | 2 src/unuran-src/methods/tdr_info.ch | 2 src/unuran-src/methods/tdr_init.ch | 2 src/unuran-src/methods/tdr_newset.ch | 2 src/unuran-src/methods/tdr_ps_debug.ch | 2 src/unuran-src/methods/tdr_ps_init.ch | 2 src/unuran-src/methods/tdr_ps_sample.ch | 2 src/unuran-src/methods/tdr_sample.ch | 2 src/unuran-src/methods/tdr_struct.h | 2 src/unuran-src/methods/unif.c | 2 src/unuran-src/methods/unif.h | 2 src/unuran-src/methods/unif_struct.h | 2 src/unuran-src/methods/unur_methods.h | 2 src/unuran-src/methods/unur_methods_source.h | 2 src/unuran-src/methods/utdr.c | 2 src/unuran-src/methods/utdr.h | 2 src/unuran-src/methods/utdr_struct.h | 2 src/unuran-src/methods/vempk.c | 2 src/unuran-src/methods/vempk.h | 2 src/unuran-src/methods/vempk_struct.h | 2 src/unuran-src/methods/vnrou.c | 2 src/unuran-src/methods/vnrou.h | 2 src/unuran-src/methods/vnrou_struct.h | 2 src/unuran-src/methods/x_gen.c | 2 src/unuran-src/methods/x_gen.h | 2 src/unuran-src/methods/x_gen_source.h | 2 src/unuran-src/methods/x_gen_struct.h | 2 src/unuran-src/parser/functparser.c | 2 src/unuran-src/parser/functparser_debug.ch | 2 src/unuran-src/parser/functparser_deriv.ch | 2 src/unuran-src/parser/functparser_eval.ch | 2 src/unuran-src/parser/functparser_init.ch | 2 src/unuran-src/parser/functparser_parser.ch | 2 src/unuran-src/parser/functparser_scanner.ch | 2 src/unuran-src/parser/functparser_source.h | 2 src/unuran-src/parser/functparser_stringgen.ch | 2 src/unuran-src/parser/functparser_struct.h | 2 src/unuran-src/parser/functparser_symbols.h | 2 src/unuran-src/parser/parser.c | 2 src/unuran-src/parser/parser.h | 2 src/unuran-src/parser/parser_source.h | 2 src/unuran-src/parser/stringparser.c | 2 src/unuran-src/parser/stringparser_lists.ch | 2 src/unuran-src/specfunct/bessel_asympt.c | 2 src/unuran-src/specfunct/cgamma.c | 2 src/unuran-src/specfunct/hypot.c | 2 src/unuran-src/specfunct/log1p.c | 2 src/unuran-src/specfunct/unur_specfunct_source.h | 2 src/unuran-src/tests/countpdf.c | 2 src/unuran-src/tests/counturn.c | 2 src/unuran-src/tests/inverror.c | 2 src/unuran-src/tests/unuran_tests.h | 2 src/unuran-src/uniform/mrg31k3p.c | 2 src/unuran-src/uniform/urng_builtin.h | 2 src/unuran-src/uniform/urng_fvoid.h | 2 src/unuran-src/uniform/urng_gsl.h | 2 src/unuran-src/uniform/urng_gslqrng.h | 2 src/unuran-src/uniform/urng_prng.h | 2 src/unuran-src/uniform/urng_randomshift.h | 2 src/unuran-src/uniform/urng_rngstreams.h | 2 src/unuran-src/unur_cookies.h | 2 src/unuran-src/unur_source.h | 2 src/unuran-src/unur_struct.h | 2 src/unuran-src/unur_typedefs.h | 2 src/unuran-src/unuran.h | 2 src/unuran-src/urng/urng.c | 2 src/unuran-src/urng/urng.h | 2 src/unuran-src/urng/urng_default.c | 2 src/unuran-src/urng/urng_set.c | 2 src/unuran-src/urng/urng_source.h | 2 src/unuran-src/urng/urng_struct.h | 2 src/unuran-src/urng/urng_unuran.c | 2 src/unuran-src/utils/debug.c | 2 src/unuran-src/utils/debug.h | 2 src/unuran-src/utils/debug_source.h | 2 src/unuran-src/utils/eigensystem.c | 2 src/unuran-src/utils/error.c | 2 src/unuran-src/utils/error.h | 2 src/unuran-src/utils/error_source.h | 2 src/unuran-src/utils/fmax.c | 2 src/unuran-src/utils/fmax_source.h | 2 src/unuran-src/utils/hooke.c | 2 src/unuran-src/utils/hooke_source.h | 2 src/unuran-src/utils/lobatto.c | 2 src/unuran-src/utils/lobatto_source.h | 2 src/unuran-src/utils/lobatto_struct.h | 2 src/unuran-src/utils/matrix.c | 2 src/unuran-src/utils/matrix_source.h | 2 src/unuran-src/utils/mrou_rectangle.c | 2 src/unuran-src/utils/mrou_rectangle_source.h | 2 src/unuran-src/utils/mrou_rectangle_struct.h | 2 src/unuran-src/utils/slist.c | 2 src/unuran-src/utils/slist.h | 2 src/unuran-src/utils/slist_struct.h | 2 src/unuran-src/utils/stream.c | 2 src/unuran-src/utils/stream.h | 2 src/unuran-src/utils/stream_source.h | 2 src/unuran-src/utils/string.c | 2 src/unuran-src/utils/string_source.h | 2 src/unuran-src/utils/string_struct.h | 2 src/unuran-src/utils/umalloc.c | 2 src/unuran-src/utils/umalloc_source.h | 2 src/unuran-src/utils/umath.c | 2 src/unuran-src/utils/umath.h | 2 src/unuran-src/utils/umath_source.h | 2 src/unuran-src/utils/unur_errno.h | 2 src/unuran-src/utils/unur_fp.c | 2 src/unuran-src/utils/unur_fp_const_source.h | 2 src/unuran-src/utils/unur_fp_source.h | 2 src/unuran-src/utils/unur_math_source.h | 2 src/unuran-src/utils/vector.c | 2 src/unuran-src/utils/vector_source.h | 2 vignettes/inputs/version.tex | 2 340 files changed, 687 insertions(+), 680 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.4 dated 2015-07-04 and 0.1.5 dated 2015-07-17
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 8 +++++--- inst/tests/runit.basicRtests.R | 11 +++++++---- 5 files changed, 27 insertions(+), 15 deletions(-)
Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Description: Functions to obtain the operational characteristics of
bioequivalence studies with 2-stage designs via simulations
- Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use both point estimate (PE) and mse from stage 1
also for the power monitoring steps.
- The third function power.2stage.fC() calculates power and sample-size
distribution of 2-stage BE studies with a futility criterion
for the PE or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
This function has a sibling power.2stage.pAF(), which performs exactly as
described in A.Fuglsang 2014
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between Power2Stage versions 0.4-1 dated 2015-06-29 and 0.4-2 dated 2015-07-17
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NAMESPACE | 6 ++ NEWS | 7 +++ R/power.R | 2 R/power_2stage_DL.R | 11 ++-- R/power_2stage_KM.R | 6 +- R/power_2stage_SSR.R | 48 +++++++++++++-------- R/print_pwrtsd_s3.R | 109 ++++++++++++++++++++++++------------------------ R/sampsiz2.R | 6 +- R/sampsiz_n0.R | 77 ++++++++++++++++++--------------- man/power.2stage.GS.Rd | 3 - man/power.2stage.fC.Rd | 4 - man/power.2stage.ssr.Rd | 14 ++++-- 14 files changed, 184 insertions(+), 143 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] (libsvm C++-code),
Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.6-4 dated 2014-09-01 and 1.6-6 dated 2015-07-17
DESCRIPTION | 14 +++++----- MD5 | 30 ++++++++++----------- NAMESPACE | 10 ++++--- R/hamming.distance.R | 6 ++-- R/matchClasses.R | 63 ++++++++++++++++++++++----------------------- R/svm.R | 40 +++++++++++++++++----------- R/tune.R | 10 +++---- build/vignette.rds |binary inst/NEWS.Rd | 21 +++++++++++++++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.Rnw | 19 +++++++++++++ inst/doc/svminternals.pdf |binary man/bclust.Rd | 2 - man/hamming.distance.Rd | 4 ++ man/tune.control.Rd | 2 - vignettes/svminternals.Rnw | 19 +++++++++++++ 16 files changed, 156 insertions(+), 84 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, and Luca Scrucca.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-47 dated 2015-05-06 and 6.0-52 dated 2015-07-17
