Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between texreg versions 1.35 dated 2015-04-28 and 1.36 dated 2015-12-08
DESCRIPTION | 29 +- MD5 | 26 - NAMESPACE | 9 R/classDefinition.R | 5 R/extract.R | 736 ++++++++++++++++++++++++++++++++++++++++----------- R/internal.R | 154 ++++++++++ R/texreg.R | 141 ++++++--- build/vignette.rds |binary inst/doc/v55i08.R | 46 +-- inst/doc/v55i08.Rnw | 52 ++- inst/doc/v55i08.pdf |binary man/extract.Rd | 86 +++++ man/texreg.Rd | 35 +- vignettes/v55i08.Rnw | 52 ++- 14 files changed, 1048 insertions(+), 323 deletions(-)
Title: Repeated Measures Proportional Odds Logistic Regression
Description: Fits linear models to repeated ordinal scores using GEE methodology.
Author: Nick Parsons
Maintainer: Nick Parsons <nick.parsons@warwick.ac.uk>
Diff between repolr versions 2.0 dated 2013-04-19 and 3.1 dated 2015-12-08
repolr-2.0/repolr/R/grepolr.R |only repolr-2.0/repolr/R/srepolr.R |only repolr-2.0/repolr/R/summary.gee.R |only repolr-2.0/repolr/data/HHSpain.rda |only repolr-2.0/repolr/data/QoL.rda |only repolr-2.0/repolr/data/achilles.rda |only repolr-2.0/repolr/man/grepolr.Rd |only repolr-2.0/repolr/man/srepolr.Rd |only repolr-2.0/repolr/man/summary.gee.Rd |only repolr-3.1/repolr/DESCRIPTION | 20 repolr-3.1/repolr/MD5 | 51 + repolr-3.1/repolr/NAMESPACE | 23 repolr-3.1/repolr/R/QIC.R | 17 repolr-3.1/repolr/R/RcppExports.R |only repolr-3.1/repolr/R/ord.expand.R | 85 ++ repolr-3.1/repolr/R/polycuts.R | 68 ++ repolr-3.1/repolr/R/print.repolr.R |only repolr-3.1/repolr/R/print.summary.repolr.R |only repolr-3.1/repolr/R/repolr.R | 872 +++++------------------------ repolr-3.1/repolr/R/summary.repolr.R |only repolr-3.1/repolr/data/HHSpain.txt.gz |only repolr-3.1/repolr/data/QoL.txt.gz |only repolr-3.1/repolr/data/achilles.txt.gz |only repolr-3.1/repolr/data/begonia.txt.gz |only repolr-3.1/repolr/data/mobility.txt.gz |only repolr-3.1/repolr/man/QIC.Rd | 30 repolr-3.1/repolr/man/begonia.Rd |only repolr-3.1/repolr/man/mobility.Rd |only repolr-3.1/repolr/man/ord.expand.Rd | 13 repolr-3.1/repolr/man/polycuts.Rd | 35 - repolr-3.1/repolr/man/repolr-package.Rd | 108 ++- repolr-3.1/repolr/man/summary.repolr.Rd |only repolr-3.1/repolr/src |only 33 files changed, 468 insertions(+), 854 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of a joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Multivariate joint frailty models for two types of recurrent events and a terminal event.
7) Joint models for longitudinal data and a terminal event.
8) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.8.1 dated 2015-11-21 and 2.8.2 dated 2015-12-08
frailtypack-2.8.1/frailtypack/src/epoce.f90 |only frailtypack-2.8.1/frailtypack/src/epoce_log.f90 |only frailtypack-2.8.1/frailtypack/vignettes/vignette.Rmd |only frailtypack-2.8.2/frailtypack/DESCRIPTION | 10 +++-- frailtypack-2.8.2/frailtypack/MD5 | 23 ++++++------ frailtypack-2.8.2/frailtypack/NEWS | 6 +++ frailtypack-2.8.2/frailtypack/R/longiPenal.R | 3 + frailtypack-2.8.2/frailtypack/R/prediction.R | 5 +- frailtypack-2.8.2/frailtypack/build |only frailtypack-2.8.2/frailtypack/inst/doc |only frailtypack-2.8.2/frailtypack/man/frailtypack-package.Rd | 2 - frailtypack-2.8.2/frailtypack/man/trivPenal.Rd | 2 - frailtypack-2.8.2/frailtypack/src/aaOptim.f90 | 15 +++++-- frailtypack-2.8.2/frailtypack/src/prediction_tri.f90 | 22 +++++------ frailtypack-2.8.2/frailtypack/vignettes/Package_summary.Rmd |only 15 files changed, 52 insertions(+), 36 deletions(-)
Title: Package for Deep Architectures and Restricted Boltzmann Machines
Description: The darch package is built on the basis of the code from G. E.
