Title: Stochastic Gradient Descent for Scalable Estimation
Description: A fast and flexible set of tools for large scale estimation. It
features many stochastic gradient methods, built-in models, visualization
tools, automated hyperparameter tuning, model checking, interval estimation,
and convergence diagnostics.
Author: Dustin Tran [aut, cre],
Panos Toulis [aut],
Tian Lian [ctb],
Ye Kuang [ctb],
Edoardo Airoldi [ctb]
Maintainer: Dustin Tran <dustin@cs.columbia.edu>
Diff between sgd versions 1.0 dated 2015-09-23 and 1.1 dated 2016-01-05
DESCRIPTION | 10 ++++----- MD5 | 22 +++++++++++--------- R/data-winequality.R |only R/plot.sgd.R | 6 ++--- R/sgd.R | 49 ++++++++++++++++++++++++++++++++------------- data |only demo/00Index | 1 demo/bench-logistic-wine.R |only inst/doc/sgd-jss.pdf |binary man/sgd.Rd | 33 ++++++++++++++++++++++-------- man/winequality.Rd |only src/Makevars.win | 2 - src/sgd.cpp | 18 ++++++++-------- src/sgd/base_sgd.h | 3 +- 14 files changed, 94 insertions(+), 50 deletions(-)
Title: Integration of Functions Over Simplices
Description: Provides methods to integrate functions over m-dimensional simplices
in n-dimensional Euclidean space. There are exact methods for polynomials and
adaptive methods for integrating an arbitrary function. Dirichlet probabilities
are calculated in certain cases.
Author: John P. Nolan, with parts based on code by Alan Genz
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between SimplicialCubature versions 1.0 dated 2014-09-24 and 1.1 dated 2016-01-05
DESCRIPTION | 19 +++-- MD5 | 22 +++--- NAMESPACE | 5 - R/SimplicialCubature.R | 125 ++++++++++++++++++++++++-------------- R/adsimp.R | 26 +++++-- R/grnmol.R | 2 demo |only man/CanonicalSimplex.Rd | 24 ++++--- man/SimplicialCubature-package.Rd | 23 +++--- man/adaptIntegrateSimplex.Rd | 25 +++++-- man/adsimp.Rd | 13 ++- man/integrateSimplexPolynomial.Rd | 2 12 files changed, 181 insertions(+), 105 deletions(-)
More information about SimplicialCubature at CRAN
Permanent link
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.8.2 dated 2015-11-27 and 2.9.0 dated 2016-01-05
DESCRIPTION | 16 MD5 | 49 - NAMESPACE | 2 R/pairs.R | 2 R/stan_csv.R | 6 R/stan_demo.R | 13 R/stan_plot.R | 2 R/stan_plot_options.R | 15 R/stanfit-class.R | 12 R/stanmodel-class.R | 296 +++--- build/vignette.rds |binary inst/NEWS | 10 inst/doc/rstan_vignette.pdf |binary inst/include/rstan/filtered_values.hpp |only inst/include/rstan/rstan_writer.hpp | 19 inst/include/rstan/stan_args.hpp | 60 - inst/include/rstan/stan_fit.hpp | 93 +- inst/include/rstan/sum_values.hpp |only inst/include/rstan/values.hpp |only man/rstan.Rd | 4 man/stan.Rd | 9 man/stan_demo.Rd | 8 man/stan_plot.Rd | 13 man/stanfit-method-plot.Rd | 19 man/stanmodel-class.Rd | 1 man/stanmodel-method-vb.Rd |only src/lang__grammars__indexes_grammar_inst.cpp |only tools/stan-functions.txt | 1236 +++++++++++++-------------- 28 files changed, 997 insertions(+), 888 deletions(-)
Title: Extract the Colors from Images
Description: A pure R implementation of the median cut algorithm.
Extracts the dominant colors from an image, and turns them into
a scale for use in plots or for fun!
Author: Joel Carlson
Maintainer: Joel Carlson <jnkcarlson@gmail.com>
Diff between RImagePalette versions 0.1.0 dated 2015-12-29 and 0.1.1 dated 2016-01-05
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 3 +++ R/quantizeImage.R |only R/scale_image.R | 11 ++++++++++- README.md | 31 +++++++++++++++++++++++++++++-- man/quantize_image.Rd |only 7 files changed, 52 insertions(+), 11 deletions(-)
Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney and Riad Jarjour
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between proftools versions 0.1-0 dated 2013-10-03 and 0.99-0 dated 2016-01-05
DESCRIPTION | 8 - MD5 | 49 +++++- NAMESPACE | 21 ++ R/plot.R |only R/prof.R |only R/proftools.R | 295 +++++++++++++++++++++-------------------- R/treemap.R |only README | 32 ++++ inst/samples/Rprof-dg.out |only inst/samples/Rprof-rec.out |only inst/samples/Rprof-rec0.out |only inst/samples/Rprof-rec1.out |only inst/samples/bootlmEx.R |only inst/samples/dg.R |only inst/samples/loops.R |only inst/samples/rec.R |only inst/samples/rec0.R |only inst/samples/rec1.R |only inst/samples/rw.R |only man/annotateSource.Rd |only man/callTreeGraphs.Rd |only man/filterProfileData.Rd |only man/flatProfile.Rd | 3 man/hotPaths.Rd |only man/plot.proftools_profData.Rd |only man/plotProfileCallGraph.Rd | 12 + man/printProfileCallGraph.Rd | 10 + man/profileCallGraph2Dot.Rd | 16 +- man/profileExpr.Rd |only man/proftools-package.Rd |only man/styles.Rd | 8 - man/summaries.Rd |only man/utils.Rd |only man/writeCallGrindFile.Rd |only vignettes |only 35 files changed, 286 insertions(+), 168 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations,
such as erosion and dilation, on data of arbitrary dimensionality. Can also
be used for finding connected components, resampling, filtering, smoothing
and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.2.0 dated 2015-08-06 and 1.3.0 dated 2016-01-05