DESCRIPTION | 16 +-- MD5 | 65 +++++++------ NAMESPACE | 23 ++++ R/aaa.R | 95 +++++++++---------- R/adaptive.R | 3 R/avNNet.R | 2 R/confusionMatrix.R | 2 R/createModel.R | 24 +++- R/findCorrelation.R | 80 ++++++++++++++-- R/lift.R | 19 ++- R/misc.R | 156 +++++++++++++++++++++++++++----- R/preProcess.R | 15 +-- R/print.train.R | 23 +++- R/resamples.R | 19 +++ R/rfe.R | 1 R/train.default.R | 38 ++++++- R/trainControl.R | 2 R/workflows.R | 3 build/vignette.rds |binary inst/NEWS.Rd | 19 +++ inst/doc/caret.R | 1 inst/doc/caret.Rnw | 1 inst/doc/caret.pdf |binary inst/models/models.RData |binary inst/models/sampling.RData |only man/caret-internal.Rd | 20 ++-- man/dummyVars.Rd | 14 ++ man/findCorrelation.Rd | 49 ++++++---- man/getSamplingInfo.Rd |only man/resamples.Rd | 5 + man/safsControl.Rd | 2 man/trainControl.Rd | 30 +++--- tests/testthat/test_BoxCox.R |only tests/testthat/test_bad_class_options.R |only tests/testthat/test_sampling_options.R |only vignettes/caret.Rnw | 1 36 files changed, 536 insertions(+), 192 deletions(-)
Title: Tinflex - Universal Non-Uniform Random Number Generator
Description: A universal non-uniform random number generator
for quite arbitrary distributions with piecewise twice
differentiable densities.
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Tinflex versions 1.0 dated 2013-05-14 and 1.1 dated 2015-07-17
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS | 5 +++++ man/Tinflex-package.Rd | 4 ++-- 5 files changed, 24 insertions(+), 15 deletions(-)
Title: Streams of Random Numbers
Description: Unified object oriented interface for multiple independent streams of random numbers from different sources.
Author: Josef Leydold <josef.leydold@wu.ac.at>
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between rstream versions 1.3.2 dated 2012-01-31 and 1.3.3 dated 2015-07-17
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- NAMESPACE | 3 ++- NEWS | 4 ++++ inst/doc/rstream.pdf |binary man/rstream-package.Rd | 4 ++-- 6 files changed, 22 insertions(+), 16 deletions(-)
Title: Interface Between R and Qt
Description: Dynamic bindings to the Qt library for calling Qt
methods and extending Qt classes from R. Other packages build upon 'qtbase'
to provide special-purpose high-level interfaces to specific parts of Qt.
Author: Michael Lawrence, Deepayan Sarkar
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between qtbase versions 1.0.9 dated 2015-05-28 and 1.0.11 dated 2015-07-17
qtbase-1.0.11/qtbase/DESCRIPTION | 6 +++--- qtbase-1.0.11/qtbase/MD5 | 16 ++++++++-------- qtbase-1.0.11/qtbase/NAMESPACE | 4 +++- qtbase-1.0.11/qtbase/inst/NOTES |only qtbase-1.0.11/qtbase/inst/doc/qtbase.pdf |binary qtbase-1.0.11/qtbase/kdebindings/CMakeLists.txt | 3 +++ qtbase-1.0.11/qtbase/src/MocProperty.cpp | 2 +- qtbase-1.0.11/qtbase/src/convert.cpp | 2 +- qtbase-1.0.11/qtbase/src/convert.hpp | 2 +- qtbase-1.0.9/qtbase/NOTES |only 10 files changed, 20 insertions(+), 15 deletions(-)
Title: Linear Mixed Effect Model Splines for Modelling and Analysis of
Time Course Data
Description: Linear Mixed effect Model Splines (lmms) implements linear mixed effect model splines for
modelling and differential expression for highly dimensional data sets:
investNoise for quality control and filterNoise for removing
non-informative trajectories; lmmSpline to model time course expression
profiles and lmmsDE performs differential expression analysis to identify
differential expression between groups, time and/or group x time
interaction.