Hinton and R. R. Salakhutdinov (available under Matlab Code for deep belief
nets). This package is for generating neural networks with many layers (deep
architectures) and train them with the method introduced by the publications
"A fast learning algorithm for deep belief nets" (G. E. Hinton, S. Osindero,
Y. W. Teh; doi: 10.1162/neco.2006.18.7.1527) and "Reducing the
dimensionality of data with neural networks" (G. E. Hinton, R. R.
Salakhutdinov; doi: 10.1126/science.1127647). This method includes a pre
training with the contrastive divergence method published by G.E Hinton
(2002; doi: 10.1162/089976602760128018) and a fine tuning with common known
training algorithms like backpropagation or conjugate gradients.
Additionally, supervised fine-tuning can be enhanced with maxout and
dropout, two recently developed techniques to improve fine-tuning for deep
learning.
Author: Martin Drees [aut, cre],
Johannes Rueckert [ctb],
Geoffrey Hinton [cph],
Ruslan Salakhutdinov [cph],
Carl Edward Rasmussen [cph],
Maintainer: Martin Drees <mdrees@stud.fh-dortmund.de>
Diff between darch versions 0.9.1 dated 2014-03-16 and 0.10.0 dated 2015-12-08
darch-0.10.0/darch/DESCRIPTION | 65 - darch-0.10.0/darch/LICENSE |only darch-0.10.0/darch/MD5 | 394 ++++--- darch-0.10.0/darch/NAMESPACE | 67 + darch-0.10.0/darch/R/backpropagation.R | 181 +-- darch-0.10.0/darch/R/darch.Add.R | 108 +- darch-0.10.0/darch/R/darch.Getter.R | 533 ++++++---- darch-0.10.0/darch/R/darch.Learn.R | 404 ++++--- darch-0.10.0/darch/R/darch.R | 116 +- darch-0.10.0/darch/R/darch.Remove.R | 19 darch-0.10.0/darch/R/darch.Reset.R | 22 darch-0.10.0/darch/R/darch.Setter.R | 180 +++ darch-0.10.0/darch/R/darchUnitFunctions.R | 345 +++--- darch-0.10.0/darch/R/dataset.R |only darch-0.10.0/darch/R/dropout.R |only darch-0.10.0/darch/R/errorFunctions.R | 55 - darch-0.10.0/darch/R/generateRBMs.R | 23 darch-0.10.0/darch/R/generateWeights.R | 18 darch-0.10.0/darch/R/interface.R |only darch-0.10.0/darch/R/loadDArch.R | 21 darch-0.10.0/darch/R/loadRBM.R | 19 darch-0.10.0/darch/R/loadRBMFFWeights.R | 21 darch-0.10.0/darch/R/makeStartEndPoints.R | 19 darch-0.10.0/darch/R/minimize.R | 78 - darch-0.10.0/darch/R/minimizeAutoencoder.R | 42 darch-0.10.0/darch/R/minimizeClassifier.R | 49 darch-0.10.0/darch/R/mnist.R |only darch-0.10.0/darch/R/net.Getter.R | 94 + darch-0.10.0/darch/R/net.R | 66 - darch-0.10.0/darch/R/net.Setter.R | 93 + darch-0.10.0/darch/R/newDArch.R | 26 darch-0.10.0/darch/R/newRBM.R | 17 darch-0.10.0/darch/R/rbm.Getter.R | 31 darch-0.10.0/darch/R/rbm.Learn.R | 146 +- darch-0.10.0/darch/R/rbm.R | 145 +- darch-0.10.0/darch/R/rbm.Reset.R | 17 darch-0.10.0/darch/R/rbm.Setter.R | 45 darch-0.10.0/darch/R/rbmUnitFunctions.R | 61 - darch-0.10.0/darch/R/rbmUpdate.R | 26 darch-0.10.0/darch/R/rpropagation.R | 128 +- darch-0.10.0/darch/R/runDArch.R | 32 darch-0.10.0/darch/R/saveDArch.R | 35 darch-0.10.0/darch/R/saveRBM.R | 23 darch-0.10.0/darch/R/saveRBMFFWeights.R | 21 darch-0.10.0/darch/README |only darch-0.10.0/darch/inst |only darch-0.10.0/darch/man/DArch-class.Rd |only darch-0.10.0/darch/man/DataSet-class.Rd |only darch-0.10.0/darch/man/Net-class.Rd |only darch-0.10.0/darch/man/RBM-class.Rd |only darch-0.10.0/darch/man/addExecOutput-DArch-method.Rd |only darch-0.10.0/darch/man/addExecOutput.Rd |only darch-0.10.0/darch/man/addLayer-DArch-method.Rd |only darch-0.10.0/darch/man/addLayer.Rd |only