Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and techniques used in the
field of pedometrics.
Author: Alessandro Samuel-Rosa [aut, cre],
Lúcia Anjos [ths],
Gustavo Vasques [ths],
Gerard Heuvelink [ths],
Tony Olsen [ctb],
Tom Kincaid [ctb],
Juan Carlos Ruiz Cuetos [ctb],
Maria Eugenia Polo Garcia [ctb],
Pablo Garcia Rodriguez [ctb],
Joshua French [ctb],
Ken Kleinman [ctb],
Dick Brus [ctb],
Frank Harrell Jr [ctb],
Ruo Xu [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.6-5 dated 2015-12-01 and 0.6-6 dated 2015-12-03
DESCRIPTION | 13 +++-- MD5 | 12 ++--- R/AAAA.R | 1 R/pedometrics.R | 4 - R/vgmICP.R | 105 +++++++++++++++++++++++---------------------- man/pedometrics-package.Rd | 4 - man/vgmICP.Rd | 46 +++++++++++-------- 7 files changed, 100 insertions(+), 85 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.4.6 dated 2015-09-21 and 0.5.0 dated 2015-12-03
Luminescence-0.4.6/Luminescence/R/readBIN2R.R |only Luminescence-0.4.6/Luminescence/R/readSPE2R.R |only Luminescence-0.4.6/Luminescence/R/readXSYG2R.R |only Luminescence-0.4.6/Luminescence/R/writeR2BIN.R |only Luminescence-0.4.6/Luminescence/man/readBIN2R.Rd |only Luminescence-0.4.6/Luminescence/man/readSPE2R.Rd |only Luminescence-0.4.6/Luminescence/man/readXSYG2R.Rd |only Luminescence-0.4.6/Luminescence/man/writeR2BIN.Rd |only Luminescence-0.5.0/Luminescence/DESCRIPTION | 53 Luminescence-0.5.0/Luminescence/MD5 | 351 +- Luminescence-0.5.0/Luminescence/NAMESPACE | 170 Luminescence-0.5.0/Luminescence/NEWS | 648 +++ Luminescence-0.5.0/Luminescence/R/Analyse_SAR.OSLdata.R | 87 Luminescence-0.5.0/Luminescence/R/CW2pHMi.R | 2 Luminescence-0.5.0/Luminescence/R/CW2pLM.R | 2 Luminescence-0.5.0/Luminescence/R/CW2pLMi.R | 2 Luminescence-0.5.0/Luminescence/R/CW2pPMi.R | 2 Luminescence-0.5.0/Luminescence/R/Luminescence-package.R | 41 Luminescence-0.5.0/Luminescence/R/RLum-class.R | 53 Luminescence-0.5.0/Luminescence/R/RLum.Analysis-class.R | 473 +- Luminescence-0.5.0/Luminescence/R/RLum.Data-class.R | 8 Luminescence-0.5.0/Luminescence/R/RLum.Data.Curve-class.R | 273 + Luminescence-0.5.0/Luminescence/R/RLum.Data.Image-class.R | 205 - Luminescence-0.5.0/Luminescence/R/RLum.Data.Spectrum-class.R | 250 - Luminescence-0.5.0/Luminescence/R/RLum.Results-class.R | 598 +-- Luminescence-0.5.0/Luminescence/R/RcppExports.R | 4 Luminescence-0.5.0/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 180 - Luminescence-0.5.0/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 82 Luminescence-0.5.0/Luminescence/R/RisoeBINfileData-class.R | 28 Luminescence-0.5.0/Luminescence/R/Second2Gray.R | 74 Luminescence-0.5.0/Luminescence/R/analyse_IRSAR.RF.R | 363 +- Luminescence-0.5.0/Luminescence/R/analyse_SAR.CWOSL.R | 1750 ++++++---- Luminescence-0.5.0/Luminescence/R/analyse_SAR.TL.R | 35 Luminescence-0.5.0/Luminescence/R/analyse_pIRIRSequence.R | 292 + Luminescence-0.5.0/Luminescence/R/apply_CosmicRayRemoval.R | 2 Luminescence-0.5.0/Luminescence/R/apply_EfficiencyCorrection.R | 2 Luminescence-0.5.0/Luminescence/R/calc_AliquotSize.R | 2 Luminescence-0.5.0/Luminescence/R/calc_CentralDose.R | 304 - Luminescence-0.5.0/Luminescence/R/calc_CommonDose.R | 1 Luminescence-0.5.0/Luminescence/R/calc_CosmicDoseRate.R | 2 Luminescence-0.5.0/Luminescence/R/calc_FadingCorr.R | 2 Luminescence-0.5.0/Luminescence/R/calc_FiniteMixture.R | 1 Luminescence-0.5.0/Luminescence/R/calc_FuchsLang2001.R | 2 Luminescence-0.5.0/Luminescence/R/calc_HomogeneityTest.R | 1 Luminescence-0.5.0/Luminescence/R/calc_IEU.R | 2 Luminescence-0.5.0/Luminescence/R/calc_MaxDose.R | 4 Luminescence-0.5.0/Luminescence/R/calc_MinDose.R | 2 Luminescence-0.5.0/Luminescence/R/calc_OSLLxTxRatio.R | 208 - Luminescence-0.5.0/Luminescence/R/calc_SourceDoseRate.R | 71 Luminescence-0.5.0/Luminescence/R/calc_Statistics.R | 55 Luminescence-0.5.0/Luminescence/R/calc_TLLxTxRatio.R | 4 Luminescence-0.5.0/Luminescence/R/calc_gSGC.R |only Luminescence-0.5.0/Luminescence/R/extract_IrradiationTimes.R | 24 Luminescence-0.5.0/Luminescence/R/fit_CWCurve.R | 2 Luminescence-0.5.0/Luminescence/R/fit_LMCurve.R | 249 - Luminescence-0.5.0/Luminescence/R/get_Layout.R | 1 Luminescence-0.5.0/Luminescence/R/get_Quote.R | 39 Luminescence-0.5.0/Luminescence/R/get_RLum.R | 67 Luminescence-0.5.0/Luminescence/R/get_Risoe.BINfileData.R | 12 Luminescence-0.5.0/Luminescence/R/get_rightAnswer.R |only Luminescence-0.5.0/Luminescence/R/internal_as.latex.table.R |only Luminescence-0.5.0/Luminescence/R/internals_RLum.R |only Luminescence-0.5.0/Luminescence/R/length_RLum.R | 6 Luminescence-0.5.0/Luminescence/R/merge_RLum.Analysis.R | 3 Luminescence-0.5.0/Luminescence/R/merge_RLum.Data.Curve.R | 10 Luminescence-0.5.0/Luminescence/R/merge_RLum.R | 134 Luminescence-0.5.0/Luminescence/R/merge_RLum.Results.R |only Luminescence-0.5.0/Luminescence/R/merge_Risoe.BINfileData.R | 22 Luminescence-0.5.0/Luminescence/R/methods_DRAC.R |only Luminescence-0.5.0/Luminescence/R/methods_RLum.R |only Luminescence-0.5.0/Luminescence/R/names_RLum.R |only Luminescence-0.5.0/Luminescence/R/plot_AbanicoPlot.R | 214 - Luminescence-0.5.0/Luminescence/R/plot_DRTResults.R | 55 Luminescence-0.5.0/Luminescence/R/plot_GrowthCurve.R | 788 +++- Luminescence-0.5.0/Luminescence/R/plot_Histogram.R | 1 Luminescence-0.5.0/Luminescence/R/plot_KDE.R | 1 Luminescence-0.5.0/Luminescence/R/plot_NRt.R |only Luminescence-0.5.0/Luminescence/R/plot_RLum.Analysis.R | 142 Luminescence-0.5.0/Luminescence/R/plot_RLum.Data.Curve.R | 10 Luminescence-0.5.0/Luminescence/R/plot_RLum.Data.Image.R | 4 Luminescence-0.5.0/Luminescence/R/plot_RLum.Data.Spectrum.R | 48 Luminescence-0.5.0/Luminescence/R/plot_RLum.R | 72 Luminescence-0.5.0/Luminescence/R/plot_RLum.Results.R | 222 - Luminescence-0.5.0/Luminescence/R/plot_RadialPlot.R | 1 Luminescence-0.5.0/Luminescence/R/plot_Risoe.BINfileData.R | 10 Luminescence-0.5.0/Luminescence/R/plot_ViolinPlot.R |only Luminescence-0.5.0/Luminescence/R/read_BIN2R.R |only Luminescence-0.5.0/Luminescence/R/read_Daybreak2R.R |only Luminescence-0.5.0/Luminescence/R/read_SPE2R.R |only Luminescence-0.5.0/Luminescence/R/read_XSYG2R.R |only Luminescence-0.5.0/Luminescence/R/replicate_RLum.R |only Luminescence-0.5.0/Luminescence/R/set_RLum.R | 112 Luminescence-0.5.0/Luminescence/R/set_Risoe.BINfileData.R | 6 Luminescence-0.5.0/Luminescence/R/structure_RLum.R | 13 Luminescence-0.5.0/Luminescence/R/template_DRAC.R |only Luminescence-0.5.0/Luminescence/R/tune_Data.R |only Luminescence-0.5.0/Luminescence/R/use_DRAC.R |only Luminescence-0.5.0/Luminescence/R/write_R2BIN.R |only Luminescence-0.5.0/Luminescence/R/zzz.R | 7 Luminescence-0.5.0/Luminescence/inst/CITATION | 22 Luminescence-0.5.0/Luminescence/inst/NEWS.Rd | 552 +++ Luminescence-0.5.0/Luminescence/inst/doc/S4classObjects.pdf |binary Luminescence-0.5.0/Luminescence/man/Analyse_SAR.OSLdata.Rd | 28 Luminescence-0.5.0/Luminescence/man/BaseDataSet.CosmicDoseRate.Rd | 3 Luminescence-0.5.0/Luminescence/man/CW2pHMi.Rd | 8 Luminescence-0.5.0/Luminescence/man/CW2pLM.Rd | 8 Luminescence-0.5.0/Luminescence/man/CW2pLMi.Rd | 8 Luminescence-0.5.0/Luminescence/man/CW2pPMi.Rd | 8 Luminescence-0.5.0/Luminescence/man/ExampleData.BINfileData.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.CW_OSL_Curve.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.DeValues.Rd | 99 Luminescence-0.5.0/Luminescence/man/ExampleData.FittingLM.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.LxTxData.