Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.3-1 dated 2016-01-28 and 1.3-4 dated 2016-07-19
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 2 +- R/pairw_oneway.R |only R/press.R | 6 ++++-- build/vignette.rds |binary man/ci.impt.Rd | 2 +- man/pairw.oneway.Rd |only man/press.rd | 5 ++++- 9 files changed, 22 insertions(+), 15 deletions(-)
Title: A Time Input Widget for Shiny
Description: Provides a time input widget for Shiny. This widget allows intuitive time input in the
'[hh]:[mm]:[ss]' or '[hh]:[mm]' (24H) format by using a separate numeric input for each time
component. The interface with R uses 'DateTimeClasses' objects. See the project page for more
information and examples.
Author: Gerhard Burger [aut, cre]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between shinyTime versions 0.1.0 dated 2016-07-18 and 0.2.0 dated 2016-07-19
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/input-time.R | 37 ++++++++++++++++++++++--------------- README.md | 22 ++++++++++++++-------- inst/www/input_binding_time.js | 3 ++- man/shinyTime.Rd | 4 ++-- man/shinyTimeExample.Rd | 4 ++-- man/timeInput.Rd | 13 +++++++++---- man/updateTimeInput.Rd | 4 ++-- 9 files changed, 67 insertions(+), 48 deletions(-)
Title: Streamline Descriptive Analysis of Quantitative Data Matrices
Description: Methods which streamline the descriptive analysis of quantitative
matrices. Matrix columns are samples while rows are features i.e. proteins, genes.
Author: Witold Wolski <wewolski@gmail.com>
Maintainer: Witold Wolski <wewolski@gmail.com>
Diff between quantable versions 0.1 dated 2015-08-07 and 0.2.2 dated 2016-07-19
quantable-0.1/quantable/man/colorscale.Rd |only quantable-0.1/quantable/man/getValuesForVolcano.Rd |only quantable-0.2.2/quantable/DESCRIPTION | 18 - quantable-0.2.2/quantable/MD5 | 103 ++++-- quantable-0.2.2/quantable/NAMESPACE | 107 +++--- quantable-0.2.2/quantable/R/CV.R |only quantable-0.2.2/quantable/R/OneSampleSingleSidedVolcano.R |only quantable-0.2.2/quantable/R/altmanbland.R | 52 +-- quantable-0.2.2/quantable/R/dat2Matrix.R |only quantable-0.2.2/quantable/R/datadescription.R | 27 - quantable-0.2.2/quantable/R/distmy.R | 84 ++--- quantable-0.2.2/quantable/R/getValuesForVolcano.R | 123 +++++-- quantable-0.2.2/quantable/R/imageWithLabels.R | 226 +++++++++++--- quantable-0.2.2/quantable/R/mypairs.R | 38 +- quantable-0.2.2/quantable/R/pairsQQ.R | 38 +- quantable-0.2.2/quantable/R/pvalCorMat.R | 82 ++--- quantable-0.2.2/quantable/R/removeNArows.R | 34 +- quantable-0.2.2/quantable/R/robustscale.R | 60 +-- quantable-0.2.2/quantable/R/roc.R |only quantable-0.2.2/quantable/R/runFun.R | 68 ++-- quantable-0.2.2/quantable/R/runrobscale.R | 106 +++--- quantable-0.2.2/quantable/R/scaleByGroup.R |only quantable-0.2.2/quantable/R/scales.R |only quantable-0.2.2/quantable/R/simpleheatmap.R | 66 ++-- quantable-0.2.2/quantable/R/split2table.R | 36 -- quantable-0.2.2/quantable/R/sumtop.R |only quantable-0.2.2/quantable/R/unpivot.R | 32 - quantable-0.2.2/quantable/R/uppertriang.R | 23 - quantable-0.2.2/quantable/R/volcanoplot.R | 134 ++++---- quantable-0.2.2/quantable/R/write.vector.R |only quantable-0.2.2/quantable/man/CV.Rd |only quantable-0.2.2/quantable/man/CVlog.Rd |only quantable-0.2.2/quantable/man/altmanbland.Rd | 61 +-- quantable-0.2.2/quantable/man/dat2Matrix.Rd |only quantable-0.2.2/quantable/man/determineCut.Rd |only quantable-0.2.2/quantable/man/distmy.Rd | 72 ++-- quantable-0.2.2/quantable/man/fisherExact.Rd |only quantable-0.2.2/quantable/man/getBlueScale.Rd |only quantable-0.2.2/quantable/man/getBlueWhiteRed.Rd |only quantable-0.2.2/quantable/man/getDiv.Rd |only quantable-0.2.2/quantable/man/getGreensScale.Rd |only quantable-0.2.2/quantable/man/getRedScale.Rd |only quantable-0.2.2/quantable/man/getTValuesForVolcano.Rd |only quantable-0.2.2/quantable/man/getWRValuesForVolcano.Rd |only quantable-0.2.2/quantable/man/imageColorscale.Rd |only quantable-0.2.2/quantable/man/imageWithLabels.Rd | 87 +++-- quantable-0.2.2/quantable/man/imageWithLabelsNoLayout.Rd |only quantable-0.2.2/quantable/man/makeROCplot.Rd |only quantable-0.2.2/quantable/man/mypairs.Rd | 51 +-- quantable-0.2.2/quantable/man/onesamplegreaterT.Rd |only quantable-0.2.2/quantable/man/pairsQQ.Rd | 49 +-- quantable-0.2.2/quantable/man/plotOneSideVolcano.Rd |only quantable-0.2.2/quantable/man/pvalCorMat.Rd | 55 +-- quantable-0.2.2/quantable/man/quantable.Rd | 22 - quantable-0.2.2/quantable/man/removeNArows.Rd | 55 +-- quantable-0.2.2/quantable/man/robustscale.Rd | 70 ++-- quantable-0.2.2/quantable/man/runFun.Rd | 76 ++-- quantable-0.2.2/quantable/man/runTICscale.Rd | 61 +-- quantable-0.2.2/quantable/man/runrobscale.Rd | 75 ++-- quantable-0.2.2/quantable/man/scaleByGroup.Rd |only quantable-0.2.2/quantable/man/simpleheatmap.Rd | 79 ++-- quantable-0.2.2/quantable/man/split2table.Rd | 48 +- quantable-0.2.2/quantable/man/sumtop.Rd |only quantable-0.2.2/quantable/man/unpivot.Rd | 44 +- quantable-0.2.2/quantable/man/uppertriang.Rd | 41 +- quantable-0.2.2/quantable/man/volcanoplot.Rd | 91 ++--- quantable-0.2.2/quantable/man/write.tab.Rd |only quantable-0.2.2/quantable/man/write.vector.Rd |only 68 files changed, 1413 insertions(+), 1081 deletions(-)
Title: Quality Control Review
Description: Allows to generate Shewhart-type charts and to obtain
numerical results of interest for a process quality control
(involving continuous, attribute or count data).
This package provides basic functionality for univariable and multivariable
quality control analysis, including: xbar, xbar-one, S, R, ewna, cusum,
mewna, mcusum and T2 charts. Additionally have nonparametric
control charts multivariate. Parametric and nonparametric Process Capability Indices.