darch-0.10.0/darch/man/addLayerField-DArch-method.Rd |only darch-0.10.0/darch/man/addLayerField.Rd |only darch-0.10.0/darch/man/applyDropoutMask.Rd |only darch-0.10.0/darch/man/backpropagation.Rd | 52 darch-0.10.0/darch/man/binSigmoidUnit.Rd | 37 darch-0.10.0/darch/man/createDataSet-ANY-ANY-missing-DataSet-method.Rd |only darch-0.10.0/darch/man/createDataSet-ANY-ANY-missing-missing-method.Rd |only darch-0.10.0/darch/man/createDataSet-ANY-missing-formula-missing-method.Rd |only darch-0.10.0/darch/man/createDataSet.Rd |only darch-0.10.0/darch/man/crossEntropyError.Rd | 18 darch-0.10.0/darch/man/darch.DataSet.Rd |only darch-0.10.0/darch/man/darch.Rd |only darch-0.10.0/darch/man/darch.default.Rd |only darch-0.10.0/darch/man/darch.formula.Rd |only darch-0.10.0/darch/man/fineTuneDArch-DArch-method.Rd |only darch-0.10.0/darch/man/fineTuneDArch.Rd |only darch-0.10.0/darch/man/generateDropoutMask.Rd |only darch-0.10.0/darch/man/generateRBMs-methods.Rd | 21 darch-0.10.0/darch/man/generateWeights.Rd | 13 darch-0.10.0/darch/man/getBatchSize-methods.Rd | 4 darch-0.10.0/darch/man/getCancel-DArch-method.Rd |only darch-0.10.0/darch/man/getCancel.Rd |only darch-0.10.0/darch/man/getCancelMessage-DArch-method.Rd |only darch-0.10.0/darch/man/getCancelMessage.Rd |only darch-0.10.0/darch/man/getDropoutHiddenLayers-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutHiddenLayers.Rd |only darch-0.10.0/darch/man/getDropoutInputLayer-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutInputLayer.Rd |only darch-0.10.0/darch/man/getDropoutMask-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutMask.Rd |only darch-0.10.0/darch/man/getDropoutMasks-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutMasks.Rd |only darch-0.10.0/darch/man/getDropoutOneMaskPerEpoch-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutOneMaskPerEpoch.Rd |only darch-0.10.0/darch/man/getEpochs-Net-method.Rd |only darch-0.10.0/darch/man/getEpochs.Rd |only darch-0.10.0/darch/man/getErrorFunction-methods.Rd | 4 darch-0.10.0/darch/man/getExecOutput-DArch-method.Rd |only darch-0.10.0/darch/man/getExecOutput.Rd |only darch-0.10.0/darch/man/getExecOutputs-DArch-method.Rd |only darch-0.10.0/darch/man/getExecOutputs.Rd |only darch-0.10.0/darch/man/getExecuteFunction-DArch-method.Rd |only darch-0.10.0/darch/man/getExecuteFunction.Rd |only darch-0.10.0/darch/man/getFF-methods.Rd | 4 darch-0.10.0/darch/man/getFinalMomentum-methods.Rd | 4 darch-0.10.0/darch/man/getFineTuneFunction-DArch-method.Rd |only darch-0.10.0/darch/man/getFineTuneFunction.Rd |only darch-0.10.0/darch/man/getGenWeightFunction-methods.Rd | 4 darch-0.10.0/darch/man/getHiddenBiases-methods.Rd | 4 darch-0.10.0/darch/man/getHiddenBiasesInc-methods.Rd | 7 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darch-0.10.0/darch/man/getMomentum-methods.Rd | 8 darch-0.10.0/darch/man/getMomentumSwitch-methods.Rd | 4 darch-0.10.0/darch/man/getNormalizeWeights-Net-method.Rd |only darch-0.10.0/darch/man/getNormalizeWeights.Rd |only darch-0.10.0/darch/man/getNumHidden-methods.Rd | 4 darch-0.10.0/darch/man/getNumVisible-methods.Rd | 7 darch-0.10.0/darch/man/getOutput-methods.Rd | 4 darch-0.10.0/darch/man/getPosPhaseData-methods.Rd | 10 darch-0.10.0/darch/man/getRBMList-DArch-method.Rd |only darch-0.10.0/darch/man/getRBMList.Rd |only darch-0.10.0/darch/man/getStats-methods.Rd | 10 darch-0.10.0/darch/man/getVisibleBiases-methods.Rd | 4 darch-0.10.0/darch/man/getVisibleBiasesInc-methods.Rd | 7 darch-0.10.0/darch/man/getVisibleUnitStates-methods.Rd | 4 darch-0.10.0/darch/man/getWeightCost-methods.Rd | 4 darch-0.10.0/darch/man/getWeightInc-methods.Rd | 4 darch-0.10.0/darch/man/getWeights-methods.Rd | 8 darch-0.10.0/darch/man/incrementEpochs-Net-method.Rd |only darch-0.10.0/darch/man/incrementEpochs.Rd |only darch-0.10.0/darch/man/linearUnit.Rd | 33 darch-0.10.0/darch/man/linearUnitDerivative.Rd | 37 darch-0.10.0/darch/man/linearUnitFunc.Rd | 31 darch-0.10.0/darch/man/loadDArch.Rd | 16 darch-0.10.0/darch/man/loadRBM.Rd | 19 darch-0.10.0/darch/man/loadRBMFFWeights.Rd | 18 darch-0.10.0/darch/man/makeStartEndPoints.Rd | 19 darch-0.10.0/darch/man/maxoutUnitDerivative.Rd |only darch-0.10.0/darch/man/minimize.Rd | 91 - darch-0.10.0/darch/man/minimizeAutoencoder.Rd | 44 darch-0.10.0/darch/man/minimizeClassifier.Rd | 52 darch-0.10.0/darch/man/mseError.Rd | 21 darch-0.10.0/darch/man/newDArch.Rd | 27 darch-0.10.0/darch/man/newRBM.Rd | 19 darch-0.10.0/darch/man/preTrainDArch-DArch-method.Rd |only darch-0.10.0/darch/man/preTrainDArch.Rd |only darch-0.10.0/darch/man/predict.DArch.Rd |only darch-0.10.0/darch/man/print.DArch.Rd |only darch-0.10.0/darch/man/provideMNIST.Rd |only darch-0.10.0/darch/man/quadraticError.Rd | 18 darch-0.10.0/darch/man/rbmUpdate.Rd | 12 darch-0.10.0/darch/man/readMNIST.Rd | 23 darch-0.10.0/darch/man/removeLayerField-methods.Rd | 11 darch-0.10.0/darch/man/resetDArch-methods.Rd | 18 darch-0.10.0/darch/man/resetExecOutput-methods.Rd | 9 darch-0.10.0/darch/man/resetRBM-methods.Rd | 7 darch-0.10.0/darch/man/rpropagation.Rd | 134 +- darch-0.10.0/darch/man/runDArch.Rd | 11 darch-0.10.0/darch/man/saveDArch-methods.Rd | 34 darch-0.10.0/darch/man/saveRBM-methods.Rd | 20 darch-0.10.0/darch/man/saveRBMFFWeights-methods.Rd | 19 darch-0.10.0/darch/man/setBatchSize-methods.Rd | 8 darch-0.10.0/darch/man/setCancel-methods.Rd | 10 darch-0.10.0/darch/man/setCancelMessage-methods.Rd | 9 darch-0.10.0/darch/man/setDropoutHiddenLayers-methods.Rd |only darch-0.10.0/darch/man/setDropoutInputLayer-methods.Rd |only darch-0.10.0/darch/man/setDropoutMask-methods.Rd |only darch-0.10.0/darch/man/setDropoutMasks-methods.Rd |only darch-0.10.0/darch/man/setDropoutOneMaskPerEpoch-set-DArch-method.Rd |only darch-0.10.0/darch/man/setDropoutOneMaskPerEpoch-set.Rd |only darch-0.10.0/darch/man/setErrorFunction-methods.Rd | 8 darch-0.10.0/darch/man/setExecuteFunction-methods.Rd | 9 darch-0.10.0/darch/man/setFF-methods.Rd | 10 darch-0.10.0/darch/man/setFinalMomentum-methods.Rd | 8 darch-0.10.0/darch/man/setFineTuneFunction-methods.Rd | 9 darch-0.10.0/darch/man/setGenWeightFunction-methods.Rd | 14 darch-0.10.0/darch/man/setHiddenBiases-methods.Rd | 12 darch-0.10.0/darch/man/setHiddenBiasesInc-methods.Rd | 9 darch-0.10.0/darch/man/setHiddenUnitFunction-methods.Rd | 8 darch-0.10.0/darch/man/setHiddenUnitStates-methods.Rd | 8 darch-0.10.0/darch/man/setInitialMomentum-set-Net-method.Rd |only darch-0.10.0/darch/man/setInitialMomentum-set.Rd |only darch-0.10.0/darch/man/setLayer-methods.Rd | 11 darch-0.10.0/darch/man/setLayerField-methods.Rd | 17 darch-0.10.0/darch/man/setLayerFunction-methods.Rd | 11 darch-0.10.0/darch/man/setLayerWeights-methods.Rd | 11 darch-0.10.0/darch/man/setLayers-methods.Rd | 9 darch-0.10.0/darch/man/setLearnRateBiasHidden-methods.Rd | 13 