Title: Modelization for Functional AutoRegressive Processes
Description: Modelizations and previsions functions for
Functional AutoRegressive processes using
nonparametric methods: functional kernel,
estimation of the covariance operator in
a subspace, ...
Author: Damon Julien <julien.damon@gmail.com>
Guillas Serge
Maintainer: Damon Julien <julien.damon@gmail.com>
Diff between far versions 0.6-4 dated 2014-12-08 and 0.6-5 dated 2015-07-20
far-0.6-4/far/INDEX |only far-0.6-5/far/DESCRIPTION | 20 +++++----- far-0.6-5/far/MD5 | 22 +++++------ far-0.6-5/far/NAMESPACE | 69 +++++++++++++++++------------------ far-0.6-5/far/R/far.R | 4 +- far-0.6-5/far/R/fdata.R | 4 +- far-0.6-5/far/R/invgen.R | 4 +- far-0.6-5/far/R/kerfon.R | 4 +- far-0.6-5/far/R/orthonormalization.R | 4 +- far-0.6-5/far/R/simul.R | 4 +- far-0.6-5/far/R/zzz.R | 4 +- far-0.6-5/far/README.md |only far-0.6-5/far/src/far.c | 2 - 13 files changed, 71 insertions(+), 70 deletions(-)
Title: Data Quality Visualization Tools for Partially Accruing Data
Description: Package for visualizing data quality of partially accruing data.
Author: Julie Eaton and Ian Painter
Maintainer: Julie Eaton <jreaton@uw.edu>
Diff between accrued versions 1.3 dated 2015-06-23 and 1.3.5 dated 2015-07-20
DESCRIPTION | 8 ++--- MD5 | 60 +++++++++++++++++++++---------------------- NAMESPACE | 5 ++- R/accruedErrors.R | 2 - R/asOf.R | 2 - R/barcode.R | 2 - R/data.accrued.R | 2 - R/lagHistogram.R | 2 - R/laggedTSarray.R | 2 - R/plot.accrued.R | 2 - R/summary.accrued.R | 2 - R/uploadPattern.R | 2 - man/accrued-package.Rd | 4 +- man/accruedDataExample.Rd | 2 - man/accruedDataILIExample.Rd | 2 - man/accruedErrors.Rd | 2 - man/asOf.Rd | 4 -- man/barcode.Rd | 8 ++--- man/data.accrued.Rd | 8 ++--- man/errorQuantileSummary.Rd | 2 - man/lagHistogram.Rd | 2 - man/laggedTSarray.Rd | 4 +- man/plot.accrued.Rd | 2 - man/plot.accruedErrors.Rd | 2 - man/plot.summary.accrued.Rd | 2 - man/print.accrued.Rd | 2 - man/print.summary.accrued.Rd | 2 - man/stackedUploadData.Rd | 2 - man/summary.accrued.Rd | 2 - man/summary.accruedErrors.Rd | 2 - man/uploadPattern.Rd | 2 - 31 files changed, 74 insertions(+), 73 deletions(-)
Title: Robust Tail Dependence Estimation
Description: Robust tail dependence estimation for bivariate models. This package is based on two papers by the authors:'Robust and bias-corrected estimation of the coefficient of tail dependence' and 'Robust and bias-corrected estimation of probabilities of extreme failure sets'. This work was supported by a research grant (VKR023480) from VILLUM FONDEN and an international project for scientific cooperation (PICS-6416).