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.LxTxOSLData.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.RLum.Analysis.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.RLum.Data.Image.Rd | 6 Luminescence-0.5.0/Luminescence/man/ExampleData.XSYG.Rd | 8 Luminescence-0.5.0/Luminescence/man/Luminescence-package.Rd | 21 Luminescence-0.5.0/Luminescence/man/RLum-class.Rd | 30 Luminescence-0.5.0/Luminescence/man/RLum.Analysis-class.Rd | 117 Luminescence-0.5.0/Luminescence/man/RLum.Data-class.Rd | 6 Luminescence-0.5.0/Luminescence/man/RLum.Data.Curve-class.Rd | 83 Luminescence-0.5.0/Luminescence/man/RLum.Data.Image-class.Rd | 77 Luminescence-0.5.0/Luminescence/man/RLum.Data.Spectrum-class.Rd | 88 Luminescence-0.5.0/Luminescence/man/RLum.Results-class.Rd | 107 Luminescence-0.5.0/Luminescence/man/Risoe.BINfileData-class.Rd | 25 Luminescence-0.5.0/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 30 Luminescence-0.5.0/Luminescence/man/Risoe.BINfileData2RLum.Data.Curve.Rd | 18 Luminescence-0.5.0/Luminescence/man/Second2Gray.Rd | 54 Luminescence-0.5.0/Luminescence/man/analyse_IRSAR.RF.Rd | 58 Luminescence-0.5.0/Luminescence/man/analyse_SAR.CWOSL.Rd | 60 Luminescence-0.5.0/Luminescence/man/analyse_SAR.TL.Rd | 11 Luminescence-0.5.0/Luminescence/man/analyse_pIRIRSequence.Rd | 78 Luminescence-0.5.0/Luminescence/man/apply_CosmicRayRemoval.Rd | 7 Luminescence-0.5.0/Luminescence/man/apply_EfficiencyCorrection.Rd | 7 Luminescence-0.5.0/Luminescence/man/as.Rd |only Luminescence-0.5.0/Luminescence/man/calc_AliquotSize.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_CentralDose.Rd | 24 Luminescence-0.5.0/Luminescence/man/calc_CommonDose.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_CosmicDoseRate.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_FadingCorr.Rd | 5 Luminescence-0.5.0/Luminescence/man/calc_FiniteMixture.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_FuchsLang2001.Rd | 7 Luminescence-0.5.0/Luminescence/man/calc_HomogeneityTest.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_IEU.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_MaxDose.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_MinDose.Rd | 7 Luminescence-0.5.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 84 Luminescence-0.5.0/Luminescence/man/calc_SourceDoseRate.Rd | 60 Luminescence-0.5.0/Luminescence/man/calc_Statistics.Rd | 11 Luminescence-0.5.0/Luminescence/man/calc_TLLxTxRatio.Rd | 9 Luminescence-0.5.0/Luminescence/man/calc_gSGC.Rd |only Luminescence-0.5.0/Luminescence/man/extract_IrradiationTimes.Rd | 21 Luminescence-0.5.0/Luminescence/man/fit_CWCurve.Rd | 7 Luminescence-0.5.0/Luminescence/man/fit_LMCurve.Rd | 84 Luminescence-0.5.0/Luminescence/man/get_Layout.Rd | 6 Luminescence-0.5.0/Luminescence/man/get_Quote.Rd | 6 Luminescence-0.5.0/Luminescence/man/get_RLum.Rd | 21 Luminescence-0.5.0/Luminescence/man/get_Risoe.BINfileData.Rd | 6 Luminescence-0.5.0/Luminescence/man/get_rightAnswer.Rd |only Luminescence-0.5.0/Luminescence/man/length_RLum.Rd | 4 Luminescence-0.5.0/Luminescence/man/merge_RLum.Analysis.Rd | 7 Luminescence-0.5.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 14 Luminescence-0.5.0/Luminescence/man/merge_RLum.Rd | 15 Luminescence-0.5.0/Luminescence/man/merge_RLum.Results.Rd | 39 Luminescence-0.5.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 12 Luminescence-0.5.0/Luminescence/man/methods_RLum.Rd |only Luminescence-0.5.0/Luminescence/man/names_RLum.Rd |only Luminescence-0.5.0/Luminescence/man/plot_AbanicoPlot.Rd | 20 Luminescence-0.5.0/Luminescence/man/plot_DRTResults.Rd | 7 Luminescence-0.5.0/Luminescence/man/plot_GrowthCurve.Rd | 92 Luminescence-0.5.0/Luminescence/man/plot_Histogram.Rd | 23 Luminescence-0.5.0/Luminescence/man/plot_KDE.Rd | 22 Luminescence-0.5.0/Luminescence/man/plot_NRt.Rd |only Luminescence-0.5.0/Luminescence/man/plot_RLum.Analysis.Rd | 29 Luminescence-0.5.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 8 Luminescence-0.5.0/Luminescence/man/plot_RLum.Data.Image.Rd | 9 Luminescence-0.5.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 33 Luminescence-0.5.0/Luminescence/man/plot_RLum.Rd | 13 Luminescence-0.5.0/Luminescence/man/plot_RLum.Results.Rd | 17 Luminescence-0.5.0/Luminescence/man/plot_RadialPlot.Rd | 6 Luminescence-0.5.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 15 Luminescence-0.5.0/Luminescence/man/plot_ViolinPlot.Rd |only Luminescence-0.5.0/Luminescence/man/read_BIN2R.Rd |only Luminescence-0.5.0/Luminescence/man/read_Daybreak2R.Rd |only Luminescence-0.5.0/Luminescence/man/read_SPE2R.Rd |only Luminescence-0.5.0/Luminescence/man/read_XSYG2R.Rd |only Luminescence-0.5.0/Luminescence/man/replicate_RLum.Rd |only Luminescence-0.5.0/Luminescence/man/sTeve.Rd | 4 Luminescence-0.5.0/Luminescence/man/set_RLum.Rd | 44 Luminescence-0.5.0/Luminescence/man/set_Risoe.BINfileData.Rd | 4 Luminescence-0.5.0/Luminescence/man/structure_RLum.Rd | 10 Luminescence-0.5.0/Luminescence/man/template_DRAC.Rd |only Luminescence-0.5.0/Luminescence/man/tune_Data.Rd |only Luminescence-0.5.0/Luminescence/man/use_DRAC.Rd |only Luminescence-0.5.0/Luminescence/man/write_R2BIN.Rd |only Luminescence-0.5.0/Luminescence/src/RcppExports.cpp | 8 Luminescence-0.5.0/Luminescence/src/analyse_IRSARRF_SRS.cpp | 47 198 files changed, 7925 insertions(+), 3594 deletions(-)
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.6 include: (1) So far mutations had been assigned to maximal one subpopulation. However mutations may not be exclusive to the assigned subpopulation but may also be present in smaller, descending subpopulations. Whether or not this is the case is now decided by leveraging the predicted phylogenetic structure of the subpopulation composition. (2) Included homozygous deletion as potential scenario when modeling (SNV,CNV) pairs with overlapping genomic location, that are propagated during distinct clonal expansions. (3) Optimized solution to improve sensitivity at cell-frequency distribution margins. Need for improvement was because subpopulation detection sensitivity correlates to centrality of subpopulation size during clustering. Tolerance of copy number and allele frequency measurement errors must be higher for marginal cell-frequencies than for central cell-frequencies, in order to counteract the reduced cluster detection sensitivity at the cell-frequency distribution margins. This is only relevant during subpopulation detection (SNV clustering), cell-frequency independent error tolerance still applies during SNV assignment. (4) Fixed a bug where incorrect data matrix conversion could occur when handing non-numerical matrix as parameter to function runExPANdS(). Further documentation and FAQ around this package is available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.6 dated 2015-11-02 and 1.6.1 dated 2015-12-03
DESCRIPTION | 12 ++++----- MD5 | 20 ++++++++-------- R/assignQuantityToSP.R | 56 +++++++++++++++++++++++++++++++++------------- R/buildMultiSamplePhylo.R | 6 ++++ R/buildPhylo.R | 40 +++++++++----------------------- R/runExPANdS.R | 11 ++++++--- inst/doc/expands.R | 2 - inst/doc/expands.Rnw | 2 - inst/doc/expands.pdf |binary man/assignQuantityToSP.Rd | 6 ++-- vignettes/expands.Rnw | 2 - 11 files changed, 88 insertions(+), 69 deletions(-)
Title: Dynamic Models in Epidemiology
Description: Mathematical models of infectious diseases in humans and animals.