darch-0.10.0/darch/man/setLearnRateBiasVisible-methods.Rd | 11 darch-0.10.0/darch/man/setLearnRateBiases-methods.Rd | 9 darch-0.10.0/darch/man/setLearnRateWeights-methods.Rd | 8 darch-0.10.0/darch/man/setLogLevel-methods.Rd | 21 darch-0.10.0/darch/man/setMomentumSwitch-methods.Rd | 8 darch-0.10.0/darch/man/setNormalizeWeights-set-Net-method.Rd |only darch-0.10.0/darch/man/setNormalizeWeights-set.Rd |only darch-0.10.0/darch/man/setNumHidden-methods.Rd | 8 darch-0.10.0/darch/man/setNumVisible-methods.Rd | 8 darch-0.10.0/darch/man/setOutput-methods.Rd | 8 darch-0.10.0/darch/man/setPosPhaseData-methods.Rd | 8 darch-0.10.0/darch/man/setRBMList-methods.Rd | 10 darch-0.10.0/darch/man/setStats-methods.Rd | 14 darch-0.10.0/darch/man/setUpdateFunction-methods.Rd | 9 darch-0.10.0/darch/man/setVisibleBiases-methods.Rd | 12 darch-0.10.0/darch/man/setVisibleBiasesInc-methods.Rd | 9 darch-0.10.0/darch/man/setVisibleUnitFunction-methods.Rd | 8 darch-0.10.0/darch/man/setVisibleUnitStates-methods.Rd | 8 darch-0.10.0/darch/man/setWeightCost-methods.Rd | 8 darch-0.10.0/darch/man/setWeightInc-methods.Rd | 8 darch-0.10.0/darch/man/setWeights-methods.Rd | 9 darch-0.10.0/darch/man/sigmUnitFunc.Rd | 32 darch-0.10.0/darch/man/sigmUnitFuncSwitch.Rd | 42 darch-0.10.0/darch/man/sigmoidUnit.Rd | 30 darch-0.10.0/darch/man/sigmoidUnitDerivative.Rd | 37 darch-0.10.0/darch/man/softmaxUnit.Rd | 32 darch-0.10.0/darch/man/softmaxUnitDerivative.Rd | 37 darch-0.10.0/darch/man/tanSigmoidUnit.Rd |only darch-0.10.0/darch/man/tanSigmoidUnitDerivative.Rd |only darch-0.10.0/darch/man/trainRBM-RBM-method.Rd |only darch-0.10.0/darch/man/trainRBM.Rd |only darch-0.10.0/darch/man/validateDataSet-DataSet-method.Rd |only darch-0.10.0/darch/man/validateDataSet.Rd |only darch-0.9.1/darch/R/package-darch.R |only darch-0.9.1/darch/R/readMNIST.R |only darch-0.9.1/darch/README.md |only darch-0.9.1/darch/man/DArch.Rd |only darch-0.9.1/darch/man/Net.Rd |only darch-0.9.1/darch/man/RBM.Rd |only darch-0.9.1/darch/man/addExecOutput-methods.Rd |only darch-0.9.1/darch/man/addLayer-methods.Rd |only darch-0.9.1/darch/man/addLayerField-methods.Rd |only darch-0.9.1/darch/man/darch-package.Rd |only darch-0.9.1/darch/man/fineTuneDArch-methods.Rd |only darch-0.9.1/darch/man/getCancel-methods.Rd |only darch-0.9.1/darch/man/getCancelMessage-methods.Rd |only darch-0.9.1/darch/man/getExecOutput-methods.Rd |only darch-0.9.1/darch/man/getExecOutputs-methods.Rd |only darch-0.9.1/darch/man/getExecuteFunction-methods.Rd |only darch-0.9.1/darch/man/getFineTuneFunction-methods.Rd |only darch-0.9.1/darch/man/getLayer-methods.Rd |only darch-0.9.1/darch/man/getLayerField-methods.Rd |only darch-0.9.1/darch/man/getLayerFunction-methods.Rd |only darch-0.9.1/darch/man/getLayerWeights-methods.Rd |only darch-0.9.1/darch/man/getLayers-methods.Rd |only darch-0.9.1/darch/man/getLearnRateBiases-methods.Rd |only darch-0.9.1/darch/man/getRBMList-methods.Rd |only darch-0.9.1/darch/man/preTrainDArch-methods.Rd |only darch-0.9.1/darch/man/setMomentum-methods.Rd |only darch-0.9.1/darch/man/trainRBM-methods.Rd |only 259 files changed, 3352 insertions(+), 2030 deletions(-)
Title: Pathway Analysis Methods for Genomewide Association Data
Description: Bayesian hierarchical methods for pathway analysis of genomewide association data: Normal/Bayes factors and Sparse Normal/Adaptive lasso. The Frequentist Fisher's product method is included as well.