Author: Miguel Flores [aut, cre],
Ruben Fernandez [ctb],
Salvador Naya [ctb],
Javier Tarrio-Saavedra [ctb]
Maintainer: Miguel Flores <ma.flores@outlook.com>
Diff between qcr versions 0.1-18 dated 2014-05-30 and 1.0 dated 2016-07-19
qcr-0.1-18/qcr/R/qcs.ewna.r |only qcr-0.1-18/qcr/data/archery1.rda |only qcr-0.1-18/qcr/data/circuit.rda |only qcr-0.1-18/qcr/data/counters.rda |only qcr-0.1-18/qcr/data/dowel1.rda |only qcr-0.1-18/qcr/data/employment.rda |only qcr-0.1-18/qcr/data/orangejuice.rda |only qcr-0.1-18/qcr/data/oxidation.rda |only qcr-0.1-18/qcr/data/pcmanufact.rda |only qcr-0.1-18/qcr/data/pistonrings.rda |only qcr-0.1-18/qcr/data/plates.rda |only qcr-0.1-18/qcr/data/presion.rda |only qcr-1.0/qcr/DESCRIPTION | 41 +++++---- qcr-1.0/qcr/MD5 | 161 +++++++++++++++++++++--------------- qcr-1.0/qcr/NAMESPACE | 59 ++++++++++++- qcr-1.0/qcr/R/mqcd.R | 18 +--- qcr-1.0/qcr/R/mqcs.R | 154 ++++++++++++++++++++++++++++++++-- qcr-1.0/qcr/R/mqcs.mcusum.r | 30 +++--- qcr-1.0/qcr/R/mqcs.mewma.r | 29 +++--- qcr-1.0/qcr/R/mqcs.t2.r | 42 +++++---- qcr-1.0/qcr/R/npqcd.R |only qcr-1.0/qcr/R/npqcs.Q.r |only qcr-1.0/qcr/R/npqcs.R |only qcr-1.0/qcr/R/npqcs.S.r |only qcr-1.0/qcr/R/npqcs.r.r |only qcr-1.0/qcr/R/plot.mqcs.R | 18 +++- qcr-1.0/qcr/R/plot.npqcs.R |only qcr-1.0/qcr/R/plot.qcs.R | 97 ++++++++------------- qcr-1.0/qcr/R/qcd.r | 85 ++----------------- qcr-1.0/qcr/R/qcr.R | 57 +++++++++--- qcr-1.0/qcr/R/qcs.R.r | 10 +- qcr-1.0/qcr/R/qcs.S.r | 10 +- qcr-1.0/qcr/R/qcs.c.r | 16 +-- qcr-1.0/qcr/R/qcs.ca.r |only qcr-1.0/qcr/R/qcs.cp.r |only qcr-1.0/qcr/R/qcs.cpn.r |only qcr-1.0/qcr/R/qcs.cusum.r | 16 +-- qcr-1.0/qcr/R/qcs.ewma.r |only qcr-1.0/qcr/R/qcs.hat.cpm.r |only qcr-1.0/qcr/R/qcs.np.r | 10 +- qcr-1.0/qcr/R/qcs.one.r | 22 ++-- qcr-1.0/qcr/R/qcs.p.r | 10 +- qcr-1.0/qcr/R/qcs.pcr.r |only qcr-1.0/qcr/R/qcs.r | 84 ++++++++++++++++-- qcr-1.0/qcr/R/qcs.u.r | 10 +- qcr-1.0/qcr/R/qcs.xbar.r | 16 +-- qcr-1.0/qcr/R/qt.r |only qcr-1.0/qcr/R/zzz.R | 2 qcr-1.0/qcr/data/archery1.RData |only qcr-1.0/qcr/data/circuit.RData |only qcr-1.0/qcr/data/counters.RData |only qcr-1.0/qcr/data/dowel1.RData |only qcr-1.0/qcr/data/employment.RData |only qcr-1.0/qcr/data/orangejuice.RData |only qcr-1.0/qcr/data/oxidation.RData |only qcr-1.0/qcr/data/pcmanufact.RData |only qcr-1.0/qcr/data/pistonrings.RData |only qcr-1.0/qcr/data/plates.RData |only qcr-1.0/qcr/data/presion.RData |only qcr-1.0/qcr/man/archery1.Rd | 8 + qcr-1.0/qcr/man/circuit.Rd | 6 - qcr-1.0/qcr/man/counters.Rd | 12 +- qcr-1.0/qcr/man/dowel1.Rd | 8 + qcr-1.0/qcr/man/employment.Rd | 12 +- qcr-1.0/qcr/man/mqcd.Rd | 11 +- qcr-1.0/qcr/man/mqcs.Rd | 12 +- qcr-1.0/qcr/man/mqcs.add.Rd |only qcr-1.0/qcr/man/mqcs.mcusum.Rd | 31 ++++-- qcr-1.0/qcr/man/mqcs.mewma.Rd | 32 ++++--- qcr-1.0/qcr/man/mqcs.t2.Rd | 31 ++++-- qcr-1.0/qcr/man/mstate.control.Rd |only qcr-1.0/qcr/man/npqcd.Rd |only qcr-1.0/qcr/man/npqcs.Q.Rd |only qcr-1.0/qcr/man/npqcs.Rd |only qcr-1.0/qcr/man/npqcs.S.Rd |only qcr-1.0/qcr/man/npqcs.add.Rd |only qcr-1.0/qcr/man/npqcs.r.Rd |only qcr-1.0/qcr/man/npstate.control.Rd |only qcr-1.0/qcr/man/orangejuice.Rd | 10 +- qcr-1.0/qcr/man/oxidation.Rd | 14 +-- qcr-1.0/qcr/man/pcmanufact.Rd | 4 qcr-1.0/qcr/man/pistonrings.Rd | 6 - qcr-1.0/qcr/man/plates.Rd | 16 ++- qcr-1.0/qcr/man/plot.mqcs.Rd | 5 - qcr-1.0/qcr/man/plot.npqcs.Rd |only qcr-1.0/qcr/man/plot.qcs.Rd | 54 ++++-------- qcr-1.0/qcr/man/presion.Rd | 12 +- qcr-1.0/qcr/man/qcd.Rd | 19 ++-- qcr-1.0/qcr/man/qcr.Rd | 18 ++-- qcr-1.0/qcr/man/qcs.R.Rd | 51 +++++------ qcr-1.0/qcr/man/qcs.Rd | 15 +-- qcr-1.0/qcr/man/qcs.S.Rd | 51 +++++------ qcr-1.0/qcr/man/qcs.add.Rd | 11 +- qcr-1.0/qcr/man/qcs.c.Rd | 40 ++++---- qcr-1.0/qcr/man/qcs.ca.Rd |only qcr-1.0/qcr/man/qcs.cp.Rd |only qcr-1.0/qcr/man/qcs.cpn.Rd |only qcr-1.0/qcr/man/qcs.cusum.Rd | 47 +++++----- qcr-1.0/qcr/man/qcs.ewma.Rd | 47 +++++----- qcr-1.0/qcr/man/qcs.hat.cpm.Rd |only qcr-1.0/qcr/man/qcs.np.Rd | 37 ++++---- qcr-1.0/qcr/man/qcs.one.Rd | 57 ++++++------ qcr-1.0/qcr/man/qcs.p.Rd | 37 ++++---- qcr-1.0/qcr/man/qcs.pcr.Rd |only qcr-1.0/qcr/man/qcs.u.Rd | 39 ++++---- qcr-1.0/qcr/man/qcs.xbar.Rd | 63 +++++++------- qcr-1.0/qcr/man/state.control.Rd | 22 ++-- 107 files changed, 1066 insertions(+), 769 deletions(-)
Title: Parameter Space Exploration with Latin Hypercubes
Description: Functions for creating Latin Hypercubes with
prescribed correlations and performing parameter space exploration.
Also implements the PLUE method.
Based on the package sensitivity, by Gilles Pujol,
Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom <andrechalom@gmail.com>
Diff between pse versions 0.4.5 dated 2016-03-14 and 0.4.6 dated 2016-07-19
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 10 ++++++++++ R/plotcv.R | 44 +++++++++++++++++++++++++++++++------------- R/plotecdf.R | 10 +++++++++- README.md | 2 ++ build/vignette.rds |binary inst/doc/multiple.pdf |binary inst/doc/pse_tutorial.pdf |binary man/plots.Rd | 5 ++++- 10 files changed, 69 insertions(+), 28 deletions(-)
Title: Penalized Regression-Based Clustering Method
Description: Clustering is unsupervised and exploratory in nature. Yet, it can be performed through penalized regression with grouping pursuit. In this package, we provide two algorithms for fitting the penalized regression-based clustering (PRclust). One algorithm is based on quadratic penalty and difference convex method. Another algorithm is based on difference convex and ADMM, called DC-ADD, which is more efficient. Generalized cross validation was provided to select the tuning parameters. Rand index, adjusted Rand index and Jaccard index were provided to estimate the agreement between estimated cluster memberships and the truth.
Author: Chong Wu, Wei Pan
Maintainer: Chong Wu <wuxx0845@umn.edu>
Diff between prclust versions 1.1 dated 2015-11-13 and 1.2 dated 2016-07-19
prclust-1.1/prclust/man/clusterStat.Rd |only prclust-1.2/prclust/DESCRIPTION | 8 prclust-1.2/prclust/MD5 | 22 prclust-1.2/prclust/NAMESPACE | 5 prclust-1.2/prclust/R/GCVOrignial.R | 45 - prclust-1.2/prclust/R/RcppExports.R | 103 -- prclust-1.2/prclust/R/stability.R |only prclust-1.2/prclust/man/GCV.Rd | 49 - prclust-1.2/prclust/man/PRclust.Rd | 57 - prclust-1.2/prclust/man/clustStat.Rd |only prclust-1.2/prclust/man/prclust-package.Rd | 13 prclust-1.2/prclust/man/stability.Rd |only prclust-1.2/prclust/src/ADMM_OrignialPRclust2.cpp | 817 +++++++++++++--------- prclust-1.2/prclust/src/RcppExports.cpp | 144 +++ 14 files changed, 771 insertions(+), 492 deletions(-)
Title: Methods for Multivariate Quadrature
Description: Provides methods to construct multivariate grids, which can be used
for multivariate quadrature. This grids can be based on different quadrature
rules like Newton-Cotes formulas (trapezoidal-, Simpson's- rule, ...) or Gauss
quadrature (Gauss-Hermite, Gauss-Legendre, ...). For the construction of the
multidimensional grid the product-rule or the combination- technique can be
applied.
Author: Constantin Weiser (HHU of Duesseldorf / Germany)
Maintainer: Constantin Weiser <weiserc@hhu.de>
Diff between mvQuad versions 1.0-5 dated 2016-02-18 and 1.0-6 dated 2016-07-19
DESCRIPTION | 13 +++++---- MD5 | 14 +++++----- R/mvQuad.R | 63 ++++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/CITATION | 2 - inst/NEWS | 7 +++++ inst/doc/mvQuad_intro.html | 20 +++++++------- man/mvQuad-package.Rd | 4 +- 8 files changed, 77 insertions(+), 46 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 (2006) <DOI:10.1162/neco.2006.18.7.1527>) and "Reducing the
dimensionality of data with neural networks" (G. E. Hinton, R. R.