Author: Jasmin Straube [aut, cre],
Kim-Anh Le Cao [aut],
Emma Huang [aut],
Dominique Gorse [ctb]
Maintainer: Jasmin Straube <j.straube@qfab.org>
Diff between lmms versions 1.2 dated 2014-11-20 and 1.3 dated 2015-07-17
lmms-1.2/lmms/INDEX |only lmms-1.3/lmms/DESCRIPTION | 33 - lmms-1.3/lmms/MD5 | 61 +- lmms-1.3/lmms/NAMESPACE | 17 lmms-1.3/lmms/R/AllClasses.R | 23 - lmms-1.3/lmms/R/deriv.lmmspline-method.R | 15 lmms-1.3/lmms/R/filterNoise-method.R | 14 lmms-1.3/lmms/R/investNoise-method.R | 7 lmms-1.3/lmms/R/lmmSpline-method.R | 184 ++++---- lmms-1.3/lmms/R/lmmsDE-method.R | 612 +++++++++++++++++++--------- lmms-1.3/lmms/R/plot.lmmsde-method.R | 204 +++++---- lmms-1.3/lmms/R/plot.lmmspline-method.R | 170 +++++-- lmms-1.3/lmms/R/predict.lmmspline-method.R | 27 + lmms-1.3/lmms/R/summary.lmmsde-methods.R | 25 + lmms-1.3/lmms/data/kidneySimTimeGroup.RData |binary lmms-1.3/lmms/man/deriv.lmmspline.Rd | 5 lmms-1.3/lmms/man/filterNoise-methods.Rd | 7 lmms-1.3/lmms/man/investNoise-methods.Rd | 9 lmms-1.3/lmms/man/lmmSpline-methods.Rd | 27 - lmms-1.3/lmms/man/lmms-class.Rd | 5 lmms-1.3/lmms/man/lmms-package.Rd | 4 lmms-1.3/lmms/man/lmmsDE-methods.Rd | 32 - lmms-1.3/lmms/man/lmmsde-class.Rd | 20 lmms-1.3/lmms/man/lmmspline-class.Rd | 9 lmms-1.3/lmms/man/noise-class.Rd | 3 lmms-1.3/lmms/man/plot.lmmsde.Rd | 15 lmms-1.3/lmms/man/plot.lmmspline.Rd | 30 + lmms-1.3/lmms/man/plot.noise.Rd | 3 lmms-1.3/lmms/man/predict.lmmspline.Rd | 5 lmms-1.3/lmms/man/summary.lmmsde.Rd | 3 lmms-1.3/lmms/man/summary.lmmspline.Rd | 3 lmms-1.3/lmms/man/summary.noise.Rd | 3 32 files changed, 1011 insertions(+), 564 deletions(-)
Title: Random Variate Generator for the GIG Distribution
Description:
Generator and density function for the
Generalized Inverse Gaussian (GIG) distribution.