Author: Marina Evangelou
Maintainer: Marina Evangelou <m.evangelou@ic.ac.uk>
Diff between PAGWAS versions 1.0 dated 2013-11-13 and 2.0 dated 2015-12-08
PAGWAS-1.0/PAGWAS/R/GWAS.analysis.R |only PAGWAS-1.0/PAGWAS/R/PAGWAS-internal.R |only PAGWAS-1.0/PAGWAS/R/TPR.FPR.R |only PAGWAS-1.0/PAGWAS/R/bf.TPR.FPR.R |only PAGWAS-1.0/PAGWAS/R/bf.area.R |only PAGWAS-1.0/PAGWAS/R/create.pathway.matrix.R |only PAGWAS-1.0/PAGWAS/R/internal.function.simulations.R |only PAGWAS-1.0/PAGWAS/R/return.a.SNAL.R |only PAGWAS-1.0/PAGWAS/R/return.bf.NBF.R |only PAGWAS-1.0/PAGWAS/R/return.hyperparameters.NBF.R |only PAGWAS-1.0/PAGWAS/R/return.s2.SNAL.R |only PAGWAS-1.0/PAGWAS/R/roc.convex.R |only PAGWAS-1.0/PAGWAS/data/list.of.parameters.rda |only PAGWAS-1.0/PAGWAS/man/create.pathway.matrix.Rd |only PAGWAS-1.0/PAGWAS/man/list.of.parameters.Rd |only PAGWAS-1.0/PAGWAS/man/return.a.SNAL.Rd |only PAGWAS-1.0/PAGWAS/man/return.bf.NBF.Rd |only PAGWAS-1.0/PAGWAS/man/return.hyperparameters.NBF.Rd |only PAGWAS-1.0/PAGWAS/man/return.s2.SNAL.Rd |only PAGWAS-1.0/PAGWAS/man/roc.convex.Rd |only PAGWAS-2.0/PAGWAS/DESCRIPTION | 16 ++-- PAGWAS-2.0/PAGWAS/MD5 | 75 +++++++------------- PAGWAS-2.0/PAGWAS/NAMESPACE | 6 + PAGWAS-2.0/PAGWAS/R/FM.chi.pvalue.R | 5 - PAGWAS-2.0/PAGWAS/R/NBF.R | 9 +- PAGWAS-2.0/PAGWAS/R/SNAL.R | 8 +- PAGWAS-2.0/PAGWAS/R/SNAL.calculation.R | 75 +++++++++----------- PAGWAS-2.0/PAGWAS/R/create.pathway.df.R |only PAGWAS-2.0/PAGWAS/R/lars.calculation.R | 1 PAGWAS-2.0/PAGWAS/R/logproby.R | 4 - PAGWAS-2.0/PAGWAS/R/matrix.inv.calculation.R | 3 PAGWAS-2.0/PAGWAS/R/matrix.invroot.calculation.R | 3 PAGWAS-2.0/PAGWAS/R/snps.to.genes.R | 8 +- PAGWAS-2.0/PAGWAS/R/snps.to.pathways.R | 35 ++------- PAGWAS-2.0/PAGWAS/data/SNPs.rda |binary PAGWAS-2.0/PAGWAS/data/genes.rda |binary PAGWAS-2.0/PAGWAS/data/genotypes.rda |binary PAGWAS-2.0/PAGWAS/data/pathways.rda |binary PAGWAS-2.0/PAGWAS/man/FM.chi.pvalue.Rd | 16 +--- PAGWAS-2.0/PAGWAS/man/NBF.Rd | 38 +++++----- PAGWAS-2.0/PAGWAS/man/PAGWAS-package.Rd | 18 ++-- PAGWAS-2.0/PAGWAS/man/SNAL.Rd | 30 ++++---- PAGWAS-2.0/PAGWAS/man/SNAL.calculation.Rd |only PAGWAS-2.0/PAGWAS/man/SNPs.Rd | 6 - PAGWAS-2.0/PAGWAS/man/create.pathway.df.Rd |only PAGWAS-2.0/PAGWAS/man/genes.Rd | 11 +- PAGWAS-2.0/PAGWAS/man/genotypes.Rd | 10 -- PAGWAS-2.0/PAGWAS/man/pathways.Rd | 6 - PAGWAS-2.0/PAGWAS/man/snps.to.genes.Rd | 12 +-- PAGWAS-2.0/PAGWAS/man/snps.to.pathways.Rd | 22 ++--- 50 files changed, 190 insertions(+), 227 deletions(-)
Title: Truncated Maximum Likelihood Fit and Robust Accelerated Failure
Time Regression for Gaussian and Log-Weibull Case
Description: R functions for the computation of the truncated maximum
likelihood and the robust accelerated failure time regression
for gaussian and log-Weibull case.