Both, deterministic and stochastic models can be simulated and plotted.
Author: Oswaldo Santos Baquero [aut, cre],
Fernando Silveira Marques [aut]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>
Diff between EpiDynamics versions 0.2 dated 2014-08-21 and 0.3.0 dated 2015-12-03
DESCRIPTION | 13 +++---- MD5 | 68 ++++++++++++++++++++------------------ NAMESPACE | 14 ++++++- NEWS | 7 +++ R/EpiDynamics-package.R | 11 +++--- R/SIR.R | 2 - R/SIR2Stages.R |only R/SISPairwiseApprox.R |only man/EpiDynamics-package.Rd | 9 ++--- man/MultiStrainPartialImmunity.Rd | 8 ++-- man/PlotMods.Rd | 16 +++++--- man/SEIR.Rd | 3 + man/SEIR4AgeClasses.Rd | 10 +++-- man/SEIRnStages.Rd | 7 ++- man/SIR.Rd | 6 ++- man/SIR2Stages.Rd |only man/SIR2TypesImports.Rd | 4 +- man/SIRAdditiveNoise.Rd | 4 +- man/SIRBirthDeath.Rd | 6 ++- man/SIRCarrierState.Rd | 8 ++-- man/SIRDemogStoch.Rd | 6 ++- man/SIRInducedMortality.Rd | 8 ++-- man/SIRInducedMortality2.Rd | 7 ++- man/SIRPartialImmunity.Rd | 10 +++-- man/SIRScaledAdditiveNoise.Rd | 8 ++-- man/SIRSinusoidalBirth.Rd | 8 ++-- man/SIRSinusoidalForcing.Rd | 12 +++--- man/SIRTauLeap.Rd | 4 +- man/SIRTermTimeForcing.Rd | 5 +- man/SIRVector.Rd | 10 +++-- man/SIS.Rd | 4 +- man/SIS2RiskGroups.Rd | 4 +- man/SISDemogStoch.Rd | 4 +- man/SISPairwiseApprox.Rd |only man/SISinusoidalTransmBrith.Rd | 4 +- man/SISnRiskGroups.Rd | 10 +++-- man/sir2AgeClasses.Rd | 6 ++- 37 files changed, 190 insertions(+), 116 deletions(-)
Title: Autoregressive Conditional Poisson
Description: Analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).
Author: Siakoulis Vasileios
Maintainer: Siakoulis Vasilios <Siakoulis.Vasilios@atticabank.gr>
Diff between acp versions 2.0 dated 2015-05-22 and 2.1 dated 2015-12-03
DESCRIPTION | 8 +++---- MD5 | 8 +++---- NAMESPACE | 5 +++- R/acp.R | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++--------- man/acp.Rd | 5 ++++ 5 files changed, 71 insertions(+), 18 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.200.2.0 dated 2015-10-31 and 0.6.300.2.0 dated 2015-12-03
ChangeLog | 25 DESCRIPTION | 8 MD5 | 124 +- inst/NEWS.Rd | 17 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloAs.h | 88 ++ inst/include/armadillo_bits/Base_bones.hpp | 6 inst/include/armadillo_bits/Base_meat.hpp | 100 +- inst/include/armadillo_bits/Cube_bones.hpp | 8 inst/include/armadillo_bits/Cube_meat.hpp | 31 inst/include/armadillo_bits/Mat_bones.hpp | 8 inst/include/armadillo_bits/Mat_meat.hpp | 35 inst/include/armadillo_bits/Proxy.hpp | 39 inst/include/armadillo_bits/arma_forward.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/auxlib_bones.hpp | 41 inst/include/armadillo_bits/auxlib_meat.hpp | 828 +++++++++++++++----- inst/include/armadillo_bits/compiler_setup.hpp | 8 inst/include/armadillo_bits/def_lapack.hpp | 99 ++ inst/include/armadillo_bits/def_superlu.hpp | 5 inst/include/armadillo_bits/diagview_meat.hpp | 12 inst/include/armadillo_bits/diskio_bones.hpp | 9 inst/include/armadillo_bits/diskio_meat.hpp | 132 --- inst/include/armadillo_bits/fft_engine.hpp | 2 inst/include/armadillo_bits/field_bones.hpp | 17 inst/include/armadillo_bits/field_meat.hpp | 210 ++++- inst/include/armadillo_bits/fn_cond.hpp | 14 inst/include/armadillo_bits/fn_det.hpp | 152 --- inst/include/armadillo_bits/fn_eig_gen.hpp | 32 inst/include/armadillo_bits/fn_inv.hpp | 195 +++- inst/include/armadillo_bits/fn_solve.hpp | 223 +++-- inst/include/armadillo_bits/fn_spsolve.hpp | 28 inst/include/armadillo_bits/glue_solve_bones.hpp | 68 + inst/include/armadillo_bits/glue_solve_meat.hpp | 184 +++- inst/include/armadillo_bits/glue_times_meat.hpp | 27 inst/include/armadillo_bits/include_superlu.hpp | 15 inst/include/armadillo_bits/memory.hpp | 14 inst/include/armadillo_bits/op_inv_bones.hpp | 4 inst/include/armadillo_bits/op_inv_meat.hpp | 8 inst/include/armadillo_bits/op_symmat_meat.hpp | 4 inst/include/armadillo_bits/op_trimat_meat.hpp | 6 inst/include/armadillo_bits/sp_auxlib_bones.hpp | 11 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 329 ++++++- inst/include/armadillo_bits/strip.hpp | 11 inst/include/armadillo_bits/subview_bones.hpp | 1 inst/include/armadillo_bits/subview_cube_bones.hpp | 1 inst/include/armadillo_bits/subview_cube_meat.hpp | 29 inst/include/armadillo_bits/subview_each_bones.hpp | 8 inst/include/armadillo_bits/subview_each_meat.hpp | 66 - inst/include/armadillo_bits/subview_elem1_meat.hpp | 2 inst/include/armadillo_bits/subview_elem2_meat.hpp | 2 inst/include/armadillo_bits/subview_field_bones.hpp | 5 inst/include/armadillo_bits/subview_field_meat.hpp | 63 + inst/include/armadillo_bits/subview_meat.hpp | 45 + inst/include/armadillo_bits/traits.hpp | 28 inst/include/armadillo_bits/typedef_elem.hpp | 24 inst/include/armadillo_bits/wall_clock_bones.hpp | 4 inst/include/armadillo_bits/wall_clock_meat.hpp | 8 inst/include/armadillo_bits/wrapper_blas.hpp | 4 inst/include/armadillo_bits/wrapper_lapack.hpp | 197 ++++ inst/include/armadillo_bits/wrapper_superlu.hpp | 46 + inst/unitTests/cpp/cube.cpp |only inst/unitTests/runit.cube.R |only 64 files changed, 2749 insertions(+), 969 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between pairwise versions 0.2.5 dated 2014-05-28 and 0.3.1 dated 2015-12-03
pairwise-0.2.5/pairwise/data/datalist |only pairwise-0.3.1/pairwise/DESCRIPTION | 22 - pairwise-0.3.1/pairwise/MD5 | 115 ++++--- pairwise-0.3.1/pairwise/NAMESPACE | 47 +++ pairwise-0.3.1/pairwise/NEWS | 31 ++ pairwise-0.3.1/pairwise/R/andersentest.pers.R |only pairwise-0.3.1/pairwise/R/grm.R | 28 + pairwise-0.3.1/pairwise/R/i.pvx.matrix.R | 5 pairwise-0.3.1/pairwise/R/i.pvx.super.R | 42 +- pairwise-0.3.1/pairwise/R/logLik.pers.R | 39 +- pairwise-0.3.1/pairwise/R/lrtest.pers.R |only pairwise-0.3.1/pairwise/R/pair.R | 59 +++ pairwise-0.3.1/pairwise/R/pairSE.R | 13 pairwise-0.3.1/pairwise/R/pairwise-package.r | 31 +- pairwise-0.3.1/pairwise/R/pairwise.item.fit.R | 2 pairwise-0.3.1/pairwise/R/pairwise.person.fit.R | 2 pairwise-0.3.1/pairwise/R/pers.R | 15 - pairwise-0.3.1/pairwise/R/plot.grm.R | 28 + pairwise-0.3.1/pairwise/R/plot.pair.R | 4 pairwise-0.3.1/pairwise/R/plot.pairSE.R | 33 +- pairwise-0.3.1/pairwise/R/plot.pers.R | 27 + pairwise-0.3.1/pairwise/R/plot.rfa.R | 5 pairwise-0.3.1/pairwise/R/simra.R |only pairwise-0.3.1/pairwise/R/summary.grm.R | 10 pairwise-0.3.1/pairwise/R/summary.pair.R | 7 pairwise-0.3.1/pairwise/R/summary.pairSE.R | 24 + pairwise-0.3.1/pairwise/R/summary.pairwise.item.fit.R |only pairwise-0.3.1/pairwise/R/summary.pairwise.person.fit.R |only pairwise-0.3.1/pairwise/R/summary.pers.R | 2 pairwise-0.3.1/pairwise/R/summary.rfa.R | 7 pairwise-0.3.1/pairwise/build/vignette.rds |binary pairwise-0.3.1/pairwise/data/bfi_cov.RData |only pairwise-0.3.1/pairwise/man/andersentest.pers.Rd |only pairwise-0.3.1/pairwise/man/bfiN.Rd | 33 +- pairwise-0.3.1/pairwise/man/bfiN_miss.Rd | 9 pairwise-0.3.1/pairwise/man/bfi_cov.Rd |only pairwise-0.3.1/pairwise/man/catprob.Rd | 31 -- pairwise-0.3.1/pairwise/man/esc.Rd | 35 -- pairwise-0.3.1/pairwise/man/ftab.Rd | 28 - pairwise-0.3.1/pairwise/man/gif.Rd | 39 -- pairwise-0.3.1/pairwise/man/grm.Rd | 142 ++------- pairwise-0.3.1/pairwise/man/iff.Rd | 66 +--- pairwise-0.3.1/pairwise/man/logLik.pers.Rd | 18 - pairwise-0.3.1/pairwise/man/lrtest.pers.Rd |only pairwise-0.3.1/pairwise/man/make.incidenz.Rd | 44 -- pairwise-0.3.1/pairwise/man/pair.Rd | 137 ++------- pairwise-0.3.1/pairwise/man/pairSE.Rd | 152 ++-------- pairwise-0.3.1/pairwise/man/pairwise-package.Rd | 192 +++---------- pairwise-0.3.1/pairwise/man/pairwise.item.fit.Rd | 38 -- pairwise-0.3.1/pairwise/man/pairwise.person.fit.Rd | 35 -- pairwise-0.3.1/pairwise/man/pers.Rd | 111 +------ pairwise-0.3.1/pairwise/man/plot.grm.Rd | 46 +-- pairwise-0.3.1/pairwise/man/plot.pair.Rd | 42 +- pairwise-0.3.1/pairwise/man/plot.pairSE.Rd | 46 +-- pairwise-0.3.1/pairwise/man/plot.pers.Rd | 43 +- pairwise-0.3.1/pairwise/man/plot.rfa.Rd | 41 +- pairwise-0.3.1/pairwise/man/ptbis.Rd | 25 - pairwise-0.3.1/pairwise/man/rfa.Rd | 84 +---- pairwise-0.3.1/pairwise/man/simra.Rd |only pairwise-0.3.1/pairwise/man/summary.grm.Rd |only pairwise-0.3.1/pairwise/man/summary.pair.Rd |only pairwise-0.3.1/pairwise/man/summary.pairSE.Rd |only pairwise-0.3.1/pairwise/man/summary.pairwise.item.fit.Rd |only pairwise-0.3.1/pairwise/man/summary.pairwise.person.fit.Rd |only pairwise-0.3.1/pairwise/man/summary.pers.Rd | 20 - pairwise-0.3.1/pairwise/man/summary.rfa.Rd |only pairwise-0.3.1/pairwise/man/tff.Rd | 67 +--- 67 files changed, 922 insertions(+), 1200 deletions(-)
Title: Streamlining Design and Deployment of Complex Workflows
Description: This framework allows you to design and implement complex
pipelines, and deploy them on your institution's computing cluster. This has
been built keeping in mind the needs of bioinformatics workflows. However, it is
easily extendable to any field where a series of steps (shell commands) are to
be executed in a (work)flow.
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between flowr versions 0.9.8.2 dated 2015-10-03 and 0.9.9.5 dated 2015-12-03
flowr-0.9.8.2/flowr/inst/scripts/flowr2 |only flowr-0.9.8.2/flowr/man/opts_flow.Rd |only flowr-0.9.8.2/flowr/tests/fastq_mutect_err1.def |only flowr-0.9.9.5/flowr/DESCRIPTION | 20 flowr-0.9.9.5/flowr/MD5 | 193 +- flowr-0.9.9.5/flowr/NAMESPACE | 6 flowr-0.9.9.5/flowr/NEWS.md | 87 + flowr-0.9.9.5/flowr/R/check-args.R | 4 flowr-0.9.9.5/flowr/R/check.R | 24 flowr-0.9.9.5/flowr/R/class-def.R | 10 flowr-0.9.9.5/flowr/R/conf.R | 45 flowr-0.9.9.5/flowr/R/errors.R | 4 flowr-0.9.9.5/flowr/R/fetch.r | 32 flowr-0.9.9.5/flowr/R/kill-flow.R | 2 flowr-0.9.9.5/flowr/R/limit_runs.R | 1 flowr-0.9.9.5/flowr/R/parse-jobids.R | 11 flowr-0.9.9.5/flowr/R/plot.R | 21 flowr-0.9.9.5/flowr/R/render-dependency.R | 9 flowr-0.9.9.5/flowr/R/rerun.R | 414 ++--- flowr-0.9.9.5/flowr/R/run.R | 84 - flowr-0.9.9.5/flowr/R/setup.R | 27 flowr-0.9.9.5/flowr/R/status.R | 39 flowr-0.9.9.5/flowr/R/submit-flow.R | 240 +-- flowr-0.9.9.5/flowr/R/submit-job.R | 6 flowr-0.9.9.5/flowr/R/submit-local.R | 2 flowr-0.9.9.5/flowr/R/to-flow.R | 780 +++++----- flowr-0.9.9.5/flowr/R/to-flowdef.R | 341 +++- flowr-0.9.9.5/flowr/R/to-flowdet.R | 2 flowr-0.9.9.5/flowr/R/to-flowmat.R | 49 flowr-0.9.9.5/flowr/R/verbose.R | 2 flowr-0.9.9.5/flowr/R/zz-db.R | 4 flowr-0.9.9.5/flowr/R/zz-parse-resources.R | 8 flowr-0.9.9.5/flowr/R/zzz.R | 4 flowr-0.9.9.5/flowr/README.md | 57 flowr-0.9.9.5/flowr/inst/CITATION |only flowr-0.9.9.5/flowr/inst/conf/flowr.conf | 14 flowr-0.9.9.5/flowr/inst/conf/local.sh | 3 flowr-0.9.9.5/flowr/inst/conf/lsf.sh | 3 flowr-0.9.9.5/flowr/inst/conf/moab.sh | 3 flowr-0.9.9.5/flowr/inst/conf/sge.sh | 3 flowr-0.9.9.5/flowr/inst/conf/slurm.sh | 3 flowr-0.9.9.5/flowr/inst/conf/torque.sh | 3 flowr-0.9.9.5/flowr/inst/conf/torque_comm.sh | 3 flowr-0.9.9.5/flowr/inst/doc/flowr_install.R | 15 flowr-0.9.9.5/flowr/inst/doc/flowr_install.Rmd | 96 + flowr-0.9.9.5/flowr/inst/doc/flowr_install.html | 103 - flowr-0.9.9.5/flowr/inst/doc/flowr_overview.R | 32 flowr-0.9.9.5/flowr/inst/doc/flowr_overview.Rmd | 148 - flowr-0.9.9.5/flowr/inst/doc/flowr_overview.html | 195 -- flowr-0.9.9.5/flowr/inst/doc/flowr_tutorial.R | 143 + flowr-0.9.9.5/flowr/inst/doc/flowr_tutorial.Rmd | 350 +++- flowr-0.9.9.5/flowr/inst/doc/flowr_tutorial.html | 408 +++-- flowr-0.9.9.5/flowr/inst/pipelines/README.md |only flowr-0.9.9.5/flowr/inst/pipelines/fastq_bam_bwa.R | 46 flowr-0.9.9.5/flowr/inst/pipelines/sleep_pipe.def | 8 flowr-0.9.9.5/flowr/inst/scripts/flowr | 377 ---- flowr-0.9.9.5/flowr/inst/scripts/flowr.v1 |only flowr-0.9.9.5/flowr/man/check.Rd | 44 flowr-0.9.9.5/flowr/man/check_args.Rd | 2 flowr-0.9.9.5/flowr/man/create_jobs_mat.Rd | 2 flowr-0.9.9.5/flowr/man/error.Rd | 2 flowr-0.9.9.5/flowr/man/fetch.Rd | 38 flowr-0.9.9.5/flowr/man/flow.Rd | 12 flowr-0.9.9.5/flowr/man/flowopts.Rd |only flowr-0.9.9.5/flowr/man/generate_flow_code.Rd | 2 flowr-0.9.9.5/flowr/man/get_unique_id.Rd | 2 flowr-0.9.9.5/flowr/man/get_wds.Rd | 2 flowr-0.9.9.5/flowr/man/job.Rd | 2 flowr-0.9.9.5/flowr/man/kill.Rd | 11 flowr-0.9.9.5/flowr/man/plot_flow.Rd | 10 flowr-0.9.9.5/flowr/man/queue.Rd | 2 flowr-0.9.9.5/flowr/man/replace_slots.Rd | 2 flowr-0.9.9.5/flowr/man/rerun.Rd | 26 flowr-0.9.9.5/flowr/man/run.Rd | 41 flowr-0.9.9.5/flowr/man/setup.Rd | 18 flowr-0.9.9.5/flowr/man/status.Rd | 18 flowr-0.9.9.5/flowr/man/submit_flow.Rd | 12 flowr-0.9.9.5/flowr/man/submit_job.Rd | 2 flowr-0.9.9.5/flowr/man/submit_run.Rd | 2 flowr-0.9.9.5/flowr/man/test_queue.Rd | 4 flowr-0.9.9.5/flowr/man/to_flow.Rd | 76 flowr-0.9.9.5/flowr/man/to_flowdef.Rd | 114 + flowr-0.9.9.5/flowr/man/to_flowdet.Rd | 4 flowr-0.9.9.5/flowr/man/to_flowmat.Rd | 45 flowr-0.9.9.5/flowr/man/verbose.Rd | 59 flowr-0.9.9.5/flowr/man/whisker_render.Rd | 6 flowr-0.9.9.5/flowr/man/write_flow_details.Rd | 2 flowr-0.9.9.5/flowr/tests/testthat.R | 2 flowr-0.9.9.5/flowr/tests/testthat/test-toflow.R | 10 flowr-0.9.9.5/flowr/vignettes/files/googl.js |only flowr-0.9.9.5/flowr/vignettes/files/logo.png |binary flowr-0.9.9.5/flowr/vignettes/files/logo_black.png |only flowr-0.9.9.5/flowr/vignettes/files/logo_blue.png |only flowr-0.9.9.5/flowr/vignettes/files/logo_green.png |only flowr-0.9.9.5/flowr/vignettes/files/logo_red.png |only flowr-0.9.9.5/flowr/vignettes/flowr_install.Rmd | 96 + flowr-0.9.9.5/flowr/vignettes/flowr_install.md |only flowr-0.9.9.5/flowr/vignettes/flowr_overview.Rmd | 148 - flowr-0.9.9.5/flowr/vignettes/flowr_overview_files/figure-html/plot_abcd-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_overview_files/figure-html/plot_one_one-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_overview_files/figure-html/plotit-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_tutorial.Rmd | 350 +++- flowr-0.9.9.5/flowr/vignettes/flowr_tutorial_files/figure-html/plot_skeleton_def-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_tutorial_files/figure-html/plot_tweaked_def-1.png |binary 104 files changed, 3209 insertions(+), 2443 deletions(-)
Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast
Clustering Using Adaptive Density Peak Detection). The work is built and
improved upon Rodriguez and Laio[2014]'s idea. ADPclust clusters data by finding
density peaks in a density-distance plot generated from local multivariate
Gaussian density estimation. It includes an automatic centroids selection and
parameter optimization algorithm, which finds the number of clusters and cluster
centroids by comparing average silhouettes on a grid of testing clustering
results; It also includes an user interactive algorithm that allows the user
to manually selects cluster centroids from a two dimensional "density-distance
plot".