Author: Christophe Dutang [aut, cre], Armelle Guillou [ctb], Yuri Goegebeur [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between RTDE versions 0.1-0 dated 2014-07-17 and 0.2-0 dated 2015-07-20
DESCRIPTION | 10 ++++------ MD5 | 14 +++++++------- NAMESPACE | 34 +++++++++++++++++++--------------- R/data-fit-probRTDE.R | 6 ++++-- inst/CITATION | 19 ++++++++----------- inst/NEWS | 5 +++++ man/Frank.Rd | 2 +- tests/test-FGM.R | 32 +++++++++++++++++++++++++------- 8 files changed, 73 insertions(+), 49 deletions(-)
Title: Analysis of Ontologies and Protein Domain Annotations
Description: There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dcGOR versions 1.0.4 dated 2014-12-03 and 1.0.5 dated 2015-07-20
DESCRIPTION | 16 - MD5 | 221 ++++++++++--------- NAMESPACE | 7 R/ClassMethod-dcGOR.r | 4 R/dcAlgo.r | 68 ++++-- R/dcAlgoPredict.r | 8 R/dcAlgoPredictGenome.r | 25 +- R/dcAlgoPredictMain.r | 31 ++ R/dcAlgoPredictPR.r |only R/dcAlgoPropagate.r | 376 ++++++++++++++++++++++------------ R/dcBuildAnno.r | 8 R/dcBuildInfoDataFrame.r | 2 R/dcBuildOnto.r | 4 R/dcDAGdomainSim.r | 16 - R/dcFunArgs.r | 17 + R/dcList2Matrix.r |only R/dcNaivePredict.r |only R/dcRDataLoader.r | 2 R/dcRWRpipeline.r | 38 +-- R/dcRWRpredict.r |only R/dcSparseMatrix.r | 21 + R/dcSupraBetter.r |only data/Ancestral_domainome.RData |binary data/InterPro.RData |binary data/InterPro2GOBP.RData |binary data/InterPro2GOCC.RData |binary data/InterPro2GOMF.RData |binary data/Pfam.RData |binary data/Pfam2GOBP.RData |binary data/Pfam2GOCC.RData |binary data/Pfam2GOMF.RData |binary data/Rfam.RData |binary data/Rfam2GOBP.RData |binary data/Rfam2GOCC.RData |binary data/Rfam2GOMF.RData |binary data/SCOP.fa.RData |binary data/SCOP.fa2DO.RData |binary data/SCOP.fa2GOBP.RData |binary data/SCOP.fa2GOCC.RData |binary data/SCOP.fa2GOMF.RData |binary data/SCOP.fa2HPMI.RData |binary data/SCOP.fa2HPON.RData |binary data/SCOP.fa2HPPA.RData |binary data/SCOP.fa2MP.RData |binary data/SCOP.sf.RData |binary data/SCOP.sf2DO.RData |binary data/SCOP.sf2GOBP.RData |binary data/SCOP.sf2GOCC.RData |binary data/SCOP.sf2GOMF.RData |binary data/SCOP.sf2HPMI.RData |binary data/SCOP.sf2HPON.RData |binary data/SCOP.sf2HPPA.RData |binary data/SCOP.sf2MP.RData |binary data/eTOL.RData |binary data/onto.DO.RData |binary data/onto.GOBP.RData |binary data/onto.GOCC.RData |binary data/onto.GOMF.RData |binary data/onto.HPMI.RData |binary data/onto.HPON.RData |binary data/onto.HPPA.RData |binary data/onto.MP.RData |binary inst/NEWS | 10 inst/staticdocs/INSTALLATIONs.md | 20 - inst/staticdocs/README.md | 2 inst/staticdocs/demo/AlgoPred.r |only inst/staticdocs/demo/List_demos.txt | 1 inst/staticdocs/docs.r | 7 inst/staticdocs/templates/footer.html | 2 man/AdjData-class.Rd | 3 man/Anno-class.Rd | 3 man/Anno-method.Rd | 3 man/AnnoData-class.Rd | 3 man/Cnetwork-class.Rd | 3 man/Cnetwork-method.Rd | 3 man/Coutput-class.Rd | 3 man/Coutput-method.Rd | 3 man/Dnetwork-class.Rd | 3 man/Dnetwork-method.Rd | 3 man/Eoutput-class.Rd | 3 man/Eoutput-method.Rd | 3 man/InfoDataFrame-class.Rd | 3 man/InfoDataFrame-method.Rd | 3 man/Onto-class.Rd | 3 man/Onto-method.Rd | 3 man/dcAlgo.Rd | 15 - man/dcAlgoPredict.Rd | 3 man/dcAlgoPredictGenome.Rd | 3 man/dcAlgoPredictMain.Rd | 3 man/dcAlgoPredictPR.Rd |only man/dcAlgoPropagate.Rd | 66 +++-- man/dcAncestralML.Rd | 3 man/dcAncestralMP.Rd | 3 man/dcBuildAnno.Rd | 3 man/dcBuildInfoDataFrame.Rd | 3 man/dcBuildOnto.Rd | 3 man/dcConverter.Rd | 3 man/dcDAGannotate.Rd | 3 man/dcDAGdomainSim.Rd | 3 man/dcDuplicated.Rd | 3 man/dcEnrichment.Rd | 3 man/dcFunArgs.Rd | 9 man/dcList2Matrix.Rd |only man/dcNaivePredict.Rd |only man/dcRDataLoader.Rd | 3 man/dcRWRpipeline.Rd | 3 man/dcRWRpredict.Rd |only man/dcSparseMatrix.Rd | 3 man/dcSplitArch.Rd | 3 man/dcSubtreeClade.Rd | 3 man/dcSubtreeTips.Rd | 3 man/dcSupraBetter.Rd |only man/dcTreeConnectivity.Rd | 3 man/onto.HPMI.Rd | 3 man/onto.HPON.Rd | 3 man/onto.HPPA.Rd | 3 man/visEnrichment.Rd | 3 117 files changed, 702 insertions(+), 414 deletions(-)