Author: Alfio Marazzi <Alfio.Marazzi@chuv.ch>, Jean-Luc Muralti
Maintainer: A. Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>
Diff between RobustAFT versions 1.3 dated 2014-11-06 and 1.4-1 dated 2015-12-08
DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- NAMESPACE | 13 ++++++++++--- man/RobustAFT-internal.Rd |only 4 files changed, 19 insertions(+), 11 deletions(-)
Title: Tools for Time Series Analysis Based on Symbolic Aggregate
Dicretization
Description: Implements z-normalization, SAX, HOT-SAX, VSM, and SAX-VSM algorithms
facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.0.1 dated 2015-10-19 and 1.0.2 dated 2015-12-08
jmotif-1.0.1/jmotif/tests/testthat/test_SAX.R |only jmotif-1.0.1/jmotif/tests/testthat/test_SAX2.R |only jmotif-1.0.2/jmotif/DESCRIPTION | 21 jmotif-1.0.2/jmotif/MD5 | 81 - jmotif-1.0.2/jmotif/NAMESPACE | 5 jmotif-1.0.2/jmotif/R/RcppExports.R | 205 +- jmotif-1.0.2/jmotif/R/data.R | 5 jmotif-1.0.2/jmotif/R/jmotif.R | 7 jmotif-1.0.2/jmotif/README.md | 131 + jmotif-1.0.2/jmotif/data/ECG0606.rda |only jmotif-1.0.2/jmotif/data/datalist | 1 jmotif-1.0.2/jmotif/man/alphabet_to_cuts.Rd | 4 jmotif-1.0.2/jmotif/man/bags_to_tfidf.Rd | 6 jmotif-1.0.2/jmotif/man/col_means.Rd | 8 jmotif-1.0.2/jmotif/man/cosine_sim.Rd | 8 jmotif-1.0.2/jmotif/man/early_abandoned_dist.Rd |only jmotif-1.0.2/jmotif/man/ecg0606.Rd |only jmotif-1.0.2/jmotif/man/euclidean_dist.Rd |only jmotif-1.0.2/jmotif/man/find_discords_brute_force.Rd |only jmotif-1.0.2/jmotif/man/find_discords_hot_sax.Rd |only jmotif-1.0.2/jmotif/man/idx_to_letter.Rd | 6 jmotif-1.0.2/jmotif/man/is_equal_mindist.Rd |only jmotif-1.0.2/jmotif/man/is_equal_str.Rd | 8 jmotif-1.0.2/jmotif/man/letter_to_idx.Rd | 6 jmotif-1.0.2/jmotif/man/letters_to_idx.Rd | 6 jmotif-1.0.2/jmotif/man/manyseries_to_wordbag.Rd | 16 jmotif-1.0.2/jmotif/man/min_dist.Rd | 4 jmotif-1.0.2/jmotif/man/paa.Rd | 8 jmotif-1.0.2/jmotif/man/sax_by_chunking.Rd | 12 jmotif-1.0.2/jmotif/man/sax_distance_matrix.Rd | 8 jmotif-1.0.2/jmotif/man/sax_via_window.Rd | 17 jmotif-1.0.2/jmotif/man/series_to_chars.Rd | 8 jmotif-1.0.2/jmotif/man/series_to_string.Rd | 8 jmotif-1.0.2/jmotif/man/series_to_wordbag.Rd | 16 jmotif-1.0.2/jmotif/man/subseries.Rd | 12 jmotif-1.0.2/jmotif/man/znorm.Rd | 9 jmotif-1.0.2/jmotif/src/RcppExports.cpp | 83 - jmotif-1.0.2/jmotif/src/jmotif.cpp | 788 ++++++++-- jmotif-1.0.2/jmotif/tests/testthat/test_SAX_simple.R |only jmotif-1.0.2/jmotif/tests/testthat/test_SAX_strategies.R |only jmotif-1.0.2/jmotif/tests/testthat/test_SAX_via_window.R |only jmotif-1.0.2/jmotif/tests/testthat/test_discord_brute_force.R |only jmotif-1.0.2/jmotif/tests/testthat/test_discord_hot_sax.R |only jmotif-1.0.2/jmotif/tests/testthat/test_early_abandoned_dist.R |only jmotif-1.0.2/jmotif/tests/testthat/test_euclidean_dist.R |only jmotif-1.0.2/jmotif/tests/testthat/test_min_dist.R | 24 jmotif-1.0.2/jmotif/tests/testthat/test_min_dist_equal.R |only jmotif-1.0.2/jmotif/tests/testthat/test_subseries.R | 7 jmotif-1.0.2/jmotif/tests/testthat/test_wordbag.R | 24 jmotif-1.0.2/jmotif/tests/testthat/test_znorm.R | 11 50 files changed, 1166 insertions(+), 397 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al (doi: 10.2307/2533043) and the two level random effects model in Beath and Heller (doi: 10.1177/1471082X0800900302). Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-5 dated 2015-11-12 and 1.0-6 dated 2015-12-08