mmand-1.2.0/mmand/src/Makevars.win |only mmand-1.3.0/mmand/DESCRIPTION | 18 +- mmand-1.3.0/mmand/MD5 | 107 ++++++++---- mmand-1.3.0/mmand/NAMESPACE | 7 mmand-1.3.0/mmand/NEWS | 17 + mmand-1.3.0/mmand/R/components.R |only mmand-1.3.0/mmand/R/kernels.R | 43 +++- mmand-1.3.0/mmand/R/morph.R | 91 +++++++--- mmand-1.3.0/mmand/README.md | 77 +++++++- mmand-1.3.0/mmand/inst/COPYRIGHTS |only mmand-1.3.0/mmand/man/binarise.Rd | 2 mmand-1.3.0/mmand/man/binary.Rd | 4 mmand-1.3.0/mmand/man/components.Rd |only mmand-1.3.0/mmand/man/display.Rd | 2 mmand-1.3.0/mmand/man/filters.Rd | 18 +- mmand-1.3.0/mmand/man/gameOfLife.Rd | 3 mmand-1.3.0/mmand/man/gaussianSmooth.Rd | 8 mmand-1.3.0/mmand/man/kernels.Rd | 36 ++-- mmand-1.3.0/mmand/man/morph.Rd | 2 mmand-1.3.0/mmand/man/morphology.Rd | 4 mmand-1.3.0/mmand/man/neighbourhood.Rd | 2 mmand-1.3.0/mmand/man/resample.Rd | 2 mmand-1.3.0/mmand/man/sampleKernelFunction.Rd | 3 mmand-1.3.0/mmand/man/symmetric.Rd |only mmand-1.3.0/mmand/man/threshold.Rd | 4 mmand-1.3.0/mmand/src/Array.cpp | 44 +++- mmand-1.3.0/mmand/src/Array.h | 80 +++++++- mmand-1.3.0/mmand/src/Componenter.cpp |only mmand-1.3.0/mmand/src/Componenter.h |only mmand-1.3.0/mmand/src/Kernel.cpp | 10 - mmand-1.3.0/mmand/src/Kernel.h | 14 - mmand-1.3.0/mmand/src/Makevars | 2 mmand-1.3.0/mmand/src/Morpher.cpp | 37 ++-- mmand-1.3.0/mmand/src/Morpher.h | 6 mmand-1.3.0/mmand/src/Resampler.cpp | 8 mmand-1.3.0/mmand/src/Resampler.h | 16 - mmand-1.3.0/mmand/src/lemon |only mmand-1.3.0/mmand/src/main.cpp | 57 +++++- mmand-1.3.0/mmand/tests/testthat/fan_components_box.rds |only mmand-1.3.0/mmand/tests/testthat/fan_components_diamond.rds |only mmand-1.3.0/mmand/tests/testthat/fan_sobel_filtered.rds |only mmand-1.3.0/mmand/tests/testthat/sobel_kernel_2d.rds |only mmand-1.3.0/mmand/tests/testthat/test-05-kernels.R | 4 mmand-1.3.0/mmand/tests/testthat/test-10-morph.R | 8 mmand-1.3.0/mmand/tests/testthat/test-25-components.R |only 45 files changed, 531 insertions(+), 205 deletions(-)
Title: Methods in Structural Reliability
Description: Various reliability analysis methods for: 1) computing
failure probability (probability that the output of a numerical
model exceeds a threshold); 2) computing the size of a sample
to estimate a quantile with a confidence level.
Author: Nicolas BOUSQUET, Gilles DEFAUX, Bertrand IOOSS, Vincent MOUTOUSSAMY,
Clement WALTER
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between mistral versions 1.1-1 dated 2014-11-25 and 2.0.0 dated 2016-01-05
mistral-1.1-1/mistral/R/FindInDatabase.R |only mistral-1.1-1/mistral/R/getSeedBelowThreshold.R |only mistral-2.0.0/mistral/DESCRIPTION | 23 mistral-2.0.0/mistral/MD5 | 82 mistral-2.0.0/mistral/NAMESPACE | 87 mistral-2.0.0/mistral/R/AKMCS.R | 884 ++++----- mistral-2.0.0/mistral/R/FORM.R | 488 ++--- mistral-2.0.0/mistral/R/IRW.R |only mistral-2.0.0/mistral/R/LSVM.R |only mistral-2.0.0/mistral/R/MP.R |only mistral-2.0.0/mistral/R/MRM.R | 1343 ++++++-------- mistral-2.0.0/mistral/R/MetaIS.R | 1246 +++++++----- mistral-2.0.0/mistral/R/MonotonicQuantileEstimation.R |only mistral-2.0.0/mistral/R/MonteCarlo.R | 323 ++- mistral-2.0.0/mistral/R/S2MART.R | 487 +++-- mistral-2.0.0/mistral/R/SMART.R | 950 ++++----- mistral-2.0.0/mistral/R/SVMLinearMonotone.R |only mistral-2.0.0/mistral/R/SubsetSimulation.R | 459 ++-- mistral-2.0.0/mistral/R/UtoX.R | 9 mistral-2.0.0/mistral/R/WilksFormula.R | 165 - mistral-2.0.0/mistral/R/generateWithAR.R | 81 mistral-2.0.0/mistral/R/limitFunction.R | 72 mistral-2.0.0/mistral/R/modelLSVM.R |only mistral-2.0.0/mistral/R/plotLSVM.R |only mistral-2.0.0/mistral/R/runifSphere.R | 31 mistral-2.0.0/mistral/R/testConvexity.R |only mistral-2.0.0/mistral/R/trainModel.R | 220 +- mistral-2.0.0/mistral/R/updateLSVM.R |only mistral-2.0.0/mistral/data |only mistral-2.0.0/mistral/man/AKMCS.Rd | 368 ++- mistral-2.0.0/mistral/man/ComputeDistributionParameter.Rd | 2 mistral-2.0.0/mistral/man/FORM.Rd | 51 mistral-2.0.0/mistral/man/IRW.Rd |only mistral-2.0.0/mistral/man/LSVM.Rd |only mistral-2.0.0/mistral/man/MP.Rd |only mistral-2.0.0/mistral/man/MRM.Rd | 208 +- mistral-2.0.0/mistral/man/MetaIS.Rd | 424 ++-- mistral-2.0.0/mistral/man/Mistral-package.Rd | 11 mistral-2.0.0/mistral/man/MonotonicQuantileEstimation.Rd |only mistral-2.0.0/mistral/man/MonteCarlo.Rd | 214 +- mistral-2.0.0/mistral/man/S2MART.Rd | 283 +- mistral-2.0.0/mistral/man/SMART.Rd | 287 +- mistral-2.0.0/mistral/man/SubsetSimulation.Rd | 245 +- mistral-2.0.0/mistral/man/UtoX.Rd | 14 mistral-2.0.0/mistral/man/kiureghian.Rd |only mistral-2.0.0/mistral/man/modelLSVM.Rd |only mistral-2.0.0/mistral/man/plotLSVM.Rd |only mistral-2.0.0/mistral/man/testConvexity.Rd |only mistral-2.0.0/mistral/man/updateLSVM.Rd |only mistral-2.0.0/mistral/man/waarts.Rd |only mistral-2.0.0/mistral/tests |only 51 files changed, 4791 insertions(+), 4266 deletions(-)
Title: The All-Configurations, Maximum-Interaction F-Test for Hidden
Additivity
Description: Computes the ACMIF test and Bonferroni-adjusted p-value of interaction in two-factor studies. Produces corresponding interaction plot and analysis of variance tables and p-values from several other tests of non-additivity.