Author: Yifan "Ethan" Xu [aut, cre],
Xiao-Feng Wang [aut]
Maintainer: Yifan "Ethan" Xu <ethan.yifanxu@gmail.com>
Diff between ADPclust versions 0.6.3 dated 2015-04-20 and 0.6.5 dated 2015-12-03
ADPclust-0.6.3/ADPclust/vignettes/ADPclust_files |only ADPclust-0.6.5/ADPclust/DESCRIPTION | 29 + ADPclust-0.6.5/ADPclust/MD5 | 60 +-- ADPclust-0.6.5/ADPclust/NAMESPACE | 6 ADPclust-0.6.5/ADPclust/R/ADPclust-package.r | 2 ADPclust-0.6.5/ADPclust/R/ADPclust.R | 67 ++- ADPclust-0.6.5/ADPclust/R/AMISE.R | 8 ADPclust-0.6.5/ADPclust/R/ROT.R | 15 ADPclust-0.6.5/ADPclust/R/findCluster.R | 10 ADPclust-0.6.5/ADPclust/R/findClusterAuto.R | 2 ADPclust-0.6.5/ADPclust/R/findFd.R | 8 ADPclust-0.6.5/ADPclust/R/plot.adpclust.R | 5 ADPclust-0.6.5/ADPclust/README.md |only ADPclust-0.6.5/ADPclust/build/vignette.rds |binary ADPclust-0.6.5/ADPclust/inst/CITATION |only ADPclust-0.6.5/ADPclust/inst/doc/ADPclust.R | 45 +- ADPclust-0.6.5/ADPclust/inst/doc/ADPclust.Rmd | 95 +++-- ADPclust-0.6.5/ADPclust/inst/doc/ADPclust.html | 410 +++++++---------------- ADPclust-0.6.5/ADPclust/man/ADPclust.Rd | 37 +- ADPclust-0.6.5/ADPclust/man/AMISE.Rd | 7 ADPclust-0.6.5/ADPclust/man/ROT.Rd | 7 ADPclust-0.6.5/ADPclust/man/clust10.Rd | 2 ADPclust-0.6.5/ADPclust/man/clust3.Rd | 2 ADPclust-0.6.5/ADPclust/man/clust5.1.Rd | 2 ADPclust-0.6.5/ADPclust/man/clust5.Rd | 2 ADPclust-0.6.5/ADPclust/man/dat_gene.Rd | 2 ADPclust-0.6.5/ADPclust/man/findCluster.Rd | 14 ADPclust-0.6.5/ADPclust/man/findClusterAuto.Rd | 6 ADPclust-0.6.5/ADPclust/man/findFd.Rd | 12 ADPclust-0.6.5/ADPclust/man/plot.adpclust.Rd | 2 ADPclust-0.6.5/ADPclust/man/summary.adpclust.Rd | 2 ADPclust-0.6.5/ADPclust/vignettes/ADPclust.Rmd | 95 +++-- 32 files changed, 467 insertions(+), 487 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.1 dated 2015-09-11 and 0.4.2 dated 2015-12-03
ChangeLog | 59 ++++++++++++++++ DESCRIPTION | 19 ++--- MD5 | 48 +++++++------ NAMESPACE | 123 ++++++++++++++++++----------------- R/RcppExports.R | 27 +++++++ R/bond.R | 4 - R/zzz.R | 22 +++++- README.md | 2 cleanup | 2 configure | 18 ++--- configure.ac | 2 inst/NEWS.Rd | 28 ++++++- inst/include/RQuantLib_RcppExports.h | 38 ++++++++++ inst/unitTests/runit.dates.R | 38 ++++++---- inst/unitTests/runit.options.R | 3 man/BondUtilities.Rd | 3 man/EuropeanOption.Rd | 8 +- man/getQuantLibCapabilities.Rd |only man/getQuantLibVersion.Rd |only src/RcppExports.cpp | 62 +++++++++++++++++ src/asian.cpp | 11 ++- src/barrier_binary.cpp | 31 ++++++++ src/implieds.cpp | 20 +++++ src/utils.cpp | 49 +++++++++++++ src/vanilla.cpp | 33 ++++++++- tests/doRUnit.R | 47 ++++++++----- 26 files changed, 540 insertions(+), 157 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtl versions 1.37-11 dated 2015-08-25 and 1.38-4 dated 2015-12-03
DESCRIPTION | 8 +- MD5 | 46 +++++++-------- R/arithscan.R | 133 --------------------------------------------- R/discan.R | 27 --------- R/read.cross.mm.R | 2 R/refineqtl.R | 7 +- R/scanone.R | 37 +----------- R/scantwo.R | 58 ------------------- R/summary.scanone.R | 111 ++----------------------------------- R/summary.scantwo.R | 69 +---------------------- R/vbscan.R | 27 --------- inst/INSTALL_ME.txt | 12 ++-- inst/README.md | 1 inst/STATUS.txt | 21 +++++++ inst/TODO.txt | 5 + inst/doc/rqtltour.pdf |binary man/max.scanone.Rd | 4 - man/max.scantwo.Rd | 12 +--- man/qtl-internal.Rd | 8 +- man/scanone.Rd | 44 +++++++------- man/summary.scanone.Rd | 18 ++---- man/summary.scanoneperm.Rd | 12 +--- man/summary.scantwo.Rd | 26 ++++---- man/summary.scantwoperm.Rd | 4 - 24 files changed, 145 insertions(+), 547 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.2 dated 2015-10-09 and 1.3 dated 2015-12-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/ChannelAttribution-package.Rd | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.2.1 dated 2015-06-04 and 1.2.2 dated 2015-12-03
ChangeLog | 4 - DESCRIPTION | 9 +- MD5 | 22 +++--- NAMESPACE | 4 + R/make_sglasso.R | 5 - R/sglasso.R | 6 - R/sglasso.fit.R | 16 +++- man/sglasso.Rd | 6 + src/sglasso_ccd_path.f90 | 148 +++++++++++++++++++++++---------------------- src/sglasso_ccd_single.f90 | 108 +++++++++++++++++--------------- src/sglasso_ccm_path.f90 | 71 ++++++++++++--------- src/sglasso_ccm_single.f90 | 46 ++++++++----- 12 files changed, 250 insertions(+), 195 deletions(-)
Title: Companion to the Forthcoming Book - R you Ready?
Description: Package contains some data and functions that
are used in my forthcoming "R you ready?" book.