DESCRIPTION | 11 MD5 | 21 - NAMESPACE | 97 +++---- R/bestlca.R | 63 ++-- R/fitAdaptRandom.R | 535 ++++++++++++++++++++-------------------- R/fitAdaptRandom2.R | 3 R/fitFixed.R | 335 ++++++++++++------------- R/randomLCA.R | 346 ++++++++++++------------- inst/NEWS | 12 man/hivtests.Rd | 5 man/randomLCA.Rd | 174 ++++++------- vignettes/randomLCA-example.tex |only 12 files changed, 811 insertions(+), 791 deletions(-)
Title: NCA Calculation and Population PK Model Diagnosis
Description: A flexible tool is presented here that can perform
(i) traditional non-compartmental analysis (NCA) and
(ii) simulation-based posterior predictive checks for a population
pharmacokinetic (PK) model using NCA metrics.
Author: Chayan Acharya [aut, cre],
Andrew C. Hooker [aut],
Siv Jonsson [aut],
Mats O. Karlsson [aut]
Maintainer: Chayan Acharya <chayan.acharya@farmbio.uu.se>
Diff between ncappc versions 0.2 dated 2015-07-16 and 0.2.1.0 dated 2015-12-08
DESCRIPTION | 11 MD5 | 70 NAMESPACE | 2 R/calc.stat.R | 24 R/dv.plot.R | 24 R/est.nca.R | 258 ++- R/histobs.plot.R | 30 R/histpop.plot.R | 27 R/nca.deviation.plot.R | 18 R/nca.npde.plot.R | 21 R/nca.pde.deviation.outlier.R | 40 R/ncappc.R | 2221 ++++++++++++++++--------------- R/read_nm_table.R |only README.md | 2 build/vignette.rds |binary inst/doc/ncappc-vignette.Rmd | 13 inst/doc/ncappc-vignette.html | 477 +++--- inst/extdata |only inst/misc/ncappcReport-NCA-PPC.Rmd | 61 inst/misc/ncappcReport-NCA-PPC.Rnw | 76 - inst/misc/ncappcReport-NCA.Rmd | 26 inst/misc/ncappcReport-NCA.Rnw | 36 man/est.nca.Rd | 30 man/nca.pde.deviation.outlier.Rd | 4 man/ncappc.Rd | 154 +- man/read_nm_table.Rd |only tests/testthat/ncappcexamples/example1.R | 29 vignettes/Deviation-vgn.png |only vignettes/HistObs-vgn.png |only vignettes/NPDE-vgn.png |only vignettes/Outlier-vgn.png |only vignettes/Sub-CommandLineArguments.Rmd | 235 +-- vignettes/Sub-EstimatedNCAmetrics.Rmd | 4 vignettes/Sub-Output.Rmd | 45 vignettes/conc-vgn.png |only vignettes/forest-vgn.png |only vignettes/histNPDE-vgn.png |only vignettes/ncappc-Schema.png |only vignettes/ncappc-vignette.Rmd | 13 vignettes/ncappc-vignette.md | 295 ++-- vignettes/ncappc-vignette.txt |only vignettes/ncappc_Schema.tif |only vignettes/popMean-vgn.png |only 43 files changed, 2365 insertions(+), 1881 deletions(-)
Title: Gapped-Kmer Support Vector Machine
Description: Imports the 'gkmSVM' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms.
Author: Mahmoud Ghandi
Maintainer: Mahmoud Ghandi <mghandi@gmail.com>
Diff between gkmSVM versions 0.55 dated 2015-06-30 and 0.65 dated 2015-12-08
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- NAMESPACE | 4 ++++ R/RcppExports.R | 12 ++++++------ R/gkmsvm_train.R | 19 +++++++++++++++---- R/gkmsvm_trainCV.R |only man/gkmSVM-package.Rd | 20 +++++++++++++------- man/gkmsvm_train.Rd | 3 ++- man/gkmsvm_trainCV.Rd |only src/EstimLogRatio.cpp | 2 +- 10 files changed, 55 insertions(+), 31 deletions(-)