Title: Nearest Neighbor Observation Imputation and Evaluation Tools
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston <ncrookston.fs@gmail.com>
Diff between yaImpute versions 1.0-24 dated 2015-05-16 and 1.0-26 dated 2015-07-20
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 5 +++++ NEWS | 8 +++++++- data/MoscowMtStJoe.RData |binary data/TallyLake.RData |binary 6 files changed, 24 insertions(+), 12 deletions(-)
Title: Variance Component Analysis
Description: ANOVA-type estimation (prediction) of random effects in linear mixed models is implemented, following
Searle et al. 1991 (ANOVA for unbalanced data). For better performance the SWEEP-Operator is now implemented
for generating the ANOVA Type-1 error sum of squares. The primary objective of this package is to perform
Variance Component Analyses (VCA). This is a special type of analysis frequently used in verifying the
precision performance of diagnostics.
The Satterthwaite approximation of the total degrees of freedom and for individual variance components is
implemented. These are used in the Chi-Squared tests against a claimed value, and in the respective confidence intervals.
Satterthwaite's approximation of denominator degrees of freedom in t-/F-tests of fixed effects are also
available.
There are several functions for extracting, random effects, fixed effects, variance-covariance
matrices of random and fixed effects. Residuals (marginal, conditional) can be extracted as raw, standardized
and studentized residuals.
Additionally, plotting methods for residuals and random effects and a variability chart are available. The latter
is useful for visualizing the variability in sub-classes emerging from the experimental design.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.1.1 dated 2015-04-27 and 1.2 dated 2015-07-20
VCA-1.1.1/VCA/data/dataEP05A2_example.RData |only VCA-1.1.1/VCA/man/dataEP05A2_example.Rd |only VCA-1.1.1/VCA/man/solveMM.Rd |only VCA-1.2/VCA/DESCRIPTION | 33 VCA-1.2/VCA/MD5 | 113 +- VCA-1.2/VCA/NAMESPACE | 23 VCA-1.2/VCA/R/plot.R | 350 ++++++- VCA-1.2/VCA/R/vca.R | 1135 ++++++++++++++++++------ VCA-1.2/VCA/data/CA19_9.RData |only VCA-1.2/VCA/data/Glucose.RData |only VCA-1.2/VCA/data/sleepstudy.RData |only VCA-1.2/VCA/inst/ChangeLog.txt | 29 VCA-1.2/VCA/inst/UnitTests/runit.VCAinference.R | 84 + VCA-1.2/VCA/inst/UnitTests/runit.anovaMM.R | 11 VCA-1.2/VCA/inst/UnitTests/runit.anovaVCA.R | 74 + VCA-1.2/VCA/inst/UnitTests/runit.misc.R | 88 + VCA-1.2/VCA/man/CA19_9.Rd |only VCA-1.2/VCA/man/Csweep.Rd |only VCA-1.2/VCA/man/DfSattHelper.Rd | 15 VCA-1.2/VCA/man/Glucose.Rd |only VCA-1.2/VCA/man/MPinv.Rd | 15 VCA-1.2/VCA/man/SattDF.Rd | 47 VCA-1.2/VCA/man/Sinv.Rd |only VCA-1.2/VCA/man/Solve.Rd |only VCA-1.2/VCA/man/Trace.Rd | 7 VCA-1.2/VCA/man/VCA-Package.Rd | 4 VCA-1.2/VCA/man/VCAinference.Rd | 246 ++--- VCA-1.2/VCA/man/anovaDF.Rd | 68 - VCA-1.2/VCA/man/anovaMM.Rd | 188 +-- VCA-1.2/VCA/man/anovaVCA.Rd | 247 ++--- VCA-1.2/VCA/man/as.matrix.VCA.Rd | 12 VCA-1.2/VCA/man/buildList.Rd | 101 -- VCA-1.2/VCA/man/coef.VCA.Rd | 14 VCA-1.2/VCA/man/fixef.Rd | 12 VCA-1.2/VCA/man/fixef.VCA.Rd | 52 - VCA-1.2/VCA/man/getAmatrix.Rd | 29 VCA-1.2/VCA/man/getCmatrix.Rd | 94 - VCA-1.2/VCA/man/getDDFM.Rd | 57 - VCA-1.2/VCA/man/getDF.Rd | 33 VCA-1.2/VCA/man/getL.Rd | 36 VCA-1.2/VCA/man/getMM.Rd | 30 VCA-1.2/VCA/man/getMat.Rd | 22 VCA-1.2/VCA/man/getSSQqf.Rd |only VCA-1.2/VCA/man/getSSQsweep.Rd |only VCA-1.2/VCA/man/getV.Rd | 27 VCA-1.2/VCA/man/getVCvar.Rd | 40 VCA-1.2/VCA/man/isBalanced.Rd | 53 - VCA-1.2/VCA/man/lsmMat.Rd | 28 VCA-1.2/VCA/man/lsmeans.Rd | 78 - VCA-1.2/VCA/man/plotRandVar.Rd | 86 - VCA-1.2/VCA/man/print.VCA.Rd | 14 VCA-1.2/VCA/man/print.VCAinference.Rd | 36 VCA-1.2/VCA/man/ranef.Rd | 12 VCA-1.2/VCA/man/ranef.VCA.Rd | 53 - VCA-1.2/VCA/man/residuals.VCA.Rd | 98 -- VCA-1.2/VCA/man/sleepstudy.Rd |only VCA-1.2/VCA/man/solveMME.Rd |only VCA-1.2/VCA/man/stepwiseVCA.Rd | 61 - VCA-1.2/VCA/man/test.fixef.Rd | 109 -- VCA-1.2/VCA/man/test.lsmeans.Rd | 35 VCA-1.2/VCA/man/varPlot.Rd | 311 ++---- VCA-1.2/VCA/man/vcov.VCA.Rd | 28 VCA-1.2/VCA/man/vcovFixed.Rd | 24 VCA-1.2/VCA/man/vcovVC.Rd | 51 - VCA-1.2/VCA/src/vca.c | 381 +++++++- 65 files changed, 2972 insertions(+), 1822 deletions(-)
Title: Tsallis q-Exp Distribution
Description: Tsallis distribution also known as the q-exponential family distribution. Provide distribution d, p, q, r functions, fitting and testing functions. Project initiated by Paul Higbie and based on Cosma Shalizi's code.
Author: Cosma Shalizi [aut] (original R code), Christophe Dutang [cre] (R code packaging)
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between tsallisqexp versions 0.9-1 dated 2015-03-17 and 0.9-2 dated 2015-07-20
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 5 +++-- build/vignette.rds |binary inst/CITATION | 24 ++++++++++++------------ inst/NEWS | 8 +++++++- inst/doc/qexpfamily.pdf |binary 7 files changed, 31 insertions(+), 24 deletions(-)
Title: SBML Integration in Package Sybil
Description: SBML (Systems Biology Markup Language) integration in sybil. Many constraint based metabolic models are published in SBML format (*.xml). Herewith is the ability to read and check SBML files in sybil provided.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut, ctb],
Deya Alzoubi [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybilSBML versions 2.0.8 dated 2014-05-21 and 2.0.10 dated 2015-07-20
DESCRIPTION | 22 ++++++++-------- LICENSE |only MD5 | 52 +++++++++++++++++++------------------- README.md |only build/vignette.rds |binary inst/NEWS.Rd | 7 +++++ inst/doc/sybilSBML.pdf |binary man/closeSBMLfile.Rd | 7 ++++- man/delSBMLmodel.Rd | 7 ++++- man/getSBMLCompartList.Rd | 7 ++++- man/getSBMLReactionsList.Rd | 7 ++++- man/getSBMLSpeciesList.Rd | 7 ++++- man/getSBMLerrors.Rd | 7 ++++- man/getSBMLlevel.Rd | 7 ++++- man/getSBMLmodId.Rd | 7 ++++- man/getSBMLmodName.Rd | 7 ++++- man/getSBMLmodel.Rd | 7 ++++- man/getSBMLnumCompart.Rd | 7 ++++- man/getSBMLnumReactions.Rd | 7 ++++- man/getSBMLnumSpecies.Rd | 7 ++++- man/getSBMLunitDefinitionsList.Rd | 7 ++++- man/getSBMLversion.Rd | 7 ++++- man/openSBMLfile.Rd | 7 ++++- man/readSBMLmod.Rd | 5 ++- man/sbmlError-class.Rd | 7 ++++- man/sbmlPtr-class.Rd | 7 ++++- man/validateSBMLdocument.Rd | 7 ++++- man/versionLibSBML.Rd | 7 ++++- 28 files changed, 170 insertions(+), 56 deletions(-)
Title: Simple GUI for Graph Based Visualization of Cluster of DNA
Sequence Reads
Description: The SeqGrapheR package provide interactive GUI for visualization of DNA sequence clusters. Details and principles of usage are described in user manual and (2010 BMC Bioinformatics 11:378). For full functionality installed NCBI blast is required.