Author: Jason A. Osborne, Christopher T. Franck and Bongseog Choi
Maintainer: Jason A. Osborne <jaosborn@ncsu.edu>
Diff between hiddenf versions 1.3 dated 2015-04-09 and 2.0 dated 2016-01-05
hiddenf-1.3/hiddenf/R/Malikfunction.R |only hiddenf-1.3/hiddenf/R/anova.hiddenf.R |only hiddenf-1.3/hiddenf/R/hiddenf.R |only hiddenf-1.3/hiddenf/R/plot.hiddenf.R |only hiddenf-1.3/hiddenf/R/print.hiddenf.R |only hiddenf-1.3/hiddenf/R/summary.hiddenf.R |only hiddenf-1.3/hiddenf/man/Malikfunction.Rd |only hiddenf-1.3/hiddenf/man/anova.hiddenf.Rd |only hiddenf-1.3/hiddenf/man/hiddenf.Rd |only hiddenf-1.3/hiddenf/man/plot.hiddenf.Rd |only hiddenf-1.3/hiddenf/man/print.hiddenf.Rd |only hiddenf-1.3/hiddenf/man/summary.hiddenf.Rd |only hiddenf-2.0/hiddenf/DESCRIPTION | 11 +- hiddenf-2.0/hiddenf/MD5 | 83 +++++++++--------- hiddenf-2.0/hiddenf/NAMESPACE | 14 ++- hiddenf-2.0/hiddenf/R/HiddenF.R |only hiddenf-2.0/hiddenf/R/KKSAPvalue.R | 119 ++++++++++++++------------- hiddenf-2.0/hiddenf/R/MalikPvalue.R | 80 ++++++++---------- hiddenf-2.0/hiddenf/R/MalikTab.R | 34 +++---- hiddenf-2.0/hiddenf/R/MandelPvalue.R | 46 +++++----- hiddenf-2.0/hiddenf/R/TukeyPvalue.R | 27 +++--- hiddenf-2.0/hiddenf/R/additivityPvalues.R | 57 ++++++------ hiddenf-2.0/hiddenf/R/anova.HiddenF.R |only hiddenf-2.0/hiddenf/R/anovaprint.r |only hiddenf-2.0/hiddenf/R/computePSS.R | 8 - hiddenf-2.0/hiddenf/R/makemtx.fcn.R | 10 +- hiddenf-2.0/hiddenf/R/maketall.fcn.R | 40 ++++----- hiddenf-2.0/hiddenf/R/plot.HiddenF.R |only hiddenf-2.0/hiddenf/R/print.HiddenF.R |only hiddenf-2.0/hiddenf/R/rconfig.fcn.R | 94 ++++++++++----------- hiddenf-2.0/hiddenf/R/rkconfig.fcn.R | 114 ++++++++++++------------- hiddenf-2.0/hiddenf/R/summary.HiddenF.R |only hiddenf-2.0/hiddenf/data/Boik.mtx.rda |binary hiddenf-2.0/hiddenf/data/Graybill.mtx.rda |binary hiddenf-2.0/hiddenf/data/cjejuni.mtx.rda |binary hiddenf-2.0/hiddenf/data/cnv1.mtx.rda |binary hiddenf-2.0/hiddenf/data/cnvall.mtx.rda |binary hiddenf-2.0/hiddenf/man/Boik.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/Graybill.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/HiddenF.Rd |only hiddenf-2.0/hiddenf/man/KKSAPvalue.Rd | 8 - hiddenf-2.0/hiddenf/man/MalikPvalue.Rd | 11 +- hiddenf-2.0/hiddenf/man/MalikTab.Rd | 10 -- hiddenf-2.0/hiddenf/man/MandelPvalue.Rd | 6 - hiddenf-2.0/hiddenf/man/TukeyPvalue.Rd | 2 hiddenf-2.0/hiddenf/man/additivityPvalues.Rd | 4 hiddenf-2.0/hiddenf/man/anova.HiddenF.Rd |only hiddenf-2.0/hiddenf/man/cjejuni.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/cnv1.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/cnvall.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/hiddenf-package.Rd | 36 +------- hiddenf-2.0/hiddenf/man/plot.HiddenF.Rd |only hiddenf-2.0/hiddenf/man/print.HiddenF.Rd |only hiddenf-2.0/hiddenf/man/summary.HiddenF.Rd |only 54 files changed, 405 insertions(+), 419 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.6 dated 2015-09-04 and 1.1.8 dated 2016-01-05
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 4 ++-- inst/doc/ExomeDepth-vignette.Rnw | 11 +++++++++-- inst/doc/ExomeDepth-vignette.pdf |binary vignettes/.install_extras |only vignettes/ExomeDepth-vignette.Rnw | 11 +++++++++-- 7 files changed, 28 insertions(+), 14 deletions(-)
Title: The Chopthin Resampler
Description: Resampling is a standard step in particle filtering and in
sequential Monte Carlo. This package implements the chopthin resampler, which
keeps a bound on the ratio between the largest and the smallest weights after
resampling.
Author: Axel Gandy and F. Din-Houn Lau
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between chopthin versions 0.2 dated 2015-12-07 and 0.2.1 dated 2016-01-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/NEWS.Rd | 6 ++++++ src/chopthin_internal.h | 1 + tests/testthat/test-chopthin_exact.R | 2 +- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Detecting of Outliers in Circular Regression
Description: Detecting of outliers in circular-circular regression models, modifying its and estimating of models parameters.