Author: Josef Leydold and Wolfgang Hormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between GIGrvg versions 0.3 dated 2014-06-04 and 0.4 dated 2015-07-17
DESCRIPTION | 14 ++++++++------ MD5 | 8 ++++---- NEWS | 5 +++++ inst/doc/README | 2 +- man/GIGrvg-package.Rd | 4 ++-- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Extra Additive Terms for GAMLSS Models
Description: Interfaces for extra smooth functions including tensor products, neural networks and decision trees.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.add versions 4.3-3 dated 2015-02-03 and 4.3-4 dated 2015-07-17
DESCRIPTION | 14 ++++---- MD5 | 8 ++-- NAMESPACE | 97 +++++++++++++++++++++++++++++---------------------------- R/gam_gamlss.R | 2 + man/tr.Rd | 2 - 5 files changed, 65 insertions(+), 58 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.3.1 dated 2015-07-15 and 0.3.2 dated 2015-07-17
FCNN4R-0.3.1/FCNN4R/src/Makevars.include |only FCNN4R-0.3.2/FCNN4R/DESCRIPTION | 8 ++-- FCNN4R-0.3.2/FCNN4R/MD5 | 13 +++---- FCNN4R-0.3.2/FCNN4R/R/mlp_net.R | 4 +- FCNN4R-0.3.2/FCNN4R/man/mlp_net-MSE-gradients.Rd | 4 +- FCNN4R-0.3.2/FCNN4R/src/Makevars | 3 + FCNN4R-0.3.2/FCNN4R/src/Makevars.win | 3 + FCNN4R-0.3.2/FCNN4R/src/interface.cpp | 38 +++++++++++++++-------- 8 files changed, 45 insertions(+), 28 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
This package allows to specify such models, transparently calls a suitable
simulator, parses the results and calculates additional summary statistics.
It supports the simulators 'ms', 'msms' and 'scrm' and can simulate
finite-sites mutation models by combining the simulators with the program
'seq-gen'.
Author: Paul Staab [aut, cre, cph],
Dirk Metzler [ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.1.0 dated 2015-07-14 and 0.1.1 dated 2015-07-17
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 9 +++++++++ build/vignette.rds |binary inst/doc/abc.Rmd | 4 ++-- inst/doc/abc.html | 6 +++--- inst/doc/installation.Rmd | 14 +++++++------- inst/doc/installation.html | 6 +++--- inst/doc/introduction.Rmd | 2 +- inst/doc/introduction.html | 2 +- src/parse_seqgen_output.cpp | 4 ++++ tests/testthat/test-simulator-seqgen.R | 5 ++++- vignettes/abc.Rmd | 4 ++-- vignettes/installation.Rmd | 14 +++++++------- vignettes/introduction.Rmd | 2 +- 15 files changed, 62 insertions(+), 46 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.0 dated 2015-06-19 and 1.6.1 dated 2015-07-17
DESCRIPTION | 9 - MD5 | 271 +++++++++++++++--------------- NAMESPACE | 43 ++++ NEWS | 80 +++++---- R/allMissing.r | 4 R/anyMissing.r | 6 R/anyNaN.r |only R/assert.r | 4 R/checkAccess.r | 8 R/checkArray.r | 9 + R/checkAtomic.r | 9 + R/checkAtomicVector.r | 9 + R/checkCharacter.r | 9 + R/checkChoice.r | 11 + R/checkClass.r | 11 + R/checkComplex.r | 9 + R/checkCount.r | 11 + R/checkDataFrame.r | 21 +- R/checkDirectory.r | 11 + R/checkEnvironment.r | 11 + R/checkFactor.r | 9 + R/checkFile.r | 11 + R/checkFlag.r | 9 + R/checkFunction.r | 32 ++- R/checkInt.r | 11 + R/checkInteger.r | 9 + R/checkIntegerish.r | 9 + R/checkList.r | 13 + R/checkLogical.r | 9 + R/checkMatrix.r | 23 +- R/checkNamed.r | 9 + R/checkNames.r | 9 + R/checkNumber.r | 8 R/checkNumeric.r | 9 + R/checkPathForOutput.r | 11 + R/checkPercentage.r | 11 + R/checkScalar.r | 12 + R/checkScalarNA.r | 11 + R/checkSetEqual.r | 11 + R/checkString.r | 14 + R/checkSubset.r | 11 + R/checkVector.r | 9 + R/coalesce.r |only R/helper.r | 13 + R/qassert.r | 11 + R/qassertr.r | 15 + R/zzz.r | 9 - build/vignette.rds |binary inst/doc/checkmate.R | 26 ++ inst/doc/checkmate.Rmd | 52 +++++ inst/doc/checkmate.html | 91 +++++++--- man/anyMissing.Rd | 10 + man/anyNaN.Rd |only man/assert.Rd | 4 man/checkAccess.Rd | 20 +- man/checkArray.Rd | 50 ++++- man/checkAtomic.Rd | 88 +++++++--- man/checkAtomicVector.Rd | 57 ++++-- man/checkCharacter.Rd | 52 ++++- man/checkChoice.Rd | 21 +- man/checkClass.Rd | 15 + man/checkComplex.Rd | 50 ++++- man/checkCount.Rd | 35 ++- man/checkDataFrame.Rd | 68 +++++-- man/checkDirectory.Rd | 21 +- man/checkEnvironment.Rd | 52 ++++- man/checkFactor.Rd | 52 ++++- man/checkFile.Rd | 21 +- man/checkFlag.Rd | 34 ++- man/checkFunction.Rd | 59 ++++-- man/checkInt.Rd | 35 ++- man/checkInteger.Rd | 52 ++++- man/checkIntegerish.Rd | 54 ++++-- man/checkList.Rd | 51 ++++- man/checkLogical.Rd | 51 ++++- man/checkMatrix.Rd | 76 +++++--- man/checkNamed.Rd | 5 man/checkNames.Rd | 15 + man/checkNull.Rd | 5 man/checkNumber.Rd | 35 ++- man/checkNumeric.Rd | 52 ++++- man/checkPathForOutput.Rd | 23 ++ man/checkPercentage.Rd | 34 ++- man/checkScalar.Rd | 32 ++- man/checkScalarNA.Rd | 31 ++- man/checkSetEqual.Rd | 20 +- man/checkString.Rd | 32 ++- man/checkSubset.Rd | 23 ++ man/checkVector.Rd | 54 ++++-- man/coalesce.Rd |only man/qassert.Rd | 12 + man/qassertr.Rd | 16 + src/all_missing.c | 6 src/all_nchar.c | 7 src/any_infinite.c | 4 src/any_missing.c | 8 src/any_nan.c |only src/any_nan.h |only src/checks.c | 259 +++++++++++++++-------------- src/checks.h | 4 src/cmessages.c | 6 src/cmessages.h | 1 tests/testthat/helper.r | 8 tests/testthat/test_anyMissing.r | 13 + tests/testthat/test_anyNaN.r |only tests/testthat/test_checkArray.r | 4 tests/testthat/test_checkAtomic.r | 4 tests/testthat/test_checkAtomicVector.r | 4 tests/testthat/test_checkCharacter.r | 5 tests/testthat/test_checkChoice.R | 4 tests/testthat/test_checkClass.r | 4 tests/testthat/test_checkComplex.r | 8 tests/testthat/test_checkCount.r | 4 tests/testthat/test_checkDataFrame.r | 36 +++- tests/testthat/test_checkEnvironment.r | 4 tests/testthat/test_checkFactor.r | 4 tests/testthat/test_checkFilesystem.r | 14 - tests/testthat/test_checkFlag.r | 4 tests/testthat/test_checkFunction.r | 10 - tests/testthat/test_checkInt.r | 12 + tests/testthat/test_checkInteger.r | 11 + tests/testthat/test_checkIntegerish.r | 11 + tests/testthat/test_checkList.r | 4 tests/testthat/test_checkLogical.r | 4 tests/testthat/test_checkMatrix.r | 4 tests/testthat/test_checkNamed.r | 4 tests/testthat/test_checkNames.r | 4 tests/testthat/test_checkNull.r | 4 tests/testthat/test_checkNumber.r | 11 + tests/testthat/test_checkNumeric.r | 11 + tests/testthat/test_checkPercentage.r | 4 tests/testthat/test_checkScalar.r | 4 tests/testthat/test_checkScalarNA.r | 1 tests/testthat/test_checkSetEqual.r | 4 tests/testthat/test_checkString.r | 4 tests/testthat/test_checkSubset.r | 4 tests/testthat/test_checkVector.r | 4 tests/testthat/test_qtest.r | 281 ++++++++++++++++---------------- tests/testthat/test_qtestr.r | 32 ++- vignettes/checkmate.Rmd | 52 +++++ 140 files changed, 2376 insertions(+), 959 deletions(-)