Author: Petr Novak
Maintainer: Petr Novak <petr@umbr.cas.cz>
Diff between SeqGrapheR versions 0.4.8.3 dated 2013-08-19 and 0.4.8.5 dated 2015-07-20
DESCRIPTION | 15 ++++---- MD5 | 10 ++--- NAMESPACE | 61 ++++++++++++++++++++--------------- R/SeqGrapheR.R | 79 ++++++++++++++++++++++++++++++++-------------- man/SeqGrapheR-package.Rd | 15 ++++---- man/SeqGrapheR.Rd | 14 ++++---- 6 files changed, 117 insertions(+), 77 deletions(-)
Title: Side Effect Risks in Hospital : Simulation and Estimation
Description: Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.
Author: Christophe Dutang and Julie Barthes
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between rhosp versions 1.06 dated 2014-12-05 and 1.07 dated 2015-07-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 14 ++++++++++---- build/vignette.rds |binary inst/CITATION | 6 +++--- 5 files changed, 20 insertions(+), 14 deletions(-)
Title: Reverse-Correlation Image-Classification Toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments (psychophysical tasks aimed at visualizing cognitive mental representations of faces).
Author: Ron Dotsch <rdotsch@gmail.com>
Maintainer: Ron Dotsch <rdotsch@gmail.com>
Diff between rcicr versions 0.3.0 dated 2015-01-23 and 0.3.2 dated 2015-07-20
ChangeLog | 32 +++ DESCRIPTION | 18 +- MD5 | 35 ++-- NAMESPACE | 14 + R/rcicr.R | 293 +++++++++++++++++++++++++++++++++- R/rcicr_2IFC.R | 132 +++------------ R/rcicr_simulations.R | 13 + man/autoscale.Rd | 7 man/batchGenerateCI.Rd |only man/batchGenerateCI2IFC.Rd | 13 + man/computeCumulativeCICorrelation.Rd |only man/generateCI.Rd | 52 ++++-- man/generateCI2IFC.Rd | 10 - man/generateCINoise.Rd |only man/generateNoiseImage.Rd | 9 - man/generateNoisePattern.Rd | 3 man/generateSinusoid.Rd | 3 man/generateStimuli2IFC.Rd | 3 man/rcicr-package.Rd | 8 man/simulateNoiseIntensities.Rd | 5 20 files changed, 482 insertions(+), 168 deletions(-)
Title: Principal Tensor Analysis on k Modes
Description: A multiway method to decompose a tensor (array) of any order, as a generalisation of SVD also supporting non-identity metrics and penalisations. 2-way SVD with these extensions is also available. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these extensions.
Author: Didier G. Leibovici <didier.leibovici@nottingham.ac.uk>
Maintainer: Didier G. Leibovici <c3s2i@free.fr>
Diff between PTAk versions 1.2-9 dated 2014-08-17 and 1.2-12 dated 2015-07-20
PTAk-1.2-12/PTAk/DESCRIPTION | 15 ++++++++------- PTAk-1.2-12/PTAk/MD5 | 9 ++++----- PTAk-1.2-12/PTAk/NAMESPACE | 12 +++++++----- PTAk-1.2-12/PTAk/inst/CITATION | 6 +++--- PTAk-1.2-12/PTAk/inst/doc/index.html | 10 +++++----- PTAk-1.2-9/PTAk/inst/doc/citation.html |only 6 files changed, 27 insertions(+), 25 deletions(-)
Title: Vignette Engine Wrapping IPython Notebooks
Description:
Calls the 'Jupyter'/'IPython' script 'nbconvert' to create vignettes from notebooks.
Those notebooks ('.ipynb' files) are files containing rich text, code, and its output.