Author: Mark Heckmann [aut, cre]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between ryouready versions 0.3 dated 2013-12-15 and 0.4 dated 2015-12-03
ryouready-0.3/ryouready/data/d.eta.txt |only ryouready-0.3/ryouready/data/d.ngo.txt |only ryouready-0.3/ryouready/data/d.superiority.txt |only ryouready-0.4/ryouready/DESCRIPTION | 24 ++--- ryouready-0.4/ryouready/MD5 | 67 ++++++++------- ryouready-0.4/ryouready/NAMESPACE | 11 ++ ryouready-0.4/ryouready/NEWS | 9 +- ryouready-0.4/ryouready/R/association_measures.r | 3 ryouready-0.4/ryouready/R/collapse_response_set.R | 23 +++-- ryouready-0.4/ryouready/R/qq-plot.R |only ryouready-0.4/ryouready/R/ryouready-package.r | 11 +- ryouready-0.4/ryouready/R/utils.r | 83 ++++++++++++++++++- ryouready-0.4/ryouready/README.md | 6 - ryouready-0.4/ryouready/data/d.eta.txt.gz |only ryouready-0.4/ryouready/data/d.ngo.txt.gz |only ryouready-0.4/ryouready/data/d.superiority.txt.gz |only ryouready-0.4/ryouready/inst |only ryouready-0.4/ryouready/man/collapse_responseset.Rd | 34 +++---- ryouready-0.4/ryouready/man/count_na.Rd |only ryouready-0.4/ryouready/man/d.eta.Rd | 5 - ryouready-0.4/ryouready/man/d.ngo.Rd | 10 +- ryouready-0.4/ryouready/man/d.superiority.Rd | 5 - ryouready-0.4/ryouready/man/eta.Rd | 25 ++--- ryouready-0.4/ryouready/man/foo.Rd | 14 +-- ryouready-0.4/ryouready/man/ggplot.qqnorm.spss.Rd |only ryouready-0.4/ryouready/man/intervals.Rd | 55 +++++------- ryouready-0.4/ryouready/man/nom.lambda.Rd | 24 ++--- ryouready-0.4/ryouready/man/nom.uncertainty.Rd | 27 ++---- ryouready-0.4/ryouready/man/ord.gamma.Rd | 16 ++- ryouready-0.4/ryouready/man/ord.somers.d.Rd | 24 ++--- ryouready-0.4/ryouready/man/ord.tau.Rd | 22 ++--- ryouready-0.4/ryouready/man/plot.qqnorm.spss.Rd |only ryouready-0.4/ryouready/man/print.nom.lambda.Rd | 12 +- ryouready-0.4/ryouready/man/print.nom.uncertainty.Rd | 12 +- ryouready-0.4/ryouready/man/print.ord.gamma.Rd | 12 +- ryouready-0.4/ryouready/man/print.ord.somersd.Rd | 12 +- ryouready-0.4/ryouready/man/print.ord.tau.Rd | 12 +- ryouready-0.4/ryouready/man/qqnorm_spss.Rd |only ryouready-0.4/ryouready/man/recode2.Rd |only ryouready-0.4/ryouready/man/rowMeans2.Rd | 45 ++++------ ryouready-0.4/ryouready/man/ryouready.Rd | 17 +-- 41 files changed, 366 insertions(+), 254 deletions(-)
Title: One-Way Independent Groups Design
Description: Two or more samples in one-way independent groups design are compared via different tests.
Author: Osman Dag, Anil Dolgun, N. Meric Konar
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 1.0 dated 2015-08-24 and 1.1 dated 2015-12-03
DESCRIPTION | 10 +++---- MD5 | 34 +++++++++++++------------- NAMESPACE | 2 - R/ag.test.R | 26 ++++++++++++++++++- R/aov.test.R | 26 ++++++++++++++++--- R/bf.test.R | 69 +++++++++++++++++++++++++---------------------------- R/james.test.R | 26 ++++++++++++++++--- R/kw.test.R | 29 +++++++++++++++++++--- R/mood.test.R | 31 +++++++++++++++++++---- R/welch.test.R | 41 +++++++++++++++++++------------ man/ag.test.Rd | 8 +++--- man/aov.test.Rd | 9 +++--- man/bf.test.Rd | 10 +++---- man/james.test.Rd | 11 +++----- man/kw.test.Rd | 9 +++--- man/mood.test.Rd | 9 +++--- man/onewaytests.Rd | 4 +-- man/welch.test.Rd | 11 +++----- 18 files changed, 233 insertions(+), 132 deletions(-)
Title: Joint Modelling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Description: Offers modelling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.
Author: Rudradev Sengupta, Nolen Joy Perualila
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
Diff between IntegratedJM versions 1.2 dated 2015-11-12 and 1.3 dated 2015-12-03
DESCRIPTION | 12 ++--- MD5 | 6 +- NEWS | 3 + R/Functions.R | 123 +++++++++++++++++++++++++++++----------------------------- 4 files changed, 75 insertions(+), 69 deletions(-)
Title: Simulation-Based Maximum Likelihood Parameter Estimation
Description: An estimation method that can use computer simulations to
approximate maximum-likelihood estimates even when the likelihood function can not
be evaluated directly. It can be applied whenever it is feasible to conduct many
simulations, but works best when the data is approximately Poisson distributed.
It was originally designed for demographic inference in evolutionary
biology. It has optional support for conducting coalescent simulation using
the 'coala' package.
Author: Paul Staab [aut, cre],
Lisha Mathew [aut],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between jaatha versions 2.7.0 dated 2014-11-26 and 3.0.0 dated 2015-12-03
jaatha-2.7.0/jaatha/NEWS |only jaatha-2.7.0/jaatha/R/RcppExports.R |only jaatha-2.7.0/jaatha/R/confidence_intervals.R |only jaatha-2.7.0/jaatha/R/demographic_model.R |only jaatha-2.7.0/jaatha/R/estimate_log_likelihood.R |only jaatha-2.7.0/jaatha/R/find_best_par_in_block.R |only jaatha-2.7.0/jaatha/R/helper_functions.R |only jaatha-2.7.0/jaatha/R/initial_search.R |only jaatha-2.7.0/jaatha/R/normalize.R |only jaatha-2.7.0/jaatha/R/package_info.R |only jaatha-2.7.0/jaatha/R/parallelization.R |only jaatha-2.7.0/jaatha/R/read_fasta.R |only jaatha-2.7.0/jaatha/R/refined_search.R |only jaatha-2.7.0/jaatha/R/run_simulations.R |only jaatha-2.7.0/jaatha/R/sim_likelihood.R |only jaatha-2.7.0/jaatha/R/sim_program.R |only jaatha-2.7.0/jaatha/R/sim_program_ms.R |only jaatha-2.7.0/jaatha/R/sim_program_msms.R |only jaatha-2.7.0/jaatha/R/sim_program_seqgen.R |only jaatha-2.7.0/jaatha/R/simulate_within_block.R |only jaatha-2.7.0/jaatha/R/sum_stat_fpc.R |only jaatha-2.7.0/jaatha/R/sum_stat_generate.R |only jaatha-2.7.0/jaatha/R/sum_stat_jsfs.R |only jaatha-2.7.0/jaatha/R/sum_stat_pmc.R |only jaatha-2.7.0/jaatha/inst/example_fasta_files |only jaatha-2.7.0/jaatha/man/Jaatha-class.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.confidenceIntervals.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.getCIsFromLogs.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.getLikelihoods.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.getStartingPoints.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.initialSearch.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.initialize.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.refinedSearch.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.setSeqgenExecutable.Rd |only jaatha-2.7.0/jaatha/man/addFeature.Rd |only jaatha-2.7.0/jaatha/man/calcJsfs.Rd |only jaatha-2.7.0/jaatha/man/calculateJsfs.Rd |only jaatha-2.7.0/jaatha/man/checkType.Rd |only jaatha-2.7.0/jaatha/man/convertSimResultsToDataFrame.Rd |only jaatha-2.7.0/jaatha/man/denormalize.Rd |only jaatha-2.7.0/jaatha/man/dm.addGrowth.Rd |only jaatha-2.7.0/jaatha/man/dm.addMigration.Rd |only jaatha-2.7.0/jaatha/man/dm.addMutation.Rd |only jaatha-2.7.0/jaatha/man/dm.addMutationRateHeterogenity.Rd |only jaatha-2.7.0/jaatha/man/dm.addOutgroup.Rd |only jaatha-2.7.0/jaatha/man/dm.addParameter.Rd |only jaatha-2.7.0/jaatha/man/dm.addRecombination.Rd |only jaatha-2.7.0/jaatha/man/dm.addSampleSize.Rd |only jaatha-2.7.0/jaatha/man/dm.addSizeChange.Rd |only jaatha-2.7.0/jaatha/man/dm.addSpeciationEvent.Rd |only jaatha-2.7.0/jaatha/man/dm.addSummaryStatistic.Rd |only jaatha-2.7.0/jaatha/man/dm.addSymmetricMigration.Rd |only jaatha-2.7.0/jaatha/man/dm.createDemographicModel.Rd |only jaatha-2.7.0/jaatha/man/dm.createThetaTauModel.Rd |only jaatha-2.7.0/jaatha/man/dm.getGroups.Rd |only jaatha-2.7.0/jaatha/man/dm.getLociLength.Rd |only jaatha-2.7.0/jaatha/man/dm.getLociNumber.Rd |only jaatha-2.7.0/jaatha/man/dm.setLociLength.Rd |only jaatha-2.7.0/jaatha/man/dm.setLociNumber.Rd |only jaatha-2.7.0/jaatha/man/dm.setMutationModel.Rd |only jaatha-2.7.0/jaatha/man/dm.simSumStats.Rd |only jaatha-2.7.0/jaatha/man/estimateLogLikelihood.Rd |only jaatha-2.7.0/jaatha/man/findBestParInBlock.Rd |only jaatha-2.7.0/jaatha/man/fitGlm.Rd |only jaatha-2.7.0/jaatha/man/fitGlmPoiTransformed.Rd |only jaatha-2.7.0/jaatha/man/fitPoiSmoothed.Rd |only jaatha-2.7.0/jaatha/man/normalize.Rd |only jaatha-2.7.0/jaatha/man/runSimulations.Rd |only jaatha-2.7.0/jaatha/man/setCores.Rd |only jaatha-2.7.0/jaatha/man/simulateWithinBlock.Rd |only jaatha-2.7.0/jaatha/src |only jaatha-2.7.0/jaatha/tests/integration |only jaatha-2.7.0/jaatha/tests/testthat/setup-custom-simulation-interface.R |only jaatha-2.7.0/jaatha/tests/testthat/setup-demographic-models.R |only jaatha-2.7.0/jaatha/tests/testthat/test-aaa-setup.R |only jaatha-2.7.0/jaatha/tests/testthat/test-calc-likelihood.R |only jaatha-2.7.0/jaatha/tests/testthat/test-confidence-intervals.R |only jaatha-2.7.0/jaatha/tests/testthat/test-demographic-model-class.R |only jaatha-2.7.0/jaatha/tests/testthat/test-estimate-likelihood.R |only jaatha-2.7.0/jaatha/tests/testthat/test-initial-search.R |only jaatha-2.7.0/jaatha/tests/testthat/test-jaatha-class.R |only jaatha-2.7.0/jaatha/tests/testthat/test-normalize.R |only jaatha-2.7.0/jaatha/tests/testthat/test-parse-ms-output.R |only jaatha-2.7.0/jaatha/tests/testthat/test-parse-seqgen-output.R |only jaatha-2.7.0/jaatha/tests/testthat/test-parse-trees.R |only jaatha-2.7.0/jaatha/tests/testthat/test-read-fasta.R |only jaatha-2.7.0/jaatha/tests/testthat/test-refined-search.