Author: Azade Ghazanfarihesari, Majid Sarmad- Ferdowsi University Of Mashhad
Maintainer: Azade Ghazanfarihesari <azade_ghazanfari@yahoo.com>
Diff between CircOutlier versions 3.1.3 dated 2015-06-09 and 3.1.4 dated 2016-01-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/Predict.R | 1 - man/CircOutlier-package.Rd | 2 +- man/DMCE.Rd | 2 +- man/MCE.Rd | 2 +- man/mce_1.Rd | 2 +- 8 files changed, 16 insertions(+), 16 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.59-5 dated 2015-08-05 and 0.62-1 dated 2016-01-05
broman-0.59-5/broman/R/loadfile.R |only broman-0.59-5/broman/README.md |only broman-0.59-5/broman/man/attachfile.Rd |only broman-0.59-5/broman/man/loadfile.Rd |only broman-0.59-5/broman/tests/testthat/test-attachload.R |only broman-0.62-1/broman/DESCRIPTION | 9 broman-0.62-1/broman/MD5 | 195 +++++++++--------- broman-0.62-1/broman/NAMESPACE | 10 broman-0.62-1/broman/R/add_commas.R | 1 broman-0.62-1/broman/R/arrowlocator.R | 1 broman-0.62-1/broman/R/cf.R | 1 broman-0.62-1/broman/R/compare_rows.R | 1 broman-0.62-1/broman/R/convert2hex.R | 2 broman-0.62-1/broman/R/dotplot.R |only broman-0.62-1/broman/R/exit.R | 1 broman-0.62-1/broman/R/fac2num.R |only broman-0.62-1/broman/R/fisher.R | 2 broman-0.62-1/broman/R/grayplot.R | 22 +- broman-0.62-1/broman/R/help.R | 1 broman-0.62-1/broman/R/histlines.R | 1 broman-0.62-1/broman/R/holmans_triangle.R | 4 broman-0.62-1/broman/R/jiggle.R |only broman-0.62-1/broman/R/kbdate.R | 1 broman-0.62-1/broman/R/manyboxplot.R | 1 broman-0.62-1/broman/R/maxabs.R |only broman-0.62-1/broman/R/mypairs.R | 1 broman-0.62-1/broman/R/myround.R | 1 broman-0.62-1/broman/R/normalize.R | 1 broman-0.62-1/broman/R/objectsizes.R | 1 broman-0.62-1/broman/R/openfile.R | 3 broman-0.62-1/broman/R/pastedot.R | 2 broman-0.62-1/broman/R/permtest.R | 1 broman-0.62-1/broman/R/pushbullet.R | 2 broman-0.62-1/broman/R/qr.R | 1 broman-0.62-1/broman/R/revrainbow.R | 1 broman-0.62-1/broman/R/rmvn.R | 1 broman-0.62-1/broman/R/runningmean.R | 2 broman-0.62-1/broman/R/simp.R | 1 broman-0.62-1/broman/R/strwidth2xlim.R | 1 broman-0.62-1/broman/R/util.R | 1 broman-0.62-1/broman/R/venn_diagram.R | 1 broman-0.62-1/broman/R/winsorize.R | 1 broman-0.62-1/broman/inst/README.md | 1 broman-0.62-1/broman/inst/STATUS.txt | 31 ++ broman-0.62-1/broman/man/add_commas.Rd | 2 broman-0.62-1/broman/man/arrowlocator.Rd | 11 - broman-0.62-1/broman/man/attrnames.Rd | 2 broman-0.62-1/broman/man/brocolors.Rd | 2 broman-0.62-1/broman/man/bromanversion.Rd | 3 broman-0.62-1/broman/man/cf.Rd | 3 broman-0.62-1/broman/man/chisq.Rd | 3 broman-0.62-1/broman/man/colwalpha.Rd | 2 broman-0.62-1/broman/man/compare_rows.Rd | 2 broman-0.62-1/broman/man/convert2hex.Rd | 3 broman-0.62-1/broman/man/done.Rd | 2 broman-0.62-1/broman/man/dotplot.Rd |only broman-0.62-1/broman/man/errors2pushbullet.Rd | 2 broman-0.62-1/broman/man/excel_fig.Rd | 2 broman-0.62-1/broman/man/exit.Rd | 2 broman-0.62-1/broman/man/fac2num.Rd |only broman-0.62-1/broman/man/fisher.Rd | 3 broman-0.62-1/broman/man/grayplot.Rd | 5 broman-0.62-1/broman/man/h.Rd | 3 broman-0.62-1/broman/man/hex2dec.Rd | 3 broman-0.62-1/broman/man/histlines.Rd | 5 broman-0.62-1/broman/man/jiggle.Rd |only broman-0.62-1/broman/man/kbdate.Rd | 3 broman-0.62-1/broman/man/lenuniq.Rd | 2 broman-0.62-1/broman/man/make.Rd | 3 broman-0.62-1/broman/man/manyboxplot.Rd | 5 broman-0.62-1/broman/man/maxabs.Rd |only broman-0.62-1/broman/man/mypairs.Rd | 3 broman-0.62-1/broman/man/myround.Rd | 3 broman-0.62-1/broman/man/normalize.Rd | 3 broman-0.62-1/broman/man/note.Rd | 2 broman-0.62-1/broman/man/objectsizes.Rd | 5 broman-0.62-1/broman/man/openfile.Rd | 3 broman-0.62-1/broman/man/paired.perm.test.Rd | 11 - broman-0.62-1/broman/man/paste..Rd | 3 broman-0.62-1/broman/man/paste00.Rd | 3 broman-0.62-1/broman/man/perm.test.Rd | 13 - broman-0.62-1/broman/man/plot_crayons.Rd | 2 broman-0.62-1/broman/man/pushbullet_devices.Rd | 2 broman-0.62-1/broman/man/qqline2.Rd | 5 broman-0.62-1/broman/man/qr2.Rd | 5 broman-0.62-1/broman/man/quantileSE.Rd | 5 broman-0.62-1/broman/man/revrainbow.Rd | 3 broman-0.62-1/broman/man/rmvn.Rd | 3 broman-0.62-1/broman/man/runningmean.Rd | 5 broman-0.62-1/broman/man/runningratio.Rd | 3 broman-0.62-1/broman/man/simp.Rd | 3 broman-0.62-1/broman/man/stop_sending_errors.Rd | 2 broman-0.62-1/broman/man/strwidth2lines.Rd | 4 broman-0.62-1/broman/man/strwidth2xlim.Rd | 9 broman-0.62-1/broman/man/switchv.Rd | 3 broman-0.62-1/broman/man/theme_karl.Rd | 3 broman-0.62-1/broman/man/triarrow.Rd | 5 broman-0.62-1/broman/man/trilines.Rd | 5 broman-0.62-1/broman/man/triplot.Rd | 3 broman-0.62-1/broman/man/tripoints.Rd | 3 broman-0.62-1/broman/man/venn.Rd | 3 broman-0.62-1/broman/man/winsorize.Rd | 3 broman-0.62-1/broman/man/xlimlabel.Rd | 9 broman-0.62-1/broman/src/count_close.c |only broman-0.62-1/broman/src/count_close.h |only broman-0.62-1/broman/tests/testthat/test-fac2num.R |only broman-0.62-1/broman/tests/testthat/test-maxabs.R |only 107 files changed, 285 insertions(+), 232 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-
of-design-space plots and similar graphics for exploring the properties of
experimental designs. The design region is explored via random sampling, which
allows for more flexibility than traditional variance dispersion graphs. A
formula interface is leveraged to provide access to complex model formulae.