Code cells can be edited and evaluated interactively.
See <http://ipython.org/notebook.html> for more information.
Author: Philipp Angerer
Maintainer: Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>
Diff between nbconvertR versions 1.0.1 dated 2015-07-08 and 1.0.2 dated 2015-07-20
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS |only R/nbconvertR.r | 26 ++++++++++++++++++++++---- inst/doc/test-vignette.pdf |binary 5 files changed, 29 insertions(+), 10 deletions(-)
Title: The Gumbel-Hougaard Copula
Description: Provides probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).
Author: Anne-Lise Caillat [ctb], Christophe Dutang [aut,cre], Veronique Larrieu [ctb] and Triet Nguyen [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between gumbel versions 1.05 dated 2014-12-05 and 1.10-1 dated 2015-07-20
gumbel-1.05/gumbel/vignettes/img |only gumbel-1.10-1/gumbel/DESCRIPTION | 12 +- gumbel-1.10-1/gumbel/MD5 | 29 ++--- gumbel-1.10-1/gumbel/NAMESPACE | 4 gumbel-1.10-1/gumbel/R/gumbel.R | 2 gumbel-1.10-1/gumbel/build/vignette.rds |binary gumbel-1.10-1/gumbel/data/windEchirolles.rda |binary gumbel-1.10-1/gumbel/data/windStMartin.rda |binary gumbel-1.10-1/gumbel/inst/CITATION | 9 - gumbel-1.10-1/gumbel/inst/doc/gumbel.Rnw | 93 ++++++++---------- gumbel-1.10-1/gumbel/inst/doc/gumbel.pdf |binary gumbel-1.10-1/gumbel/vignettes/gumbel-concordance.tex |only gumbel-1.10-1/gumbel/vignettes/gumbel.Rnw | 93 ++++++++---------- gumbel-1.10-1/gumbel/vignettes/gumbel.tex |only 14 files changed, 115 insertions(+), 127 deletions(-)
Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut],
Bas Kempen [ctb],
Gerard Heuvelink [ctb],
Brendan Malone [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between GSIF versions 0.4-6 dated 2015-05-11 and 0.4-7 dated 2015-07-20
DESCRIPTION | 10 +++--- MD5 | 40 ++++++++++++++------------ NAMESPACE | 52 ++++++++++++++++++---------------- R/AAAA.R | 69 ++++++++++++++++++++++++---------------------- R/MaxEnt.R | 2 - R/TT2tri.R | 4 +- R/WPSworldgrids.R | 6 ++-- R/as.geosamples.R | 2 - R/fit.gstatModel.R | 41 ++++++++++++++++----------- R/fit.regModel.R | 14 ++++----- R/fit.vgmModel.R | 3 +- R/merge.R | 34 +++++++++++----------- R/predict.gstatModel.R | 27 +++++++++--------- R/sample.grid.R |only R/spc.R | 4 +- man/MaxEnt.Rd | 3 +- man/fit.gstatModel.Rd | 16 +++++----- man/fit.regModel.Rd | 7 ++-- man/fit.vgmModel.Rd | 2 - man/predict.gstatModel.Rd | 4 +- man/sample.grid.Rd |only man/spline.krige.Rd | 2 - 22 files changed, 180 insertions(+), 162 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria. Optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between GNE versions 0.99-0 dated 2014-07-31 and 0.99-1 dated 2015-07-20
DESCRIPTION | 11 +++++------ MD5 | 17 +++++++++-------- NAMESPACE | 5 +++++ build/vignette.rds |binary inst/NEWS | 6 ++++++ inst/TODOlist.txt | 2 ++ inst/doc/GNE-howto.Rnw | 11 +---------- inst/doc/GNE-howto.pdf |binary man/eqsolve.depr.Rd |only vignettes/GNE-howto.Rnw | 11 +---------- 10 files changed, 29 insertions(+), 34 deletions(-)
Title: Predicting and Forecasting Time Series via GMDH-Type Neural
Network Algorithms
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to predict and forecast a univariate time series.