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sim-likelihood.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sim-program.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simprog-ms.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simprog-msms.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simprog-seqgen.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simulate-within-block.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sumstat-fpc.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sumstat-jsfs.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sumstat-pmc.R |only jaatha-2.7.0/jaatha/tests/testthat/test-zzz-temp-files.R |only jaatha-3.0.0/jaatha/DESCRIPTION | 62 - jaatha-3.0.0/jaatha/MD5 | 171 +-- jaatha-3.0.0/jaatha/NAMESPACE | 66 - jaatha-3.0.0/jaatha/NEWS.md |only jaatha-3.0.0/jaatha/R/block.R | 143 +- jaatha-3.0.0/jaatha/R/boot_jaatha.R |only jaatha-3.0.0/jaatha/R/coala_interface.R |only jaatha-3.0.0/jaatha/R/fit_glm.R | 157 -- jaatha-3.0.0/jaatha/R/initialization.R |only jaatha-3.0.0/jaatha/R/jaatha.R | 525 +--------- jaatha-3.0.0/jaatha/R/jaatha_data.R |only jaatha-3.0.0/jaatha/R/jaatha_log.R |only jaatha-3.0.0/jaatha/R/jaatha_model.R |only jaatha-3.0.0/jaatha/R/likelihood.R |only jaatha-3.0.0/jaatha/R/par_ranges.R |only jaatha-3.0.0/jaatha/R/simulation_cache.R |only jaatha-3.0.0/jaatha/R/stat_basic.R |only jaatha-3.0.0/jaatha/R/stat_cube.R |only jaatha-3.0.0/jaatha/R/tools.R |only jaatha-3.0.0/jaatha/README.md | 101 + jaatha-3.0.0/jaatha/build |only jaatha-3.0.0/jaatha/inst/CITATION | 30 jaatha-3.0.0/jaatha/inst/doc |only jaatha-3.0.0/jaatha/man/boot_jaatha.Rd |only jaatha-3.0.0/jaatha/man/coarsen_jsfs.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_data.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_model.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_model.coalmodel.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_model.function.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_stat.Rd |only jaatha-3.0.0/jaatha/man/estimate_llh.Rd |only jaatha-3.0.0/jaatha/man/jaatha-package.Rd | 20 jaatha-3.0.0/jaatha/man/jaatha.Rd |only jaatha-3.0.0/jaatha/tests/testthat/test-block.R |only jaatha-3.0.0/jaatha/tests/testthat/test-coala-interface.R |only jaatha-3.0.0/jaatha/tests/testthat/test-fit-glm.R | 82 - jaatha-3.0.0/jaatha/tests/testthat/test-initialization.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-data.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-function.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-log.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-model.R |only jaatha-3.0.0/jaatha/tests/testthat/test-likelihood.R |only jaatha-3.0.0/jaatha/tests/testthat/test-par-ranges.R |only jaatha-3.0.0/jaatha/tests/testthat/test-sim-cache.R |only jaatha-3.0.0/jaatha/tests/testthat/test-stat-cubes.R |only jaatha-3.0.0/jaatha/tests/testthat/test-tools.R |only jaatha-3.0.0/jaatha/tests/testthat/test-zzz-bootstrapping.R |only jaatha-3.0.0/jaatha/vignettes |only 145 files changed, 428 insertions(+), 929 deletions(-)
Title: Tools for Autoregressive Conditional Duration Models
Description: Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.
Author: Markus Belfrage
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
Diff between ACDm versions 1.0.2 dated 2015-07-16 and 1.0.3 dated 2015-12-03
DESCRIPTION | 8 MD5 | 31 +-- R/computeDurations.R | 75 ++++--- R/diurnalAdj.R | 19 + R/plotHistAcd.R | 2 data/adjDurData.RData |binary data/durData.RData |binary inst/NEWS.Rd |only man/computeDurations.Rd | 10 - man/data.Rd | 2 man/diurnalAdj.Rd | 3 man/plotDescTrans.Rd | 4 man/plotHazard.Rd | 3 man/plotHistAcd.Rd | 3 man/plotScatterAcd.Rd | 4 man/resiDensityAcd.Rd | 8 src/computeDurations.c | 458 ++++++++++++++++++++++++------------------------ 17 files changed, 341 insertions(+), 289 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.2 dated 2015-10-19 and 1.6.5 dated 2015-12-03
TMB-1.6.2/TMB/inst/include/tmbutils/R_inla.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/array.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/autodiff.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/density.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/kronecker.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/matexp.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/order.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/romberg.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/splines.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/spmat.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils_extra.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/vector.cpp |only TMB-1.6.5/TMB/DESCRIPTION | 14 - TMB-1.6.5/TMB/MD5 | 122 +++++++------- TMB-1.6.5/TMB/NAMESPACE | 5 TMB-1.6.5/TMB/NEWS | 34 +++ TMB-1.6.5/TMB/R/TMB.R | 102 +++++++---- TMB-1.6.5/TMB/R/header_tool.R |only TMB-1.6.5/TMB/R/mcmc.R |only TMB-1.6.5/TMB/R/sdreport.R | 87 +++++++-- TMB-1.6.5/TMB/inst/COPYRIGHTS | 2 TMB-1.6.5/TMB/inst/examples/mcmc_examples.R |only TMB-1.6.5/TMB/inst/examples/simple.cpp | 5 TMB-1.6.5/TMB/inst/include/Rstream.hpp | 8 TMB-1.6.5/TMB/inst/include/TMB.hpp | 28 ++- TMB-1.6.5/TMB/inst/include/Vectorize.hpp | 114 ------------- TMB-1.6.5/TMB/inst/include/atomic_macro.hpp | 12 - TMB-1.6.5/TMB/inst/include/atomic_math.hpp | 9 - TMB-1.6.5/TMB/inst/include/checkpoint_macro.hpp | 6 TMB-1.6.5/TMB/inst/include/config.hpp | 25 +- TMB-1.6.5/TMB/inst/include/convenience.hpp | 24 ++ TMB-1.6.5/TMB/inst/include/convert.hpp | 33 +-- TMB-1.6.5/TMB/inst/include/cppad/local/ad_fun.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/for_jac_sweep.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/forward0sweep.hpp | 20 +- TMB-1.6.5/TMB/inst/include/cppad/local/forward1sweep.hpp | 16 - TMB-1.6.5/TMB/inst/include/cppad/local/forward2sweep.hpp | 20 +- TMB-1.6.5/TMB/inst/include/cppad/local/fun_construct.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/kasper.hpp | 28 +-- TMB-1.6.5/TMB/inst/include/cppad/local/near_equal_ext.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/optimize.hpp | 12 - TMB-1.6.5/TMB/inst/include/cppad/local/print_for.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/rev_hes_sweep.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/rev_jac_sweep.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/reverse.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/reverse_sweep.hpp | 20 +- TMB-1.6.5/TMB/inst/include/cppad/memory_leak.hpp | 17 - TMB-1.6.5/TMB/inst/include/cppad/near_equal.hpp | 7 TMB-1.6.5/TMB/inst/include/cppad/speed_test.hpp | 27 +-- TMB-1.6.5/TMB/inst/include/cppad/thread_alloc.hpp | 13 - TMB-1.6.5/TMB/inst/include/cppad/time_test.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/track_new_del.hpp | 41 ++-- TMB-1.6.5/TMB/inst/include/cppad/vector.hpp | 4 TMB-1.6.5/TMB/inst/include/precompile.hpp |only TMB-1.6.5/TMB/inst/include/start_parallel.hpp | 20 +- TMB-1.6.5/TMB/inst/include/tmb_core.hpp | 108 +++++++----- TMB-1.6.5/TMB/inst/include/tmbutils/R_inla.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/array.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/autodiff.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/density.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/kronecker.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/matexp.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/order.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/romberg.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/splines.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/spmat.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/tmbutils.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/tmbutils_extra.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/vector.hpp |only TMB-1.6.5/TMB/man/MakeADFun.Rd | 14 - TMB-1.6.5/TMB/man/compile.Rd | 2 TMB-1.6.5/TMB/man/mcmc.Rd |only TMB-1.6.5/TMB/man/mcmc.hmc.Rd |only TMB-1.6.5/TMB/man/mcmc.nuts.Rd |only TMB-1.6.5/TMB/man/mcmc.rwm.Rd |only TMB-1.6.5/TMB/man/precompile.Rd | 41 +++- TMB-1.6.5/TMB/man/sdreport.Rd | 54 +++++- TMB-1.6.5/TMB/man/summary.sdreport.Rd | 3 79 files changed, 638 insertions(+), 509 deletions(-)
Title: Software for the Analysis of Genetic Architecture
Description: Implements an information theory approach to the analysis of line
cross data providing model averaged results of parameter estimates and
unconditional standard errors. Also includes functions to provide a
visualization of models space, custom plots of multi-model inference results, and traditional
line cross analysis plots.