Graphics can be constructed simultaneously for multiple experimental designs
and/or multiple model formulae. Instead of using pointwise optimization to
find the minimum and maximum scaled prediction variance curves, which can be
inaccurate and time consuming, this package uses quantile regression as an
alternative.
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.1.2 dated 2015-10-26 and 1.1.3 dated 2016-01-05
DESCRIPTION | 27 +++++++++++++++------------ MD5 | 28 ++++++++++++++-------------- NAMESPACE | 2 +- build/vignette.rds |binary inst/CITATION | 2 +- man/GJ54.Rd | 2 +- man/LHS.Rd | 5 +++-- man/meanspv.Rd | 4 ++-- man/plot.spv.Rd | 23 ++++++++++++----------- man/print.spv.Rd | 4 ++-- man/runif_sphere.Rd | 6 ++++-- man/sampler.Rd | 10 +++++----- man/spv.Rd | 9 +++++---- man/stdrange.Rd | 2 +- man/vdg-package.Rd | 24 ++++++++++++------------ 15 files changed, 78 insertions(+), 70 deletions(-)
Title: GAMLSS Data
Description: Data for GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.data versions 4.3-0 dated 2015-07-16 and 4.3-2 dated 2016-01-05
DESCRIPTION | 8 ++--- MD5 | 74 +++++++++++++++++++++++++----------------------- data/CD4.rda |binary data/LGAclaims.rda |binary data/Mums.rda |binary data/VictimsOfCrime.rda |binary data/acidity.rda |binary data/aep.rda |binary data/aids.rda |binary data/alveolar.rda |binary data/computer.rda |binary data/datalist | 3 + data/db.rda |binary data/dbbmi.rda |binary data/fabric.rda |binary data/film30.rda |binary data/film90.rda |binary data/glass.rda |binary data/glasses.RData |only data/hodges.rda |binary data/hodges1.rda |binary data/lice.rda |binary data/margolin.rda |binary data/meta.rda |only data/mvi.rda |binary data/mviBig.rda |binary data/parzen.rda |binary data/polio.rda |binary data/rent.rda |binary data/rent99.polys.rda |binary data/rent99.rda |binary data/respInf.rda |only data/species.rda |binary data/stylo.rda |binary data/tensile.rda |binary data/tse.rda |binary data/usair.rda |binary data/vas5.rda |binary man/glasses.Rd |only man/meta.Rd |only man/respInf.Rd |only 41 files changed, 47 insertions(+), 38 deletions(-)
Title: Unimodal Additive Hazards Model
Description: Nonparametric estimation of a unimodal or U-shape covariate effect under additive hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>
Diff between uniah versions 0.3 dated 2015-12-28 and 0.4 dated 2016-01-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/print.uniah.R | 4 ++-- R/uniah.R | 24 ++++++++++++------------ R/uniah.ti.known.R | 10 +++++----- R/uniah.ti.unknown.R | 9 +++++---- man/uniah-package.Rd | 4 ++-- man/uniah.Rd | 18 +++++++++--------- 8 files changed, 46 insertions(+), 45 deletions(-)
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.0 dated 2015-07-20 and 1.0.1 dated 2016-01-05
timedelay-1.0.0/timedelay/R/logprofilelikelihood.R |only timedelay-1.0.0/timedelay/man/logprofilelikelihood.Rd |only timedelay-1.0.1/timedelay/DESCRIPTION | 11 timedelay-1.0.1/timedelay/MD5 | 18 timedelay-1.0.1/timedelay/NAMESPACE | 6 timedelay-1.0.1/timedelay/R/bayesian.R | 269 ++++++------ timedelay-1.0.1/timedelay/R/entirelogprofilelikelihood.R | 37 + timedelay-1.0.1/timedelay/man/bayesian.Rd | 65 -- timedelay-1.0.1/timedelay/man/entirelogprofilelikelihood.Rd | 22 timedelay-1.0.1/timedelay/man/simple.Rd | 2 timedelay-1.0.1/timedelay/man/timedelay-package.Rd | 98 +--- 11 files changed, 249 insertions(+), 279 deletions(-)
Title: Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>
Diff between pcadapt versions 2.1 dated 2015-12-18 and 2.1.1 dated 2016-01-05
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- inst/doc/pcadapt.Rmd | 30 +++++++----------------------- inst/doc/pcadapt.html | 34 ++++++++++------------------------ man/pcadapt-package.Rd | 4 ++-- vignettes/pcadapt.Rmd | 30 +++++++----------------------- 6 files changed, 36 insertions(+), 82 deletions(-)
Title: Least-Squares Bilinear Clustering for Three-Way Data
Description: Functions for performing least-squares bilinear clustering of
three-way data. The method uses the bilinear decomposition (or biadditive
model) to model two-way matrix slices while clustering over the third way.