Salakhutdinov (2006) <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, cph],
Johannes Rueckert [ctb],
Christoph M. Friedrich [ctb],
Geoffrey Hinton [cph],
Ruslan Salakhutdinov [cph],
Carl Edward Rasmussen [cph],
Maintainer: Martin Drees <mdrees@stud.fh-dortmund.de>
Diff between darch versions 0.10.0 dated 2015-12-08 and 0.12.0 dated 2016-07-19
darch-0.10.0/darch/R/darch.Remove.R |only darch-0.10.0/darch/R/darch.Reset.R |only darch-0.10.0/darch/R/generateWeights.R |only darch-0.10.0/darch/R/interface.R |only darch-0.10.0/darch/R/loadRBM.R |only darch-0.10.0/darch/R/loadRBMFFWeights.R |only darch-0.10.0/darch/R/net.R |only darch-0.10.0/darch/R/net.Setter.R |only darch-0.10.0/darch/R/newRBM.R |only darch-0.10.0/darch/R/rbm.Getter.R |only darch-0.10.0/darch/R/rbm.R |only darch-0.10.0/darch/R/rbm.Setter.R |only darch-0.10.0/darch/R/saveRBM.R |only darch-0.10.0/darch/R/saveRBMFFWeights.R |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/applyDropoutMask.Rd |only darch-0.10.0/darch/man/binSigmoidUnit.Rd |only darch-0.10.0/darch/man/darch.DataSet.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/generateRBMs-methods.Rd |only darch-0.10.0/darch/man/generateWeights.Rd |only darch-0.10.0/darch/man/getBatchSize-methods.Rd |only 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/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 |only 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 |only darch-0.10.0/darch/man/getFinalMomentum-methods.Rd |only 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 |only darch-0.10.0/darch/man/getHiddenBiases-methods.Rd |only darch-0.10.0/darch/man/getHiddenBiasesInc-methods.Rd |only darch-0.10.0/darch/man/getHiddenUnitStates-methods.Rd |only darch-0.10.0/darch/man/getInitialMomentum-Net-method.Rd |only darch-0.10.0/darch/man/getInitialMomentum.Rd |only darch-0.10.0/darch/man/getLayer-DArch-method.Rd |only darch-0.10.0/darch/man/getLayer.Rd |only darch-0.10.0/darch/man/getLayerField-DArch-method.Rd |only darch-0.10.0/darch/man/getLayerField.Rd |only darch-0.10.0/darch/man/getLayerFunction-DArch-method.Rd |only darch-0.10.0/darch/man/getLayerFunction.Rd |only darch-0.10.0/darch/man/getLayerWeights-DArch-method.Rd |only darch-0.10.0/darch/man/getLayerWeights.Rd |only darch-0.10.0/darch/man/getLayers-DArch-method.Rd |only darch-0.10.0/darch/man/getLayers.Rd |only darch-0.10.0/darch/man/getLearnRateBiasHidden-methods.Rd |only darch-0.10.0/darch/man/getLearnRateBiasVisible-methods.Rd |only darch-0.10.0/darch/man/getLearnRateBiases-DArch-method.Rd |only darch-0.10.0/darch/man/getLearnRateBiases.Rd |only darch-0.10.0/darch/man/getLearnRateWeights-methods.Rd |only darch-0.10.0/darch/man/getMomentum-methods.Rd |only darch-0.10.0/darch/man/getMomentumSwitch-methods.Rd |only 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 |only darch-0.10.0/darch/man/getNumVisible-methods.Rd |only darch-0.10.0/darch/man/getOutput-methods.Rd |only darch-0.10.0/darch/man/getPosPhaseData-methods.Rd |only 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 |only darch-0.10.0/darch/man/getVisibleBiases-methods.Rd |only darch-0.10.0/darch/man/getVisibleBiasesInc-methods.Rd |only darch-0.10.0/darch/man/getVisibleUnitStates-methods.Rd |only darch-0.10.0/darch/man/getWeightCost-methods.Rd |only darch-0.10.0/darch/man/getWeightInc-methods.Rd |only darch-0.10.0/darch/man/getWeights-methods.Rd |only 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/linearUnitDerivative.Rd |only darch-0.10.0/darch/man/linearUnitFunc.Rd |only darch-0.10.0/darch/man/loadRBM.Rd |only darch-0.10.0/darch/man/loadRBMFFWeights.Rd |only darch-0.10.0/darch/man/maxoutUnitDerivative.Rd |only darch-0.10.0/darch/man/newRBM.Rd |only darch-0.10.0/darch/man/quadraticError.Rd |only darch-0.10.0/darch/man/removeLayerField-methods.Rd |only darch-0.10.0/darch/man/resetDArch-methods.Rd |only darch-0.10.0/darch/man/resetExecOutput-methods.Rd |only darch-0.10.0/darch/man/resetRBM-methods.Rd |only darch-0.10.0/darch/man/saveDArch-methods.Rd |only darch-0.10.0/darch/man/saveRBM-methods.Rd |only darch-0.10.0/darch/man/saveRBMFFWeights-methods.Rd |only darch-0.10.0/darch/man/setBatchSize-methods.Rd |only darch-0.10.0/darch/man/setCancel-methods.Rd |only darch-0.10.0/darch/man/setCancelMessage-methods.Rd |only 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 |only darch-0.10.0/darch/man/setExecuteFunction-methods.Rd |only darch-0.10.0/darch/man/setFF-methods.Rd |only darch-0.10.0/darch/man/setFinalMomentum-methods.Rd |only darch-0.10.0/darch/man/setFineTuneFunction-methods.Rd |only darch-0.10.0/darch/man/setGenWeightFunction-methods.Rd |only darch-0.10.0/darch/man/setHiddenBiases-methods.Rd |only darch-0.10.0/darch/man/setHiddenBiasesInc-methods.Rd |only darch-0.10.0/darch/man/setHiddenUnitFunction-methods.Rd |only darch-0.10.0/darch/man/setHiddenUnitStates-methods.Rd |only 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 |only darch-0.10.0/darch/man/setLayerField-methods.Rd |only darch-0.10.0/darch/man/setLayerFunction-methods.Rd |only darch-0.10.0/darch/man/setLayerWeights-methods.Rd |only darch-0.10.0/darch/man/setLayers-methods.Rd |only darch-0.10.0/darch/man/setLearnRateBiasHidden-methods.Rd |only darch-0.10.0/darch/man/setLearnRateBiasVisible-methods.Rd |only darch-0.10.0/darch/man/setLearnRateBiases-methods.Rd |only darch-0.10.0/darch/man/setLearnRateWeights-methods.Rd |only darch-0.10.0/darch/man/setLogLevel-methods.Rd |only darch-0.10.0/darch/man/setMomentumSwitch-methods.Rd |only 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 |only darch-0.10.0/darch/man/setNumVisible-methods.Rd |only darch-0.10.0/darch/man/setOutput-methods.Rd |only darch-0.10.0/darch/man/setPosPhaseData-methods.Rd |only darch-0.10.0/darch/man/setRBMList-methods.Rd |only darch-0.10.0/darch/man/setStats-methods.Rd |only darch-0.10.0/darch/man/setUpdateFunction-methods.Rd |only darch-0.10.0/darch/man/setVisibleBiases-methods.Rd |only darch-0.10.0/darch/man/setVisibleBiasesInc-methods.Rd |only darch-0.10.0/darch/man/setVisibleUnitFunction-methods.Rd |only darch-0.10.0/darch/man/setVisibleUnitStates-methods.Rd |only darch-0.10.0/darch/man/setWeightCost-methods.Rd |only darch-0.10.0/darch/man/setWeightInc-methods.Rd |only darch-0.10.0/darch/man/setWeights-methods.Rd |only darch-0.10.0/darch/man/sigmUnitFunc.Rd |only darch-0.10.0/darch/man/sigmUnitFuncSwitch.Rd |only darch-0.10.0/darch/man/sigmoidUnitDerivative.Rd |only darch-0.10.0/darch/man/softmaxUnitDerivative.Rd |only 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-0.12.0/darch/DESCRIPTION | 49 darch-0.12.0/darch/MD5 | 358 +---- darch-0.12.0/darch/NAMESPACE | 187 -- darch-0.12.0/darch/R/RcppExports.R |only darch-0.12.0/darch/R/autosave.R |only darch-0.12.0/darch/R/backpropagation.R | 261 ++- darch-0.12.0/darch/R/benchmark.R |only darch-0.12.0/darch/R/bootstrap.R |only darch-0.12.0/darch/R/caret.R |only darch-0.12.0/darch/R/compat.R |only darch-0.12.0/darch/R/config.R |only darch-0.12.0/darch/R/darch.Add.R | 70 - darch-0.12.0/darch/R/darch.Class.R |only darch-0.12.0/darch/R/darch.Getter.R | 492 ------- darch-0.12.0/darch/R/darch.Learn.R | 576 ++++++-- darch-0.12.0/darch/R/darch.R | 654 ++++++++-- darch-0.12.0/darch/R/darch.Setter.R | 461 ------- darch-0.12.0/darch/R/darchUnitFunctions.R | 361 ++--- darch-0.12.0/darch/R/dataset.R | 549 ++++---- darch-0.12.0/darch/R/dropout.R | 52 darch-0.12.0/darch/R/errorFunctions.R | 97 - darch-0.12.0/darch/R/generateRBMs.R | 70 - darch-0.12.0/darch/R/generateWeightsFunctions.R |only darch-0.12.0/darch/R/loadDArch.R | 43 darch-0.12.0/darch/R/log.R |only darch-0.12.0/darch/R/makeStartEndPoints.R | 37 darch-0.12.0/darch/R/minimize.R | 62 darch-0.12.0/darch/R/minimizeAutoencoder.R | 176 +- darch-0.12.0/darch/R/minimizeClassifier.R | 234 ++- darch-0.12.0/darch/R/mnist.R | 68 - darch-0.12.0/darch/R/momentum.R |only darch-0.12.0/darch/R/net.Class.R |only darch-0.12.0/darch/R/net.Getter.R | 296 ---- darch-0.12.0/darch/R/newDArch.R | 59 darch-0.12.0/darch/R/params.R |only darch-0.12.0/darch/R/plot.R |only darch-0.12.0/darch/R/predict.R |only darch-0.12.0/darch/R/print.R |only darch-0.12.0/darch/R/rbm.Class.R |only darch-0.12.0/darch/R/rbm.Learn.R | 167 +- darch-0.12.0/darch/R/rbm.Reset.R | 55 darch-0.12.0/darch/R/rbmUnitFunctions.R | 136 +- darch-0.12.0/darch/R/rbmUpdate.R | 103 - darch-0.12.0/darch/R/rpropagation.R | 288 +++- darch-0.12.0/darch/R/runDArch.R | 136 +- darch-0.12.0/darch/R/saveDArch.R | 67 - darch-0.12.0/darch/R/test.R |only darch-0.12.0/darch/R/util.R |only darch-0.12.0/darch/R/weightUpdateFunctions.R |only darch-0.12.0/darch/README | 2 darch-0.12.0/darch/man/DArch-class.Rd | 61 darch-0.12.0/darch/man/DataSet.Rd |only darch-0.12.0/darch/man/Net.Rd |only darch-0.12.0/darch/man/RBM.Rd |only darch-0.12.0/darch/man/addLayer-DArch-method.Rd | 5 darch-0.12.0/darch/man/addLayer.Rd | 7 darch-0.12.0/darch/man/addLayerField-DArch-method.Rd | 4 darch-0.12.0/darch/man/addLayerField.Rd | 4 darch-0.12.0/darch/man/backpropagation.Rd | 73 - darch-0.12.0/darch/man/contr.ltfr.Rd |only darch-0.12.0/darch/man/createDataSet-ANY-ANY-missing-DataSet-method.Rd | 7 darch-0.12.0/darch/man/createDataSet-ANY-ANY-missing-missing-method.Rd | 14 darch-0.12.0/darch/man/createDataSet-ANY-missing-formula-missing-method.Rd | 19 darch-0.12.0/darch/man/createDataSet.Rd | 8 darch-0.12.0/darch/man/crossEntropyError.Rd | 29 darch-0.12.0/darch/man/darch.Rd | 641 ++++++--- darch-0.12.0/darch/man/darchBench.Rd |only darch-0.12.0/darch/man/darchModelInfo.Rd |only darch-0.12.0/darch/man/darchTest.Rd |only darch-0.12.0/darch/man/exponentialLinearUnit.Rd |only darch-0.12.0/darch/man/fineTuneDArch-DArch-method.Rd | 36 darch-0.12.0/darch/man/fineTuneDArch.Rd | 67 - darch-0.12.0/darch/man/generateDropoutMask.Rd | 6 darch-0.12.0/darch/man/generateRBMs-DArch-method.Rd |only darch-0.12.0/darch/man/generateWeightsGlorotNormal.Rd |only darch-0.12.0/darch/man/generateWeightsGlorotUniform.Rd |only darch-0.12.0/darch/man/generateWeightsHeNormal.Rd |only darch-0.12.0/darch/man/generateWeightsHeUniform.Rd |only darch-0.12.0/darch/man/generateWeightsNormal.Rd |only darch-0.12.0/darch/man/generateWeightsUniform.Rd |only darch-0.12.0/darch/man/getDropoutMask.Rd | 3 darch-0.12.0/darch/man/getMomentum.Rd |only darch-0.12.0/darch/man/linearUnit.Rd | 39 darch-0.12.0/darch/man/linearUnitRbm.Rd |only darch-0.12.0/darch/man/loadDArch.Rd | 22 darch-0.12.0/darch/man/makeStartEndPoints.Rd | 11 darch-0.12.0/darch/man/maxoutUnit.Rd |only darch-0.12.0/darch/man/maxoutWeightUpdate.Rd |only darch-0.12.0/darch/man/minimize.Rd | 36 darch-0.12.0/darch/man/minimizeAutoencoder.Rd | 69 - darch-0.12.0/darch/man/minimizeClassifier.Rd | 80 - darch-0.12.0/darch/man/mseError.Rd | 23 darch-0.12.0/darch/man/newDArch.Rd | 29 darch-0.12.0/darch/man/plot.DArch.Rd |only darch-0.12.0/darch/man/preTrainDArch-DArch-method.Rd | 20 darch-0.12.0/darch/man/preTrainDArch.Rd | 23 darch-0.12.0/darch/man/predict.DArch.Rd | 47 darch-0.12.0/darch/man/print.DArch.Rd | 25 darch-0.12.0/darch/man/provideMNIST.Rd | 12 darch-0.12.0/darch/man/rbmUpdate.Rd | 24 darch-0.12.0/darch/man/readMNIST.Rd | 9 darch-0.12.0/darch/man/rectifiedLinearUnit.Rd |only darch-0.12.0/darch/man/resetRBM.Rd |only darch-0.12.0/darch/man/rmseError.Rd |only darch-0.12.0/darch/man/rpropagation.Rd | 115 + darch-0.12.0/darch/man/runDArch.Rd | 35 darch-0.12.0/darch/man/runDArchDropout.Rd |only darch-0.12.0/darch/man/saveDArch.Rd |only darch-0.12.0/darch/man/setDarchParams.Rd |only darch-0.12.0/darch/man/setDropoutMask-set.Rd |only darch-0.12.0/darch/man/setLogLevel.Rd |only darch-0.12.0/darch/man/show-DArch-method.Rd |only darch-0.12.0/darch/man/sigmoidUnit.Rd | 40 darch-0.12.0/darch/man/sigmoidUnitRbm.Rd |only darch-0.12.0/darch/man/softmaxUnit.Rd | 42 darch-0.12.0/darch/man/softplusUnit.Rd |only darch-0.12.0/darch/man/tanhUnit.Rd |only darch-0.12.0/darch/man/tanhUnitRbm.Rd |only darch-0.12.0/darch/man/trainRBM.Rd | 40 darch-0.12.0/darch/man/validateDataSet-DataSet-method.Rd | 5 darch-0.12.0/darch/man/validateDataSet.Rd | 5 darch-0.12.0/darch/man/weightDecayWeightUpdate.Rd |only darch-0.12.0/darch/src |only 285 files changed, 4043 insertions(+), 3858 deletions(-)
Title: Simulates Correlated Multinomial Responses
Description: Simulates correlated multinomial responses conditional on a marginal model specification.
Author: Anestis Touloumis [aut, cre]
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between SimCorMultRes versions 1.4.0 dated 2015-12-14 and 1.4.1 dated 2016-07-19
SimCorMultRes-1.4.0/SimCorMultRes/inst/doc/SCMRvin.R |only SimCorMultRes-1.4.0/SimCorMultRes/inst/doc/SCMRvin.Rnw |only SimCorMultRes-1.4.0/SimCorMultRes/inst/doc/SCMRvin.pdf |only SimCorMultRes-1.4.0/SimCorMultRes/vignettes/SCMRvin-concordance.tex |only SimCorMultRes-1.4.0/SimCorMultRes/vignettes/SCMRvin.Rnw |only SimCorMultRes-1.4.0/SimCorMultRes/vignettes/SCMRvin.tex |only SimCorMultRes-1.4.1/SimCorMultRes/DESCRIPTION | 21 - SimCorMultRes-1.4.1/SimCorMultRes/MD5 | 46 +- SimCorMultRes-1.4.1/SimCorMultRes/NAMESPACE | 7 SimCorMultRes-1.4.1/SimCorMultRes/R/rbin.R | 120 ++++--- SimCorMultRes-1.4.1/SimCorMultRes/R/rmult.bcl.R | 109 ++++-- SimCorMultRes-1.4.1/SimCorMultRes/R/rmult.clm.R | 148 +++++---- SimCorMultRes-1.4.1/SimCorMultRes/R/rmult.crm.R | 158 +++++----- SimCorMultRes-1.4.1/SimCorMultRes/R/rnorta.R | 37 +- SimCorMultRes-1.4.1/SimCorMultRes/R/rsmvnorm.R | 37 +- SimCorMultRes-1.4.1/SimCorMultRes/build/vignette.rds |binary SimCorMultRes-1.4.1/SimCorMultRes/inst/CITATION | 10 SimCorMultRes-1.4.1/SimCorMultRes/inst/NEWS | 9 SimCorMultRes-1.4.1/SimCorMultRes/inst/doc/SimCorMultRes.R |only SimCorMultRes-1.4.1/SimCorMultRes/inst/doc/SimCorMultRes.Rnw |only SimCorMultRes-1.4.1/SimCorMultRes/inst/doc/SimCorMultRes.pdf |only SimCorMultRes-1.4.1/SimCorMultRes/man/SimCorMultRes-package.Rd | 26 - SimCorMultRes-1.4.1/SimCorMultRes/man/rbin.Rd | 85 +++-- SimCorMultRes-1.4.1/SimCorMultRes/man/rmult.bcl.Rd | 84 +++-- SimCorMultRes-1.4.1/SimCorMultRes/man/rmult.clm.Rd | 85 +++-- SimCorMultRes-1.4.1/SimCorMultRes/man/rmult.crm.Rd | 70 ++-- SimCorMultRes-1.4.1/SimCorMultRes/man/rnorta.Rd | 67 +++- SimCorMultRes-1.4.1/SimCorMultRes/man/rsmvnorm.Rd | 20 - SimCorMultRes-1.4.1/SimCorMultRes/vignettes/SimCorMultRes.Rnw |only 29 files changed, 699 insertions(+), 440 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, Rasch copula model, faceted and
hierarchical rater models, ordinal IRT model (ISOP),
DETECT statistic, local structural equation modeling (LSEM),
mean and covariance structure modelling for multivariate normally
distributed data.