Author: Heath Blackmon and Jeffery P. Demuth
Maintainer: Heath Blackmon <coleoguy@gmail.com>
Diff between SAGA versions 1.0 dated 2015-09-07 and 2.0.0 dated 2015-12-03
SAGA-1.0/SAGA/inst/Cmatrix.mp.csv |only SAGA-1.0/SAGA/inst/doc/model-averaged-analysis.html |only SAGA-1.0/SAGA/vignettes/1.png |only SAGA-1.0/SAGA/vignettes/2.png |only SAGA-1.0/SAGA/vignettes/3.png |only SAGA-1.0/SAGA/vignettes/4.png |only SAGA-1.0/SAGA/vignettes/5.png |only SAGA-1.0/SAGA/vignettes/6.png |only SAGA-2.0.0/SAGA/DESCRIPTION | 15 SAGA-2.0.0/SAGA/MD5 | 43 - SAGA-2.0.0/SAGA/NAMESPACE | 12 SAGA-2.0.0/SAGA/R/AICtoMW.R |only SAGA-2.0.0/SAGA/R/AnalyzeCrossesMM.R | 151 ++++-- SAGA-2.0.0/SAGA/R/DisplayCmatrix.R | 15 SAGA-2.0.0/SAGA/R/cohortID.R |only SAGA-2.0.0/SAGA/R/plot.genarch.R |only SAGA-2.0.0/SAGA/R/plotObserved.R |only SAGA-2.0.0/SAGA/build/vignette.rds |binary SAGA-2.0.0/SAGA/inst/cmatrix.esd.csv |only SAGA-2.0.0/SAGA/inst/cmatrix.xy.csv |only SAGA-2.0.0/SAGA/inst/cmatrix.zw.csv |only SAGA-2.0.0/SAGA/inst/doc/model-averaged-analysis.R | 72 ++ SAGA-2.0.0/SAGA/inst/doc/model-averaged-analysis.Rmd | 442 ++++++++++++++---- SAGA-2.0.0/SAGA/inst/doc/model-averaged-analysis.pdf |only SAGA-2.0.0/SAGA/inst/genome.scale.csv |only SAGA-2.0.0/SAGA/man/AICtoMW.Rd |only SAGA-2.0.0/SAGA/man/AnalyzeCrossesMM.Rd | 19 SAGA-2.0.0/SAGA/man/DisplayCmatrix.Rd | 8 SAGA-2.0.0/SAGA/man/SAGA-package.Rd | 6 SAGA-2.0.0/SAGA/man/cohortID.Rd |only SAGA-2.0.0/SAGA/man/plot.genarch.Rd |only SAGA-2.0.0/SAGA/man/plotObserved.Rd |only SAGA-2.0.0/SAGA/vignettes/model-averaged-analysis.Rmd | 442 ++++++++++++++---- 33 files changed, 924 insertions(+), 301 deletions(-)
Title: Random Ferns Classifier
Description: An R implementation of the random ferns classifier by Ozuysal et al., modified for generic and multi-label classification and featuring OOB error approximation and importance measure.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>
Diff between rFerns versions 1.1.0 dated 2014-11-30 and 2.0.0 dated 2015-12-03
rFerns-1.1.0/rFerns/man/rFerns.predict.Rd |only rFerns-2.0.0/rFerns/DESCRIPTION | 8 - rFerns-2.0.0/rFerns/MD5 | 22 +-- rFerns-2.0.0/rFerns/NAMESPACE | 12 + rFerns-2.0.0/rFerns/R/ferns.R | 206 ++++++++++++++++++++++++++---- rFerns-2.0.0/rFerns/R/tools.R |only rFerns-2.0.0/rFerns/inst/NEWS | 10 + rFerns-2.0.0/rFerns/man/merge.rFerns.Rd |only rFerns-2.0.0/rFerns/man/predict.rFerns.Rd |only rFerns-2.0.0/rFerns/man/rFerns.Rd | 132 +++++++++++-------- rFerns-2.0.0/rFerns/src/fern.h | 155 ++++++++++++++++++++++ rFerns-2.0.0/rFerns/src/ferns.c | 43 ++++-- rFerns-2.0.0/rFerns/src/forest.h | 145 +++++++++------------ rFerns-2.0.0/rFerns/src/tools.h | 25 +++ 14 files changed, 564 insertions(+), 194 deletions(-)
Title: Partial and Semi-Partial (Part) Correlation
Description: Calculates partial and semi-partial
(part) correlations along with p-value.
Author: Seongho Kim
Maintainer: Seongho Kim <biostatistician.kim@gmail.com>
Diff between ppcor versions 1.0 dated 2011-06-15 and 1.1 dated 2015-12-03
ppcor-1.0/ppcor/R/ppcor_v1.R |only ppcor-1.1/ppcor/DESCRIPTION | 14 ++++++++------ ppcor-1.1/ppcor/MD5 |only ppcor-1.1/ppcor/NAMESPACE |only ppcor-1.1/ppcor/R/ppcor_v1.01.R |only ppcor-1.1/ppcor/man/pcor.Rd | 10 ++++------ ppcor-1.1/ppcor/man/pcor.test.Rd | 10 ++++------ ppcor-1.1/ppcor/man/ppcor-package.Rd | 12 +++++------- ppcor-1.1/ppcor/man/spcor.Rd | 10 ++++------ ppcor-1.1/ppcor/man/spcor.test.Rd | 10 ++++------ 10 files changed, 29 insertions(+), 37 deletions(-)
Title: Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre],
Pei Wang Developer [aut],
Zhidong Tu Developer [aut],
Won-min Song Developer [aut],
Adele Cutler Developer [ctb],
Leo Breiman Developer [ctb],
Andy Liaw Developer [ctb],
Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>
Diff between JRF versions 0.1-1 dated 2015-11-20 and 0.1-2 dated 2015-12-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/JRF.Rd | 34 ++++++++++++++++++---------------- man/importance.Rd | 11 ++++++----- 4 files changed, 30 insertions(+), 27 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.1 dated 2015-09-22 and 2.0.2 dated 2015-12-03
DESCRIPTION | 28 ++ MD5 | 70 +++---- NAMESPACE | 4 R/GHCN_FUNCTIONS.R | 361 ++++++++++++++++++++++++++++++++++--- R/SSURGO_FUNCTIONS.R | 43 ++-- R/UTILITY_FUNCTIONS.R | 18 + man/curl_download.Rd | 2 man/download_ghcn_daily_station.Rd | 2 man/download_huc4.Rd | 2 man/download_itrdb.Rd | 4 man/download_ned_tile.Rd | 8 man/download_nhd_subregion.Rd | 2 man/download_ssurgo_inventory.Rd | 2 man/download_ssurgo_study_area.Rd | 4 man/extract_ssurgo_data.Rd | 4 man/get_ghcn_daily.Rd | 152 ++++++++++++++- man/get_ghcn_daily_station.Rd | 142 ++++++++++++++ man/get_ghcn_inventory.Rd | 4 man/get_huc4.Rd | 6 man/get_itrdb.Rd | 16 - man/get_ned.Rd | 4 man/get_ned_tile.Rd | 8 man/get_nhd.Rd | 6 man/get_nhd_subregion.Rd | 4 man/get_ssurgo.Rd | 8 man/get_ssurgo_inventory.Rd | 4 man/get_ssurgo_study_area.Rd | 10 - man/pkg_test.Rd | 2 man/polygon_from_extent.Rd | 4 man/read_crn.Rd | 4 man/read_crn_data.Rd | 4 man/read_crn_metadata.Rd | 4 man/sequential_duplicated.Rd | 2 man/spdf_from_polygon.Rd | 2 man/station_to_data_frame.Rd |only man/substr_right.Rd | 2 man/unwrap_rows.Rd |only 37 files changed, 789 insertions(+), 153 deletions(-)