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH versions 1.0 dated 2014-11-25 and 1.1 dated 2015-07-20
DESCRIPTION | 11 ++++--- MD5 | 12 ++++---- NAMESPACE | 13 +++++++- R/fcast.R | 87 ++++++++++++++++++++++++++++++++++++++++++++++------------ man/GMDH.Rd | 7 +--- man/cancer.Rd | 2 - man/fcast.Rd | 10 +++--- 7 files changed, 100 insertions(+), 42 deletions(-)
Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and
where to focus code optimization, using Amdahl's law and visual aids
based on line profiling. Amdahl's profiler organises profiling output
files (planned inclusion of memory profiling in the next major release)
in a visually appealing way. It is meant to help to balance development
vs. execution time by helping to identify the most promising sections
of code to optimize and projecting potential gains. The package is
an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>
Diff between aprof versions 0.2.4 dated 2014-11-20 and 0.2.5 dated 2015-07-20
DESCRIPTION | 25 +- MD5 | 23 +- NAMESPACE | 2 R/aprof.R | 461 +++++++++++++++++++++++++------------------------ inst |only man/aprof.Rd | 15 + man/is.aprof.Rd | 3 man/plot.Rd | 11 - man/print.Rd | 3 man/profileplot.Rd | 3 man/readLineDensity.Rd | 3 man/summary.Rd | 3 man/targetedSummary.Rd | 3 13 files changed, 292 insertions(+), 263 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.5.5 dated 2015-07-16 and 1.5.6 dated 2015-07-20
DESCRIPTION | 6 +-- MD5 | 12 +++--- src/data_frame.h | 18 ---------- src/extptr.h | 33 +++++++++--------- src/grange.h | 5 +- src/gtf.h | 60 ++++++++++++++++----------------- src/tokenize.h | 99 +++++++++++++++++++++++++++---------------------------- 7 files changed, 107 insertions(+), 126 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using MCMC.
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between bsts versions 0.6.1 dated 2014-12-04 and 0.6.2 dated 2015-07-20
bsts-0.6.1/bsts/R/plot_dynamic_distribution.R |only bsts-0.6.1/bsts/man/PlotDynamicDistribution.Rd |only bsts-0.6.1/bsts/man/plot.seasonal.effect.Rd |only bsts-0.6.2/bsts/DESCRIPTION | 9 - bsts-0.6.2/bsts/MD5 | 36 ++-- bsts-0.6.2/bsts/NAMESPACE | 12 + bsts-0.6.2/bsts/R/add.seasonal.R | 8 - bsts-0.6.2/bsts/R/bsts.R | 178 ++++++++++++++--------- bsts-0.6.2/bsts/R/compare.bsts.models.R | 3 bsts-0.6.2/bsts/R/mixed.frequency.R | 46 ++--- bsts-0.6.2/bsts/R/plot.dynamic.distribution.R |only bsts-0.6.2/bsts/R/plot_seasonal_effect.R | 57 ++++--- bsts-0.6.2/bsts/data/iclaims.RData |only bsts-0.6.2/bsts/man/bsts.Rd | 13 + bsts-0.6.2/bsts/man/iclaims.Rd |only bsts-0.6.2/bsts/man/plot.bsts.Rd | 35 ++++ bsts-0.6.2/bsts/man/plot.bsts.mixed.Rd | 4 bsts-0.6.2/bsts/man/plot.bsts.prediction.Rd | 10 - bsts-0.6.2/bsts/man/plot.bsts.predictors.Rd | 2 bsts-0.6.2/bsts/man/plot.dynamic.distribution.Rd |only bsts-0.6.2/bsts/man/residuals.bsts.Rd |only bsts-0.6.2/bsts/src/btlm.cc | 4 bsts-0.6.2/bsts/src/state_space.cc | 1 23 files changed, 272 insertions(+), 146 deletions(-)
Title: R Version of GENetic Optimization Using Derivatives
Description: A genetic algorithm plus derivative optimizer.