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 1.11-0 dated 2016-05-30 and 1.12-2 dated 2016-07-19
sirt-1.11-0/sirt/man/rasch.pml.Rd |only sirt-1.12-2/sirt/DESCRIPTION | 14 sirt-1.12-2/sirt/MD5 | 246 ++-- sirt-1.12-2/sirt/NAMESPACE | 328 +++-- sirt-1.12-2/sirt/R/CallSwitch.R |only sirt-1.12-2/sirt/R/Q3.R |only sirt-1.12-2/sirt/R/Q3.testlet.R |only sirt-1.12-2/sirt/R/R2conquest.R |only sirt-1.12-2/sirt/R/amh.R | 140 +- sirt-1.12-2/sirt/R/amh_compare_estimators.R |only sirt-1.12-2/sirt/R/amh_eval_prior.R |only sirt-1.12-2/sirt/R/amh_ic.R | 22 sirt-1.12-2/sirt/R/amh_loglike.R | 10 sirt-1.12-2/sirt/R/amh_posterior.R |only sirt-1.12-2/sirt/R/amh_proposal_refresh.R | 22 sirt-1.12-2/sirt/R/amh_sampling.R | 51 sirt-1.12-2/sirt/R/anova_sirt.R | 8 sirt-1.12-2/sirt/R/bounds_parameters.R |only sirt-1.12-2/sirt/R/btm.R | 112 + sirt-1.12-2/sirt/R/btm_fit.R | 29 sirt-1.12-2/sirt/R/categorize.R | 31 sirt-1.12-2/sirt/R/coef.mlnormal.R |only sirt-1.12-2/sirt/R/coef.pmle.R |only sirt-1.12-2/sirt/R/confint.mlnormal.R |only sirt-1.12-2/sirt/R/confint.pmle.R |only sirt-1.12-2/sirt/R/decategorize.R | 13 sirt-1.12-2/sirt/R/dimproper.R |only sirt-1.12-2/sirt/R/ginverse_sym.R |only sirt-1.12-2/sirt/R/hard_thresholding.R |only sirt-1.12-2/sirt/R/invariance.alignment2.R | 27 sirt-1.12-2/sirt/R/logLik.mlnormal.R |only sirt-1.12-2/sirt/R/logLik.pmle.R |only sirt-1.12-2/sirt/R/loglike_mvnorm.R |only sirt-1.12-2/sirt/R/lsem.MGM.stepfunctions.R | 11 sirt-1.12-2/sirt/R/lsem.estimate.R | 54 sirt-1.12-2/sirt/R/lsem.fitsem.R | 44 sirt-1.12-2/sirt/R/lsem.group.moderator.R | 10 sirt-1.12-2/sirt/R/lsem.helper.R | 8 sirt-1.12-2/sirt/R/lsem.parameter.summary.R | 19 sirt-1.12-2/sirt/R/lsem.permutationTest.R | 42 sirt-1.12-2/sirt/R/lsem.residualize.R | 38 sirt-1.12-2/sirt/R/mcmc_WaldTest.R | 45 sirt-1.12-2/sirt/R/mcmc_coef.R | 4 sirt-1.12-2/sirt/R/mcmc_confint.R | 14 sirt-1.12-2/sirt/R/mcmc_derivedPars.R | 6 sirt-1.12-2/sirt/R/mcmc_plot.R | 4 sirt-1.12-2/sirt/R/mcmc_summary.R | 48 sirt-1.12-2/sirt/R/mcmc_vcov.R | 8 sirt-1.12-2/sirt/R/mcmclist2coda.R | 21 sirt-1.12-2/sirt/R/md.pattern.sirt.R | 21 sirt-1.12-2/sirt/R/mlnormal.R |only sirt-1.12-2/sirt/R/mlnormalCheckMatrixListDifference.R |only sirt-1.12-2/sirt/R/mlnormalMatrix2List.R |only sirt-1.12-2/sirt/R/mlnormal_abs_approx.R |only sirt-1.12-2/sirt/R/mlnormal_adjust_numdiff_parameter.R |only sirt-1.12-2/sirt/R/mlnormal_as_vector_names.R |only sirt-1.12-2/sirt/R/mlnormal_covmat_add_ridge.R |only sirt-1.12-2/sirt/R/mlnormal_create_disp.R |only sirt-1.12-2/sirt/R/mlnormal_equal_list_matrices.R |only sirt-1.12-2/sirt/R/mlnormal_equal_matrix.R |only sirt-1.12-2/sirt/R/mlnormal_eval_penalty.R |only sirt-1.12-2/sirt/R/mlnormal_eval_penalty_update_theta.R |only sirt-1.12-2/sirt/R/mlnormal_eval_priors.R |only sirt-1.12-2/sirt/R/mlnormal_eval_priors_derivative.R |only sirt-1.12-2/sirt/R/mlnormal_eval_priors_derivative2.R |only sirt-1.12-2/sirt/R/mlnormal_fill_matrix_from_list.R |only sirt-1.12-2/sirt/R/mlnormal_fit_function_ml.R |only sirt-1.12-2/sirt/R/mlnormal_ic.R |only sirt-1.12-2/sirt/R/mlnormal_information_matrix_reml.R |only sirt-1.12-2/sirt/R/mlnormal_linear_regression_bayes.R |only sirt-1.12-2/sirt/R/mlnormal_log_2pi.R |only sirt-1.12-2/sirt/R/mlnormal_log_det.R |only sirt-1.12-2/sirt/R/mlnormal_parameter_change.R |only sirt-1.12-2/sirt/R/mlnormal_postproc_eval_posterior.R |only sirt-1.12-2/sirt/R/mlnormal_postproc_parameters.R |only sirt-1.12-2/sirt/R/mlnormal_proc.R |only sirt-1.12-2/sirt/R/mlnormal_proc_control.R |only sirt-1.12-2/sirt/R/mlnormal_proc_variance_shortcut.R |only sirt-1.12-2/sirt/R/mlnormal_proc_variance_shortcut_XY_R.R |only sirt-1.12-2/sirt/R/mlnormal_proc_variance_shortcut_XY_Rcpp.R |only sirt-1.12-2/sirt/R/mlnormal_proc_variance_shortcut_Z_R.R |only sirt-1.12-2/sirt/R/mlnormal_proc_variance_shortcut_Z_Rcpp.R |only sirt-1.12-2/sirt/R/mlnormal_process_prior.R |only sirt-1.12-2/sirt/R/mlnormal_sqrt_diag.R |only sirt-1.12-2/sirt/R/mlnormal_update_V_R.R |only sirt-1.12-2/sirt/R/mlnormal_update_V_Rcpp.R |only sirt-1.12-2/sirt/R/mlnormal_update_beta.R |only sirt-1.12-2/sirt/R/mlnormal_update_beta_GLS.R |only sirt-1.12-2/sirt/R/mlnormal_update_beta_XVX_R.R |only sirt-1.12-2/sirt/R/mlnormal_update_beta_XVX_Rcpp.R |only sirt-1.12-2/sirt/R/mlnormal_update_beta_iterations_penalty.R |only sirt-1.12-2/sirt/R/mlnormal_update_beta_iterations_priors.R |only sirt-1.12-2/sirt/R/mlnormal_update_control_list.R |only sirt-1.12-2/sirt/R/mlnormal_update_ml_derivative_V.R |only sirt-1.12-2/sirt/R/mlnormal_update_theta_ml.R |only sirt-1.12-2/sirt/R/mlnormal_update_theta_newton_step.R |only sirt-1.12-2/sirt/R/mlnormal_verbose_f0.R |only sirt-1.12-2/sirt/R/mlnormal_verbose_f1.R |only sirt-1.12-2/sirt/R/mlnormal_verbose_f2.R |only sirt-1.12-2/sirt/R/parmsummary_extend.R |only sirt-1.12-2/sirt/R/plot.lsem.R | 27 sirt-1.12-2/sirt/R/pmle.R |only sirt-1.12-2/sirt/R/pmle_data_proc.R |only sirt-1.12-2/sirt/R/pmle_eval_posterior.R |only sirt-1.12-2/sirt/R/pmle_ic.R |only sirt-1.12-2/sirt/R/pmle_process_prior.R |only sirt-1.12-2/sirt/R/pow.R |only sirt-1.12-2/sirt/R/print.mlnormal.R |only sirt-1.12-2/sirt/R/prior_extract_density.R |only sirt-1.12-2/sirt/R/prior_model_pars_CleanString.R |only sirt-1.12-2/sirt/R/prior_model_parse.R |only sirt-1.12-2/sirt/R/rasch.conquest.R | 580 ---------- sirt-1.12-2/sirt/R/rasch.pml2.R | 434 ------- sirt-1.12-2/sirt/R/soft_thresholding.R |only sirt-1.12-2/sirt/R/summary.amh.R | 38 sirt-1.12-2/sirt/R/summary.mlnormal.R |only sirt-1.12-2/sirt/R/summary.pmle.R |only sirt-1.12-2/sirt/R/summary_round_helper.R |only sirt-1.12-2/sirt/R/testlet.yen.q3.R |only sirt-1.12-2/sirt/R/tracemat.R |only sirt-1.12-2/sirt/R/vcov.mlnormal.R |only sirt-1.12-2/sirt/R/vcov.pmle.R |only sirt-1.12-2/sirt/R/xxirt.R | 70 - sirt-1.12-2/sirt/R/xxirt_EAP.R | 14 sirt-1.12-2/sirt/R/xxirt_IRT.se.R | 12 sirt-1.12-2/sirt/R/xxirt_ThetaDistribution_extract_freeParameters.R | 11 sirt-1.12-2/sirt/R/xxirt_coef.R | 6 sirt-1.12-2/sirt/R/xxirt_compute_itemprobs.R | 24 sirt-1.12-2/sirt/R/xxirt_compute_likelihood.R | 14 sirt-1.12-2/sirt/R/xxirt_compute_posterior.R | 44 sirt-1.12-2/sirt/R/xxirt_compute_priorDistribution.R | 8 sirt-1.12-2/sirt/R/xxirt_createDiscItem.R | 8 sirt-1.12-2/sirt/R/xxirt_createItemList.R | 20 sirt-1.12-2/sirt/R/xxirt_createParTable.R | 76 - sirt-1.12-2/sirt/R/xxirt_createThetaDistribution.R | 10 sirt-1.12-2/sirt/R/xxirt_data_proc.R | 57 sirt-1.12-2/sirt/R/xxirt_hessian.R | 23 sirt-1.12-2/sirt/R/xxirt_ic.R | 16 sirt-1.12-2/sirt/R/xxirt_modifyParTable.R | 28 sirt-1.12-2/sirt/R/xxirt_mstep_ThetaParameters.R | 61 - sirt-1.12-2/sirt/R/xxirt_mstep_itemParameters.R | 53 sirt-1.12-2/sirt/R/xxirt_mstep_itemParameters_evalPrior.R | 33 sirt-1.12-2/sirt/R/xxirt_parTheta_extract_freeParameters.R | 6 sirt-1.12-2/sirt/R/xxirt_partable_extract_freeParameters.R | 10 sirt-1.12-2/sirt/R/xxirt_partable_include_freeParameters.R | 7 sirt-1.12-2/sirt/R/xxirt_postproc_parameters.R | 35 sirt-1.12-2/sirt/R/xxirt_proc_ParTable.R | 72 - sirt-1.12-2/sirt/R/xxirt_vcov.R | 4 sirt-1.12-2/sirt/R/yen.q3.R | 102 - sirt-1.12-2/sirt/R/zzz.R | 34 sirt-1.12-2/sirt/inst/NEWS | 46 sirt-1.12-2/sirt/man/CallSwitch.Rd |only sirt-1.12-2/sirt/man/Q3.Rd | 4 sirt-1.12-2/sirt/man/Q3.testlet.Rd | 4 sirt-1.12-2/sirt/man/R2conquest.Rd | 18 sirt-1.12-2/sirt/man/amh.Rd | 202 ++- sirt-1.12-2/sirt/man/data.activity.itempars.Rd | 2 sirt-1.12-2/sirt/man/equating.rasch.Rd | 7 sirt-1.12-2/sirt/man/loglike_mvnorm.Rd |only sirt-1.12-2/sirt/man/mlnormal.Rd |only sirt-1.12-2/sirt/man/nedelsky.sim.Rd | 42 sirt-1.12-2/sirt/man/parmsummary_extend.Rd |only sirt-1.12-2/sirt/man/prior_model_parse.Rd |only sirt-1.12-2/sirt/man/rasch.pml3.Rd |only sirt-1.12-2/sirt/man/rinvgamma2.Rd | 20 sirt-1.12-2/sirt/man/sim.raschtype.Rd | 10 sirt-1.12-2/sirt/man/sirt-defunct.Rd |only sirt-1.12-2/sirt/man/sirt-package.Rd | 554 +++++---- sirt-1.12-2/sirt/man/sirt-utilities.Rd |only sirt-1.12-2/sirt/man/xxirt.Rd | 40 sirt-1.12-2/sirt/man/xxirt_createParTable.Rd | 15 sirt-1.12-2/sirt/src/mlnormal_helper_functions.cpp |only 172 files changed, 1885 insertions(+), 2466 deletions(-)
Title: Functions for Statistics Classes at Carleton College
Description: Includes commands for bootstrapping and permutation tests, a command for created grouped bar plots, and a demo of the quantile-normal plot for data drawn from different distributions.