Up to four different types of clusters are included, one for each term of the
bilinear decomposition. In this way, matrices are clustered simultaneously on
(a subset of) their overall means, row margins, column margins and row-column
interactions. The orthogonality of the bilinear model results in separability of
the joint clustering problem into four separate ones. Three of these subproblems
are specific k-means problems, while a special algorithm is implemented for the
interactions. Plotting methods are provided, including biplots for the low-rank
approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between lsbclust versions 1.0.3 dated 2015-08-14 and 1.0.4 dated 2016-01-05
DESCRIPTION | 31 +++++++++-------- MD5 | 76 ++++++++++++++++++++++---------------------- NAMESPACE | 5 +- R/T3Clusf.R |only R/plot.col.kmeans.R | 2 - R/plot.int.lsbclust.R | 7 +--- R/plot.ovl.kmeans.R | 20 +++++++++-- R/plot.row.kmeans.R | 2 - data/dcars.rda |binary data/lov.rda |binary data/supermarkets.rda |binary inst/CITATION | 2 - man/ClustMeans.Rd | 2 - man/KMeansW.Rd | 14 ++++---- man/LossMat.Rd | 2 - man/T3Clusf.Rd |only man/bicomp.Rd | 10 ++--- man/cmat.Rd | 2 - man/dcars.Rd | 12 +++--- man/genproc.Rd | 4 +- man/indarr.Rd | 4 +- man/int.lsbclust.Rd | 10 ++--- man/lov.Rd | 30 ++++++++--------- man/lsbclust-package.Rd | 2 - man/lsbclust.Rd | 16 ++++----- man/lsbclusttoclue.Rd | 2 - man/orc.lsbclust.Rd | 18 +++++----- man/plot.bicomp.Rd | 6 +-- man/plot.col.kmeans.Rd | 2 - man/plot.int.lsbclust.Rd | 40 +++++++++++------------ man/plot.lsbclust.Rd | 4 +- man/plot.ovl.kmeans.Rd | 2 - man/plot.row.kmeans.Rd | 2 - man/plot.step.lsbclust.Rd | 4 +- man/print.lsbclust.Rd | 2 - man/sim.lsbclust.Rd | 2 - man/step.lsbclust.Rd | 32 +++++++++--------- man/summary.int.lsbclust.Rd | 2 - man/summary.lsbclust.Rd | 2 - man/supermarkets.Rd | 6 +-- 40 files changed, 197 insertions(+), 182 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 4.3-6 dated 2015-09-03 and 4.3-7 dated 2016-01-05
gamlss-4.3-6/gamlss/R/histSmo-6-03-12.R |only gamlss-4.3-7/gamlss/DESCRIPTION | 8 +-- gamlss-4.3-7/gamlss/MD5 | 36 +++++++-------- gamlss-4.3-7/gamlss/NAMESPACE | 22 ++++++++- gamlss-4.3-7/gamlss/R/cy.R | 21 ++++++++- gamlss-4.3-7/gamlss/R/gamlss.R | 43 +++++++++--------- gamlss-4.3-7/gamlss/R/histSmo.R |only gamlss-4.3-7/gamlss/R/lo_new.R | 54 +++++++++++++---------- gamlss-4.3-7/gamlss/R/pb_03-02-2014.R | 2 gamlss-4.3-7/gamlss/R/pb_goingtozero.R | 21 ++++++++- gamlss-4.3-7/gamlss/R/pb_new.R | 37 +++++++++++++++- gamlss-4.3-7/gamlss/R/pbm_new.R | 73 +++++++++++++++++++++++++++++++- gamlss-4.3-7/gamlss/R/random.R | 50 ++++++++++++++++++++- gamlss-4.3-7/gamlss/R/re_gamlss_lme.R | 12 +++-- gamlss-4.3-7/gamlss/R/term.plot-new.R | 44 +++++++++++++------ gamlss-4.3-7/gamlss/inst/doc/NEWS.txt | 42 ++++++++++++------ gamlss-4.3-7/gamlss/man/histSmo.Rd | 54 ++++++++++++++++------- gamlss-4.3-7/gamlss/man/lo.Rd | 7 +-- gamlss-4.3-7/gamlss/man/ps.Rd | 8 +++ gamlss-4.3-7/gamlss/man/random.Rd | 2 20 files changed, 400 insertions(+), 136 deletions(-)
Title: Constrained Dual Scaling for Detecting Response Styles
Description: This is an implementation of constrained dual scaling for
detecting response styles in categorical data, including utility functions. The
procedure involves adding additional columns to the data matrix representing the
boundaries between the rating categories. The resulting matrix is then doubled
and analyzed by dual scaling. One-dimensional solutions are sought which provide
optimal scores for the rating categories. These optimal scores are constrained
to follow monotone quadratic splines. Clusters are introduced within which the
response styles can vary. The type of response style present in a cluster can
be diagnosed from the optimal scores for said cluster, and this can be used to
construct an imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between cds versions 1.0.2 dated 2015-08-15 and 1.0.3 dated 2016-01-05
DESCRIPTION | 30 ++++++++++--------- MD5 | 76 ++++++++++++++++++++++++------------------------- NAMESPACE | 2 - R/G.start.R | 39 ++++++++++++++----------- R/cds.R | 28 ++++++++++++------ inst/CITATION | 2 - man/G.start.Rd | 8 +++-- man/Lfun.G.upd.Rd | 4 +- man/Lfun.Rd | 2 - man/addbounds.Rd | 4 +- man/approxloads.Rd | 2 - man/calc.wt.bubbles.Rd | 4 +- man/cds-package.Rd | 2 - man/cds.Rd | 16 +++++++--- man/cds.sim.Rd | 8 ++--- man/cdstoclue.Rd | 2 - man/clean.scales.Rd | 2 - man/create.ind.Rd | 2 - man/create.rs.Rd | 2 - man/createcdsdata.Rd | 4 +- man/datsim.Rd | 2 - man/gen.cop.Rd | 8 ++--- man/genPCA.Rd | 2 - man/group.ALS.Rd | 2 - man/indmat.Rd | 2 - man/ispline.Rd | 2 - man/orthprocr.Rd | 2 - man/plot.cds.Rd | 2 - man/plot.cdslist.Rd | 2 - man/print.cds.Rd | 2 - man/print.cdsdata.Rd | 2 - man/rcormat.Rd | 2 - man/rcovmat.Rd | 2 - man/sensory.Rd | 5 +-- man/sensory.aux.Rd | 3 + man/simpca.Rd | 2 - man/trQnorm.Rd | 2 - man/trRnorm.Rd | 2 - man/updateG.Rd | 2 - 39 files changed, 161 insertions(+), 126 deletions(-)
Title: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS
Proteomics Data
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: George Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Maintainer: George Rosenberger <rosenberger@imsb.biol.ethz.ch>
Diff between aLFQ versions 1.3.2 dated 2014-09-29 and 1.3.3 dated 2016-01-05
aLFQ-1.3.2/aLFQ/data/aa.index.rda |only aLFQ-1.3.2/aLFQ/man/aa.index.Rd |only aLFQ-1.3.3/aLFQ/DESCRIPTION | 18 +-- aLFQ-1.3.3/aLFQ/MD5 | 18 +-- aLFQ-1.3.3/aLFQ/NAMESPACE | 108 +++++++++++----------- aLFQ-1.3.3/aLFQ/R/ALF.R | 2 aLFQ-1.3.3/aLFQ/R/apexFeatures.R | 7 - aLFQ-1.3.3/aLFQ/inst/CITATION | 2 aLFQ-1.3.3/aLFQ/man/ALF.Rd | 2 aLFQ-1.3.3/aLFQ/man/aLFQ.package.Rd | 12 +- aLFQ-1.3.3/aLFQ/tests/Examples/aLFQ-Ex.Rout.save | 109 ----------------------- 11 files changed, 88 insertions(+), 190 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.22 dated 2015-10-27 and 1.4.23 dated 2016-01-05
DESCRIPTION | 8 +- MD5 | 10 +- R/invgauss.R | 143 +++++++++++++++++++++++++++++------------- inst/NEWS | 5 + man/invgauss.Rd | 4 - tests/statmod-Tests.Rout.save | 10 +- 6 files changed, 121 insertions(+), 59 deletions(-)
Title: Plant Root System Markup Language (RSML) File Processing
Description: Read and analyse Root System Markup Language (RSML) files, used to
store plant root system architecture data. More information can be found
at the address <http://rootsystemml.github.io/>.