Author: Walter R. Mebane, Jr. <wmebane@umich.edu>,
Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Maintainer: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Diff between rgenoud versions 5.7-12 dated 2013-06-28 and 5.7-12.4 dated 2015-07-20
rgenoud-5.7-12.4/rgenoud/ChangeLog | 12 +++++ rgenoud-5.7-12.4/rgenoud/DESCRIPTION | 19 ++++--- rgenoud-5.7-12.4/rgenoud/MD5 | 20 ++++---- rgenoud-5.7-12.4/rgenoud/R/rgenoud.R | 60 +++++++++++++++---------- rgenoud-5.7-12.4/rgenoud/R/zzz.R | 4 - rgenoud-5.7-12.4/rgenoud/build |only rgenoud-5.7-12.4/rgenoud/inst/doc/Figures |only rgenoud-5.7-12.4/rgenoud/inst/doc/rgenoud.bib |only rgenoud-5.7-12.4/rgenoud/inst/doc/rgenoud.pdf |binary rgenoud-5.7-12.4/rgenoud/tests/tests.R | 2 rgenoud-5.7-12.4/rgenoud/tests/tests.Rout.save | 19 ++----- rgenoud-5.7-12/rgenoud/COPYING |only rgenoud-5.7-12/rgenoud/COPYRIGHTS |only 13 files changed, 77 insertions(+), 59 deletions(-)
Title: Person Fit
Description: Several person-fit statistics (PFSs) are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro <j.n.tendeiro@rug.nl>
Diff between PerFit versions 1.3.1 dated 2015-03-18 and 1.4 dated 2015-07-20
DESCRIPTION | 17 +--- MD5 | 100 +++++++++++------------ NAMESPACE | 2 R/ADE.R | 46 +++++++--- R/Accessory.R | 113 +++++++++++++++----------- R/C.Sato.R | 19 ++-- R/Cstar.R | 24 ++++- R/Cutoff.R | 36 ++++---- R/Flagged.R | 26 +++--- R/G.R | 15 +-- R/Gnormed.R | 18 ++-- R/Gnormedpoly.R | 94 ++++++++++++++++------ R/Gpoly.R | 14 +-- R/Hotdeck.R | 24 ++--- R/Ht.R | 25 +++-- R/MissingValues.R | 8 + R/NCI.R | 20 ++-- R/NPModel.R | 27 +++--- R/NPModelPoly.R | 32 +++---- R/PModel.R | 12 +- R/PModelPoly.R | 10 +- R/PRF.R | 70 +++++++++------- R/PerFitPFS.R | 180 +++++++++++++++++++++--------------------- R/PerFitSE.R | 15 +-- R/PlotPerFit.R | 38 ++++---- R/SanityChecks.R | 40 ++++----- R/SummaryPerFit.R | 2 R/U3.R | 36 ++++++-- R/U3poly.R | 119 +++++++++++++++++++++------- R/ZU3.R | 41 +++++++-- R/lz.R | 14 +-- R/lzpoly.R | 18 +--- R/lzstar.R | 29 +++--- R/rpbis.R | 7 - data/InadequacyData.RData |binary data/IntelligenceData.RData |binary data/PhysFuncData.RData |binary man/ADE.KB.Rd | 10 +- man/C.index.Rd | 184 +++++++++++++++++++++---------------------- man/G.Rd | 186 ++++++++++++++++++++++---------------------- man/Gpoly.Rd | 180 +++++++++++++++++++++--------------------- man/Ht.Rd | 172 ++++++++++++++++++++-------------------- man/NCI.Rd | 160 ++++++++++++++++++------------------- man/PRFplot.Rd | 8 - man/PerFit-package.Rd | 11 ++ man/PerFitPFS.Rd | 4 man/U3.Rd | 186 ++++++++++++++++++++++---------------------- man/U3poly.Rd | 6 - man/lz.Rd | 8 - man/lzpoly.Rd | 164 +++++++++++++++++++------------------- man/r.pbis.Rd | 146 +++++++++++++++++----------------- 51 files changed, 1472 insertions(+), 1244 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.5 dated 2015-06-26 and 1.2.7 dated 2015-07-20
DESCRIPTION | 10 ++-- MD5 | 14 +++--- NAMESPACE | 11 ++++ NEWS | 9 +++ R/Utilities.R | 93 +++++++++++++++++++++++++++++++++++++---- R/user_functions.R | 7 +-- src/icenReg_files/ic_par.cpp | 10 ++-- src/icenReg_files/ic_sp_ch.cpp | 8 +-- 8 files changed, 131 insertions(+), 31 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: Maximum likelihood estimators are obtained via an EM algorithm.
Author: Andrew Karl, Yan Yang, and Sharon Lohr
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.0-2 dated 2014-06-22 and 3.0-3 dated 2015-07-20
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 6 +++++- NEWS | 3 +++ man/GPvam-package.Rd | 4 ++-- man/GPvam.Rd | 7 ++++--- man/plot.Rd | 11 ++++++++--- 7 files changed, 36 insertions(+), 23 deletions(-)
Title: Generalized Least Squares with Measurement Error
Description: Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between GLSME versions 1.0.2 dated 2014-08-20 and 1.0.3 dated 2015-07-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 11 ++++++----- R/GLSME.R | 6 +++++- 4 files changed, 18 insertions(+), 13 deletions(-)