Author: Laura Chihara
Maintainer: Laura Chihara <lchihara@carleton.edu>
Diff between CarletonStats versions 1.2 dated 2015-12-15 and 1.3 dated 2016-07-19
DESCRIPTION | 12 +- MD5 | 42 +++---- R/CarletonStats-internal.R | 262 +++++++++++++++++++++++---------------------- R/anovaSummarized.R | 18 +-- R/boot.default.R | 114 +++++++++---------- R/boot.formula.R | 18 +-- R/bootCor.R | 42 +++---- R/bootPaired.R | 36 +++--- R/confIntDemo.R | 48 ++++---- R/corDemo.R | 1 R/groupedBar.default.R | 5 R/groupedBar.formula.R | 18 +-- R/permTest.default.R | 4 R/permTestCor.R | 36 +++--- R/permTestPaired.R | 36 +++--- R/qqPlotDemo.R | 16 +- R/stemPlot.default.R | 38 +++--- R/stemPlot.formula.R | 22 +-- data/Icecream.rda |binary data/Milkshakes.rda |binary data/states03.rda |binary man/groupedBar.Rd | 19 +-- 22 files changed, 401 insertions(+), 386 deletions(-)
Title: Serial Limiting Dilution Assay Statistics
Description: Calculates maximum likelihood estimate, exact and asymptotic confidence intervals, and exact and asymptotic goodness of fit p-values for infectious units per million (IUPM) from serial limiting dilution assays. This package uses the likelihood equation, exact PGOF, and exact confidence intervals described in Meyers et al. (1994) <http://jcm.asm.org/content/32/3/732.full.pdf>.
Author: Michael Hudgens, Ilana Trumble, Andrew Allmon
Maintainer: Ilana Trumble <itrumble@unc.edu>
Diff between SLDAssay versions 1.4 dated 2016-06-29 and 1.5 dated 2016-07-19
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 1 + R/IUPM.R | 28 ++++++++++++++++++++++++---- man/get.iupm.Rd | 7 +++++-- 5 files changed, 40 insertions(+), 16 deletions(-)
Title: Designing multi-arm multi-stage studies
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 0.9 dated 2016-06-14 and 1.0 dated 2016-07-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/mams.R | 8 ++++++++ inst/NEWS | 6 ++++++ 4 files changed, 21 insertions(+), 7 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++.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.6 dated 2016-06-29 and 1.7 dated 2016-07-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/ChannelAttribution-package.Rd | 4 ++-- src/ChannelAttribution.cpp | 23 +++++++++++++---------- 4 files changed, 22 insertions(+), 19 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Import 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded
'ReadStat' C library <https://github.com/WizardMac/ReadStat>. Package includes
preliminary support for writing 'Stata' and 'SPSS' formats.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between haven versions 0.2.0 dated 2015-04-08 and 0.2.1 dated 2016-07-19
DESCRIPTION | 15 ++++++++------- MD5 | 29 +++++++++++++++-------------- NAMESPACE | 2 +- R/haven.R | 2 -- R/utils.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/datetimes.html | 16 ++++++++++------ man/as_factor.Rd | 2 +- man/hms.Rd | 2 +- man/labelled.Rd | 2 +- man/read_dta.Rd | 2 +- man/read_sas.Rd | 7 ++----- man/read_spss.Rd | 2 +- man/zap_empty.Rd | 2 +- vignettes/rsconnect |only 16 files changed, 44 insertions(+), 43 deletions(-)
Title: Generate, Visualise, and Compare Fast and Frugal Decision Trees
Description: Fast and Frugal Trees (FFTs) are very simple decision trees for
classifying cases (i.e.; breast cancer patients) into one of two classes (e.g.;
no cancer vs. true cancer). FFTs can be preferable to more complex algorithms (such as
logistic regression) because they are easy to communicate and implement, and are
robust against noisy data. This package contains several functions that allow users
to create, visualize, and test FFts from their input their own data.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>
Diff between FFTrees versions 1.0.1 dated 2016-07-12 and 1.1.0 dated 2016-07-19
FFTrees-1.0.1/FFTrees/R/applyfft_function.R |only FFTrees-1.0.1/FFTrees/R/simfft_function.R |only FFTrees-1.0.1/FFTrees/R/simfftplot_function.R |only FFTrees-1.0.1/FFTrees/inst/doc/simfft_function.R |only FFTrees-1.0.1/FFTrees/inst/doc/simfft_function.Rmd |only FFTrees-1.0.1/FFTrees/inst/doc/simfft_function.html |only FFTrees-1.0.1/FFTrees/man/applyfft.Rd |only FFTrees-1.0.1/FFTrees/man/simfft.Rd |only FFTrees-1.0.1/FFTrees/man/simfftplot.Rd |only FFTrees-1.0.1/FFTrees/vignettes/simfft_function.Rmd |only FFTrees-1.1.0/FFTrees/DESCRIPTION | 15 FFTrees-1.1.0/FFTrees/MD5 | 98 + FFTrees-1.1.0/FFTrees/NAMESPACE | 16 FFTrees-1.1.0/FFTrees/R/auc_function.R |only FFTrees-1.1.0/FFTrees/R/cartpred_function.R |only FFTrees-1.1.0/FFTrees/R/classtable_function.R | 48 FFTrees-1.1.0/FFTrees/R/cuerank_function.R | 23 FFTrees-1.1.0/FFTrees/R/fft_function.R | 1014 +++----------------- FFTrees-1.1.0/FFTrees/R/growffts_function.R |only FFTrees-1.1.0/FFTrees/R/heartdisease_doc.R | 2 FFTrees-1.1.0/FFTrees/R/income_doc.R | 2 FFTrees-1.1.0/FFTrees/R/lrpred_function.R |only FFTrees-1.1.0/FFTrees/R/mushrooms_doc.R | 2 FFTrees-1.1.0/FFTrees/R/plotfft_function.R | 884 +++++++++-------- FFTrees-1.1.0/FFTrees/R/predictfft_function.R |only FFTrees-1.1.0/FFTrees/R/summaryfft_function.R |only FFTrees-1.1.0/FFTrees/R/titanic_doc.R | 2 FFTrees-1.1.0/FFTrees/R/transparent_function.R |only FFTrees-1.1.0/FFTrees/build/vignette.rds |binary FFTrees-1.1.0/FFTrees/data/breastcancer.RData |binary FFTrees-1.1.0/FFTrees/data/mushrooms.RData |binary FFTrees-1.1.0/FFTrees/inst/doc/fft_examples.R |only FFTrees-1.1.0/FFTrees/inst/doc/fft_examples.Rmd |only FFTrees-1.1.0/FFTrees/inst/doc/fft_examples.html |only FFTrees-1.1.0/FFTrees/inst/doc/fft_function.R | 37 FFTrees-1.1.0/FFTrees/inst/doc/fft_function.Rmd | 79 - FFTrees-1.1.0/FFTrees/inst/doc/fft_function.html | 331 ++---- FFTrees-1.1.0/FFTrees/inst/doc/fft_overview.R | 12 FFTrees-1.1.0/FFTrees/inst/doc/fft_overview.Rmd | 16 FFTrees-1.1.0/FFTrees/inst/doc/fft_overview.html | 10 FFTrees-1.1.0/FFTrees/inst/doc/fft_plot.R | 37 FFTrees-1.1.0/FFTrees/inst/doc/fft_plot.Rmd | 78 - FFTrees-1.1.0/FFTrees/inst/doc/fft_plot.html | 78 - FFTrees-1.1.0/FFTrees/man/auc.Rd |only FFTrees-1.1.0/FFTrees/man/cart.pred.Rd |only FFTrees-1.1.0/FFTrees/man/classtable.Rd | 17 FFTrees-1.1.0/FFTrees/man/cuerank.Rd | 5 FFTrees-1.1.0/FFTrees/man/fft.Rd | 36 FFTrees-1.1.0/FFTrees/man/grow.ffts.Rd |only FFTrees-1.1.0/FFTrees/man/heartdisease.Rd | 2 FFTrees-1.1.0/FFTrees/man/income.Rd | 2 FFTrees-1.1.0/FFTrees/man/lr.pred.Rd |only FFTrees-1.1.0/FFTrees/man/mushrooms.Rd | 2 FFTrees-1.1.0/FFTrees/man/plot.fft.Rd | 42 FFTrees-1.1.0/FFTrees/man/predict.fft.Rd |only FFTrees-1.1.0/FFTrees/man/summary.fft.Rd |only FFTrees-1.1.0/FFTrees/man/titanic.Rd | 2 FFTrees-1.1.0/FFTrees/man/transparent.Rd |only FFTrees-1.1.0/FFTrees/vignettes/fft_examples.Rmd |only FFTrees-1.1.0/FFTrees/vignettes/fft_examples.md |only FFTrees-1.1.0/FFTrees/vignettes/fft_function.Rmd | 79 - FFTrees-1.1.0/FFTrees/vignettes/fft_function.md |only FFTrees-1.1.0/FFTrees/vignettes/fft_overview.Rmd | 16 FFTrees-1.1.0/FFTrees/vignettes/fft_overview.md |only FFTrees-1.1.0/FFTrees/vignettes/fft_plot.Rmd | 78 - FFTrees-1.1.0/FFTrees/vignettes/fft_plot.md |only 66 files changed, 1086 insertions(+), 1979 deletions(-)
Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Delaporte versions 2.3.1 dated 2016-06-17 and 3.0.0 dated 2016-07-19
DESCRIPTION | 8 +-- MD5 | 16 +++--- NAMESPACE | 2 R/Delaporte.R | 38 ++++++++++----- inst/NEWS.Rd | 51 ++++++++++++++------- man/Delaporte-package.Rd | 6 +- man/Delaporte.Rd | 25 +++++----- src/Delaporte.cpp | 106 ++++++++++++++++++++++++++------------------ tests/testthat/test-delap.r | 27 ++++++++++- 9 files changed, 181 insertions(+), 98 deletions(-)
More information about VariableScreening at CRAN
Permanent link
Title: Time-Weighted Dynamic Time Warping for Satellite Image Time
Series Analysis
Description: Provides an implementation of the Time-Weighted Dynamic Time
Warping (TWDTW) method for land use and land cover mapping using satellite
image time series. TWDTW is based on the Dynamic Time Warping technique and
has achieved high accuracy for land use and land cover classification using
satellite data. The method is based on comparing unclassified satellite image
time series with a set of known temporal patterns (e.g. phenological cycles
associated with the vegetation). Using 'dtwSat' the user can build temporal
patterns for land cover types, apply the TWDTW analysis for satellite datasets,
visualize the results of the time series analysis, produce land cover maps, and
create temporal plots for land cover change analysis.