Author: Guillaume Lobet
Maintainer: Guillaume Lobet <guillaume.lobet@ulg.ac.be>
Diff between rsml versions 1.2 dated 2014-11-18 and 1.3 dated 2016-01-05
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/plant_functions.R | 17 ++++++++++++++--- R/root_functions.R | 3 +++ R/rsmlToList.R | 4 ++-- 6 files changed, 31 insertions(+), 15 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System for
Automated Geoscientific Analyses) from within R by running the command
line version of SAGA. This package furthermore provides several R functions
for handling ASCII grids, including a flexible framework for applying local
functions (including predict methods of fitted models) and focal functions to
multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 0.94-4 dated 2015-11-05 and 0.94-5 dated 2016-01-05
DESCRIPTION | 10 +-- MD5 | 14 ++-- R/RSAGA-core.R | 4 - R/RSAGA-modules.R | 128 ++++++++++++++++++++++++++++++++++++------ R/RSAGA-package.R | 2 inst/doc/RSAGA-landslides.pdf |binary man/RSAGA-package.Rd | 2 man/rsaga.import.gdal.Rd | 94 +++++++++++++++++++++++++++++- 8 files changed, 219 insertions(+), 35 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Description: A collection of tools for approximating the 'PDQ' functions
(respectively, the cumulative distribution, density, and quantile) of
probability distributions via classical expansions involving moments and
cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between PDQutils versions 0.1.2 dated 2015-06-15 and 0.1.3 dated 2016-01-05
DESCRIPTION | 16 +++++++++------- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 10 +++++++++- R/PDQutils.r | 13 ++++++++++++- R/gram_charlier.r | 4 ++-- README.md | 5 ++++- build/vignette.rds |binary inst/doc/PDQutils.R | 2 +- inst/doc/PDQutils.Rnw | 2 +- inst/doc/PDQutils.pdf |binary man/AS269.Rd | 39 ++++++++++++++++++++------------------- man/NEWS.Rd | 17 +++++++++++------ man/PDQutils.Rd | 42 +++++++++++++++++++++--------------------- man/cumulant2moment.Rd | 2 +- man/dapx_edgeworth.Rd | 10 +++++----- man/dapx_gca.Rd | 32 ++++++++++++++++---------------- man/moment2cumulant.Rd | 2 +- man/qapx_cf.Rd | 26 +++++++++++++------------- man/rapx_cf.Rd | 8 ++++---- vignettes/PDQutils.Rnw | 2 +- 20 files changed, 150 insertions(+), 120 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-5 dated 2015-11-02 and 0.7-6 dated 2016-01-05
DESCRIPTION | 15 MD5 | 24 - NAMESPACE | 4 R/metaplus.R | 5 R/mymle.R | 308 +++++++++---------- R/profilenorm.metaplus.R | 260 +++++++++------- R/profilet.metaplus.R | 743 ++++++++++++++++++++++++++++++++--------------- data/cdp.RData |binary inst/NEWS | 10 man/metaplus-package.Rd | 24 - man/metaplus.Rd | 100 ++++++ man/outlierProbs.Rd | 65 ++-- man/testOutliers.Rd | 2 13 files changed, 979 insertions(+), 581 deletions(-)
Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, randomForest, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between visreg versions 2.2-0 dated 2015-04-22 and 2.2-1 dated 2016-01-05
DESCRIPTION | 8 +++--- MD5 | 25 +++++++++++--------- NAMESPACE | 4 ++- NEWS | 8 ++++++ R/Response.R | 47 ++++++++++---------------------------- R/Terms.R | 6 +--- R/setupF.R | 10 ++++---- R/setupV.R | 7 +++-- R/setupV2.R | 6 ++-- R/visreg2d.R | 1 R/visregPlot.R | 7 +++-- R/visregPred.R |only R/visregResid.R |only inst/tests/nonstandard-packages.R |only tests/visreg-mlm.R | 1 15 files changed, 61 insertions(+), 69 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.9.0 dated 2015-10-20 and 2.10.0 dated 2016-01-05
R.filesets-2.10.0/R.filesets/DESCRIPTION | 16 R.filesets-2.10.0/R.filesets/MD5 | 79 +- R.filesets-2.10.0/R.filesets/NAMESPACE | 3 R.filesets-2.10.0/R.filesets/NEWS | 24 R.filesets-2.10.0/R.filesets/R/Arguments.EXTRAS.R | 21 R.filesets-2.10.0/R.filesets/R/ChecksumFile.R | 14 R.filesets-2.10.0/R.filesets/R/GenericDataFile.R | 334 +++------- R.filesets-2.10.0/R.filesets/R/GenericDataFileSet.PARALLEL.R | 18 R.filesets-2.10.0/R.filesets/R/GenericDataFileSet.R | 79 -- R.filesets-2.10.0/R.filesets/R/GenericDataFileSet.getChecksum.R | 2 R.filesets-2.10.0/R.filesets/R/GenericTabularFileSet.R | 5 R.filesets-2.10.0/R.filesets/R/TabularTextFile.R | 2 R.filesets-2.10.0/R.filesets/R/fullname.R | 10 R.filesets-2.10.0/R.filesets/R/utils.R |only R.filesets-2.10.0/R.filesets/man/ChecksumFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/GenericDataFile.Rd | 2 R.filesets-2.10.0/R.filesets/man/GenericDataFileSet.Rd | 1 R.filesets-2.10.0/R.filesets/man/GenericTabularFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/Non-documented_objects.Rd | 3 R.filesets-2.10.0/R.filesets/man/RDataFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/RdsFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/TabularTextFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/anyNA.GenericDataFileSet.Rd | 4 R.filesets-2.10.0/R.filesets/man/compareChecksum.GenericDataFile.Rd | 2 R.filesets-2.10.0/R.filesets/man/extract.GenericDataFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/getChecksum.GenericDataFile.Rd | 7 R.filesets-2.10.0/R.filesets/man/hasBeenModified.GenericDataFile.Rd | 6 R.filesets-2.10.0/R.filesets/man/readChecksum.GenericDataFile.Rd | 3 R.filesets-2.10.0/R.filesets/man/validateChecksum.GenericDataFile.Rd | 3 R.filesets-2.10.0/R.filesets/man/writeChecksum.GenericDataFile.Rd | 2 R.filesets-2.10.0/R.filesets/tests/ChecksumFile.R |only R.filesets-2.10.0/R.filesets/tests/GenericDataFile.R | 143 ++++ R.filesets-2.10.0/R.filesets/tests/GenericDataFileSet,dsApply.R | 10 R.filesets-2.10.0/R.filesets/tests/GenericDataFileSet,sortBy.R | 5 R.filesets-2.10.0/R.filesets/tests/GenericDataFileSet.R | 75 ++ R.filesets-2.10.0/R.filesets/tests/RDataFileSet.R |only R.filesets-2.10.0/R.filesets/tests/RdsFileSet.R | 2 R.filesets-2.10.0/R.filesets/tests/TabularTextFile,extend.R | 35 - R.filesets-2.10.0/R.filesets/tests/TabularTextFile.R | 6 R.filesets-2.10.0/R.filesets/tests/TabularTextFileSet.R | 8 R.filesets-2.10.0/R.filesets/tests/fullname.R |only R.filesets-2.10.0/R.filesets/tests/readDataFrame.R | 5 R.filesets-2.9.0/R.filesets/man/seq.GenericDataFileSet.Rd |only 43 files changed, 519 insertions(+), 422 deletions(-)
Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the likeLTD guide provided,
or Balding, D.J. (2013) <doi: 10.1073/pnas.1219739110>.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>
Diff between likeLTD versions 6.0.1 dated 2015-12-18 and 6.0.2 dated 2016-01-05
DESCRIPTION | 10 +-- MD5 | 12 ++-- build/vignette.rds |binary inst/doc/likeLTDguide.pdf |binary inst/doc/usage.pdf |binary src/gammaDist.cpp | 10 +-- src/maximizePeaks.cpp | 117 ++++++++++++++++++++-------------------------- 7 files changed, 67 insertions(+), 82 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputed cross-validation. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included(for C++ matrix operations); uses Marloes Maathuis's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.3.1 dated 2015-12-10 and 1.3.2 dated 2016-01-05
icenReg-1.3.1/icenReg/build |only icenReg-1.3.1/icenReg/data/essIncData.RData |only icenReg-1.3.1/icenReg/data/essIncData_small.RData |only icenReg-1.3.1/icenReg/inst |only icenReg-1.3.1/icenReg/man/ICNPMLE.Rd |only icenReg-1.3.1/icenReg/man/abs_inv.Rd |only icenReg-1.3.1/icenReg/man/essIncData.Rd |only icenReg-1.3.1/icenReg/man/essIncData_small.Rd |only icenReg-1.3.1/icenReg/man/icenReg_cv.Rd |only icenReg-1.3.1/icenReg/man/optCliq.Rd |only icenReg-1.3.1/icenReg/man/simBVCen.Rd |only icenReg-1.3.1/icenReg/vignettes |only icenReg-1.3.2/icenReg/DESCRIPTION | 14 ++-- icenReg-1.3.2/icenReg/MD5 | 63 +++++++------------ icenReg-1.3.2/icenReg/NAMESPACE | 12 +-- icenReg-1.3.2/icenReg/R/Utilities.R | 1 icenReg-1.3.2/icenReg/R/referenceClasses.R | 11 +++ icenReg-1.3.2/icenReg/R/user_functions.R | 35 ++++++---- icenReg-1.3.2/icenReg/data/IR_diabetes.RData |only icenReg-1.3.2/icenReg/man/IR_diabetes.Rd |only icenReg-1.3.2/icenReg/man/diag_baseline.Rd | 17 +---- icenReg-1.3.2/icenReg/man/diag_covar.Rd | 28 +++----- icenReg-1.3.2/icenReg/man/getFitEsts.Rd | 4 - icenReg-1.3.2/icenReg/man/getSCurves.Rd | 57 +++++++++-------- icenReg-1.3.2/icenReg/man/ic_par.Rd | 26 ++++--- icenReg-1.3.2/icenReg/man/ic_sp.Rd | 49 +++++++------- icenReg-1.3.2/icenReg/man/imputeCens.Rd | 10 +-- icenReg-1.3.2/icenReg/man/miceData.Rd | 14 ++-- icenReg-1.3.2/icenReg/man/predict.icenReg_fit.Rd | 7 +- icenReg-1.3.2/icenReg/man/simIC_weib.Rd | 26 ++++--- icenReg-1.3.2/icenReg/man/unpublishedRdFiles |only icenReg-1.3.2/icenReg/src/icenReg_files/ic_par.cpp | 4 - icenReg-1.3.2/icenReg/src/icenReg_files/ic_sp_ch.cpp | 4 - 33 files changed, 193 insertions(+), 189 deletions(-)