Author: Victor Maus [aut, cre]
Maintainer: Victor Maus <vwmaus1@gmail.com>
Diff between dtwSat versions 0.2.0 dated 2016-07-10 and 0.2.1 dated 2016-07-19
dtwSat-0.2.0/dtwSat/src/bestmathces.f |only dtwSat-0.2.1/dtwSat/DESCRIPTION | 26 ++++----- dtwSat-0.2.1/dtwSat/MD5 | 64 ++++++++++++----------- dtwSat-0.2.1/dtwSat/NAMESPACE | 1 dtwSat-0.2.1/dtwSat/NEWS.md | 5 + dtwSat-0.2.1/dtwSat/R/data.R | 4 - dtwSat-0.2.1/dtwSat/R/dtw.R | 21 ++++++- dtwSat-0.2.1/dtwSat/R/dwtSat.R |only dtwSat-0.2.1/dtwSat/R/getTimeSeries.R | 10 +++ dtwSat-0.2.1/dtwSat/R/plotArea.R | 3 - dtwSat-0.2.1/dtwSat/R/plotChanges.R | 3 - dtwSat-0.2.1/dtwSat/R/plotDistance.R | 5 - dtwSat-0.2.1/dtwSat/R/plotMaps.R | 3 - dtwSat-0.2.1/dtwSat/R/twdtw.R | 7 +- dtwSat-0.2.1/dtwSat/R/twdtwApply.R | 3 - dtwSat-0.2.1/dtwSat/R/twdtwClassify.R | 5 + dtwSat-0.2.1/dtwSat/R/zzz.R | 3 - dtwSat-0.2.1/dtwSat/build/vignette.rds |binary dtwSat-0.2.1/dtwSat/inst/doc/applying_twdtw.R | 26 +++++++-- dtwSat-0.2.1/dtwSat/inst/doc/applying_twdtw.Rmd | 54 +++++++++++++------ dtwSat-0.2.1/dtwSat/inst/doc/applying_twdtw.pdf |binary dtwSat-0.2.1/dtwSat/inst/doc/images_array.pdf |only dtwSat-0.2.1/dtwSat/inst/doc/images_ts.pdf |only dtwSat-0.2.1/dtwSat/man/dtwSat.Rd |only dtwSat-0.2.1/dtwSat/man/example_ts.Rd | 3 - dtwSat-0.2.1/dtwSat/man/example_ts.list.Rd | 3 - dtwSat-0.2.1/dtwSat/man/getTimeSeries.Rd | 2 dtwSat-0.2.1/dtwSat/man/plotArea.Rd | 3 - dtwSat-0.2.1/dtwSat/man/plotChanges.Rd | 3 - dtwSat-0.2.1/dtwSat/man/plotDistance.Rd | 5 - dtwSat-0.2.1/dtwSat/man/plotMaps.Rd | 3 - dtwSat-0.2.1/dtwSat/man/twdtwApply.Rd | 3 - dtwSat-0.2.1/dtwSat/man/twdtwClassify.Rd | 5 + dtwSat-0.2.1/dtwSat/src/bestmatches.f |only dtwSat-0.2.1/dtwSat/src/computecost.f | 4 - dtwSat-0.2.1/dtwSat/vignettes/.install_extras | 4 - dtwSat-0.2.1/dtwSat/vignettes/applying_twdtw.Rmd | 54 +++++++++++++------ 37 files changed, 204 insertions(+), 131 deletions(-)
Title: Estimation of the Relative Importance of Factors Affecting
Species Distribution Based on Stability Concept
Description: From output files obtained from the software ModestR, the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between SPEDInstabR versions 1.0 dated 2016-06-25 and 1.1 dated 2016-07-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 +- R/ContrMap.R | 12 +++++++----- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Includes also
utilities for sequence data management under the ACNUC system.
Author: Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 3.2-0 dated 2016-07-07 and 3.3-0 dated 2016-07-19
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- R/extractseqs.R | 53 ++++++++++++++++++++++++++++++++++++++--------------- man/extractseqs.Rd | 7 ++++--- 4 files changed, 54 insertions(+), 30 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.5 dated 2016-05-14 and 0.12.6 dated 2016-07-19
ChangeLog | 110 +++++++++ DESCRIPTION | 8 MD5 | 97 ++++---- NAMESPACE | 5 R/Attributes.R | 141 ++++++++++++ README.md | 16 - build/Rcpp.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 51 ++++ inst/doc/Rcpp-FAQ.R | 35 +-- inst/doc/Rcpp-FAQ.Rnw | 66 +++++ inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.Rnw | 278 +++++++++++++++++-------- inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.Rnw | 2 inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 18 + inst/include/Rcpp.h | 2 inst/include/Rcpp/String.h | 17 - inst/include/Rcpp/algorithm.h |only inst/include/Rcpp/config.h | 4 inst/include/Rcpp/exceptions.h | 49 ++-- inst/include/Rcpp/print.h | 8 inst/include/Rcpp/sugar/functions/max.h | 22 - inst/include/Rcpp/sugar/functions/min.h | 22 - inst/include/Rcpp/sugar/functions/na_omit.h | 9 inst/include/Rcpp/sugar/operators/divides.h | 12 - inst/include/Rcpp/sugar/operators/minus.h | 12 - inst/include/Rcpp/sugar/operators/plus.h | 25 +- inst/include/Rcpp/sugar/operators/times.h | 24 +- inst/include/Rcpp/vector/Matrix.h | 14 - inst/include/Rcpp/vector/VectorBase.h | 2 inst/unitTests/cpp/algorithm.cpp |only inst/unitTests/cpp/sugar.cpp | 5 inst/unitTests/runit.String.R | 6 inst/unitTests/runit.algorithm.R |only inst/unitTests/runit.sugar.R | 10 man/cppFunction.Rd | 9 man/evalCpp.Rd | 10 man/sourceCpp.Rd | 15 - src/attributes.cpp | 310 ++++++++++++++++------------ vignettes/Rcpp-FAQ.Rnw | 66 +++++ vignettes/Rcpp-quickref.Rnw | 278 +++++++++++++++++-------- vignettes/Rcpp-sugar.Rnw | 2 vignettes/Rcpp.bib | 18 + 51 files changed, 1275 insertions(+), 503 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
Description: Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can in
general be programmed on. A useful OptPath object (archive) to log function
evaluations is also provided.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Karin Schork [ctb],
Jakob Richter [aut],
Pascal Kerschke [aut]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between ParamHelpers versions 1.7 dated 2016-02-03 and 1.8 dated 2016-07-19
ParamHelpers-1.7/ParamHelpers/R/extractParamSetFromSooFunction.R |only ParamHelpers-1.7/ParamHelpers/R/isMissingValue.R |only ParamHelpers-1.7/ParamHelpers/man/extractParamSetFromSooFunction.Rd |only ParamHelpers-1.7/ParamHelpers/tests/testthat/test_extractParamSetFromSooFunction.R |only ParamHelpers-1.8/ParamHelpers/DESCRIPTION | 28 - ParamHelpers-1.8/ParamHelpers/LICENSE | 2 ParamHelpers-1.8/ParamHelpers/MD5 | 186 +++++----- ParamHelpers-1.8/ParamHelpers/NAMESPACE | 17 ParamHelpers-1.8/ParamHelpers/NEWS | 18 ParamHelpers-1.8/ParamHelpers/R/LearnerParam.R | 22 - ParamHelpers-1.8/ParamHelpers/R/OptPath.R | 12 ParamHelpers-1.8/ParamHelpers/R/OptPathDF.R | 2 ParamHelpers-1.8/ParamHelpers/R/OptPathDF_as_data_frame.R | 27 - ParamHelpers-1.8/ParamHelpers/R/OptPathDF_getter.R | 6 ParamHelpers-1.8/ParamHelpers/R/OptPathDF_setter.R | 21 - ParamHelpers-1.8/ParamHelpers/R/OptPath_getter.R | 19 - ParamHelpers-1.8/ParamHelpers/R/OptPath_plotEAF.R | 9 ParamHelpers-1.8/ParamHelpers/R/OptPath_plotYTraces.R | 23 - ParamHelpers-1.8/ParamHelpers/R/OptPath_plotter.R | 6 ParamHelpers-1.8/ParamHelpers/R/OptPath_setter.R | 10 ParamHelpers-1.8/ParamHelpers/R/ParamSet.R | 8 ParamHelpers-1.8/ParamHelpers/R/aParam.R | 44 +- ParamHelpers-1.8/ParamHelpers/R/convertDiscrete.R | 21 - ParamHelpers-1.8/ParamHelpers/R/convertParamSetToIrace.R | 26 - ParamHelpers-1.8/ParamHelpers/R/convertTypesToCInts.R | 6 ParamHelpers-1.8/ParamHelpers/R/dfRowsToList.R | 2 ParamHelpers-1.8/ParamHelpers/R/filterParams.R | 36 + ParamHelpers-1.8/ParamHelpers/R/generateDesign.R | 23 - ParamHelpers-1.8/ParamHelpers/R/generateGridDesign.R | 26 - ParamHelpers-1.8/ParamHelpers/R/generateRandomDesign.R | 17 ParamHelpers-1.8/ParamHelpers/R/getBounds.R | 15 ParamHelpers-1.8/ParamHelpers/R/getDefaults.R | 1 ParamHelpers-1.8/ParamHelpers/R/getParamIds.R | 44 +- ParamHelpers-1.8/ParamHelpers/R/getParamLengths.R | 3 ParamHelpers-1.8/ParamHelpers/R/getParamNr.R | 3 ParamHelpers-1.8/ParamHelpers/R/getParamSet.R |only ParamHelpers-1.8/ParamHelpers/R/getParamTypes.R | 3 ParamHelpers-1.8/ParamHelpers/R/getRequiredParamNames.R |only ParamHelpers-1.8/ParamHelpers/R/getTypeStrings.R |only ParamHelpers-1.8/ParamHelpers/R/hasFiniteBoxConstraints.R | 3 ParamHelpers-1.8/ParamHelpers/R/hasForbidden.R | 2 ParamHelpers-1.8/ParamHelpers/R/hasRequires.R | 4 ParamHelpers-1.8/ParamHelpers/R/hasTrafo.R | 6 ParamHelpers-1.8/ParamHelpers/R/hasType.R | 22 - ParamHelpers-1.8/ParamHelpers/R/isFeasible.R | 108 +++-- ParamHelpers-1.8/ParamHelpers/R/isForbidden.R | 4 ParamHelpers-1.8/ParamHelpers/R/isRequiresOk.R | 2 ParamHelpers-1.8/ParamHelpers/R/isType.R | 45 +- ParamHelpers-1.8/ParamHelpers/R/isVector.R | 23 + ParamHelpers-1.8/ParamHelpers/R/makeLearnerParamFuns.R | 1 ParamHelpers-1.8/ParamHelpers/R/makeParamFuns.R | 50 -- ParamHelpers-1.8/ParamHelpers/R/paramValueToString.R | 12 ParamHelpers-1.8/ParamHelpers/R/renderOptPathPlot.R | 5 ParamHelpers-1.8/ParamHelpers/R/renderOptPathPlot_helpers.R | 85 ++-- ParamHelpers-1.8/ParamHelpers/R/renderOptPathPlot_workers.R | 119 +++--- ParamHelpers-1.8/ParamHelpers/R/sample.R | 7 ParamHelpers-1.8/ParamHelpers/R/trafo.R | 38 +- ParamHelpers-1.8/ParamHelpers/R/updateParVals.R |only ParamHelpers-1.8/ParamHelpers/R/utils.R | 14 ParamHelpers-1.8/ParamHelpers/man/LearnerParam.Rd | 42 +- ParamHelpers-1.8/ParamHelpers/man/Param.Rd | 25 - ParamHelpers-1.8/ParamHelpers/man/addOptPathEl.Rd | 8 ParamHelpers-1.8/ParamHelpers/man/as.data.frame.OptPathDF.Rd | 1 ParamHelpers-1.8/ParamHelpers/man/filterParams.Rd | 24 + ParamHelpers-1.8/ParamHelpers/man/generateDesign.Rd | 11 ParamHelpers-1.8/ParamHelpers/man/generateGridDesign.Rd | 9 ParamHelpers-1.8/ParamHelpers/man/generateRandomDesign.Rd | 10 ParamHelpers-1.8/ParamHelpers/man/getLower.Rd | 3 ParamHelpers-1.8/ParamHelpers/man/getParamIds.Rd | 6 ParamHelpers-1.8/ParamHelpers/man/getParamSet.Rd |only ParamHelpers-1.8/ParamHelpers/man/getTypeStrings.Rd |only ParamHelpers-1.8/ParamHelpers/man/hasFiniteBoxConstraints.Rd | 6 ParamHelpers-1.8/ParamHelpers/man/hasType.Rd | 6 ParamHelpers-1.8/ParamHelpers/man/isFeasible.Rd | 23 - ParamHelpers-1.8/ParamHelpers/man/isType.Rd | 3 ParamHelpers-1.8/ParamHelpers/man/isVector.Rd |only ParamHelpers-1.8/ParamHelpers/man/makeParamSet.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/paramValueToString.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/plotYTraces.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/renderOptPathPlot.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/renderYTraces.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/sampleValue.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/sampleValues.Rd | 2 ParamHelpers-1.8/ParamHelpers/man/trafoValue.Rd | 4 ParamHelpers-1.8/ParamHelpers/man/updateParVals.Rd |only ParamHelpers-1.8/ParamHelpers/tests/testthat/Rplots.pdf |binary ParamHelpers-1.8/ParamHelpers/tests/testthat/helper_zzz.R | 2 ParamHelpers-1.8/ParamHelpers/tests/testthat/test_OptPath.R | 34 + ParamHelpers-1.8/ParamHelpers/tests/testthat/test_ParamSet.R | 19 - ParamHelpers-1.8/ParamHelpers/tests/testthat/test_convertParamSetToIrace.R | 21 + ParamHelpers-1.8/ParamHelpers/tests/testthat/test_dropParams.R | 2 ParamHelpers-1.8/ParamHelpers/tests/testthat/test_filterParams.R | 36 + ParamHelpers-1.8/ParamHelpers/tests/testthat/test_forbidden.R | 2 ParamHelpers-1.8/ParamHelpers/tests/testthat/test_generateDesign.R | 19 - ParamHelpers-1.8/ParamHelpers/tests/testthat/test_getParamTypes.R | 5 ParamHelpers-1.8/ParamHelpers/tests/testthat/test_getRequiredParamNames.R |only ParamHelpers-1.8/ParamHelpers/tests/testthat/test_hasIsType.R | 17 ParamHelpers-1.8/ParamHelpers/tests/testthat/test_isFeasible.R |only ParamHelpers-1.8/ParamHelpers/tests/testthat/test_isVector.R |only ParamHelpers-1.8/ParamHelpers/tests/testthat/test_renderOptPathPlot.R | 40 +- ParamHelpers-1.8/ParamHelpers/tests/testthat/test_trafo.R | 24 + ParamHelpers-1.8/ParamHelpers/tests/testthat/test_updateParVals.R |only 102 files changed, 978 insertions(+), 674 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 0.70 dated 2016-06-27 and 0.71.0 dated 2016-07-19
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- man/gkmSVM-package.Rd | 2 +- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Antigoni Kaliontzopoulou, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 3.0.1 dated 2016-03-25 and 3.0.2 dated 2016-07-19
DESCRIPTION | 10 MD5 | 106 ++-- NAMESPACE | 2 NEWS | 26 + R/advanced.procD.lm.r | 285 ++++++++---- R/bilat.symmetry.r | 121 +++-- R/compare.evol.rates.r | 48 +- R/compare.multi.evol.rates.r | 43 + R/geomorph.support.code.r | 903 ++++++++++++++++++++++++++++++++-------- R/geomorph.utils.r | 279 +++++++----- R/gpagen.r | 20 R/integration.test.r | 12 R/modularity.test.r | 38 + R/morphol.disparity.r | 34 + R/phylo.integration.r | 23 - R/phylo.modularity.r | 40 + R/physignal.r | 42 + R/plotGMPhyloMorphoSpace.r | 2 R/plotRefToTarget.r | 37 + R/plotTangentSpace.r | 121 +++-- R/procD.allometry.r | 42 + R/procD.lm.r | 26 - R/procD.pgls.r | 20 R/readland.nts.r | 4 R/readland.tps.r | 4 R/trajectory.analysis.r | 9 R/two.b.pls.r | 19 R/writeland.tps.r | 6 man/advanced.procD.lm.Rd | 47 +- man/bilat.symmetry.Rd | 86 ++- man/compare.evol.rates.Rd | 7 man/compare.multi.evol.rates.Rd | 6 man/gpagen.Rd | 4 man/integration.test.Rd | 6 man/modularity.test.Rd | 8 man/morphol.disparity.Rd | 11 man/phylo.integration.Rd | 6 man/phylo.modularity.Rd | 5 man/physignal.Rd | 5 man/plot.bilat.symmetry.Rd | 2 man/plot.pls.Rd | 9 man/plot.procD.allometry.Rd | 43 + man/plotRefToTarget.Rd | 4 man/plotTangentSpace.Rd | 43 + man/print.plotTangentSpace.Rd |only man/print.procD.lm.Rd | 2 man/procD.allometry.Rd | 6 man/procD.lm.Rd | 8 man/procD.pgls.Rd | 5 man/readland.nts.Rd | 4 man/summary.bilat.symmetry.Rd | 2 man/summary.plotTangentSpace.Rd |only man/trajectory.analysis.Rd | 5 man/two.b.pls.Rd | 12 man/writeland.tps.Rd | 4 55 files changed, 1900 insertions(+), 762 deletions(-)
Title: Data Integration Feature for Force.com and Salesforce.com
Description: Insert, update,
retrieve, delete and bulk operate datasets with a SaaS based CRM
Salesforce.com and a PaaS based application platform Force.com from R.
Author: Takekatsu Hiramura [aut, cre],
Steven Mortimer [ctb],
Alexis Iglauer [ctb]
Maintainer: Takekatsu Hiramura <thira@plavox.info>
Diff between RForcecom versions 1.0 dated 2016-07-01 and 1.1 dated 2016-07-19
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/RForcecom.R | 5 +++-- R/rforcecom.query.R | 2 +- R/rforcecom.search.R | 2 +- man/RForcecom.Rd | 2 +- 7 files changed, 18 insertions(+), 17 deletions(-)