Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.1 dated 2015-10-05 and 0.8.2 dated 2015-10-14
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS | 11 ++- R/MulticoreFuture.R | 2 R/futureAssign.R | 2 R/globals.R | 62 ++++++++++++++--- demo/mandelbrot.R | 4 - man/eager.Rd | 136 +++++++++++++++++++-------------------- man/multicore.Rd | 166 ++++++++++++++++++++++++------------------------ tests/demo.R |only tests/dotdotdot.R | 6 + tests/futureAssign_OP.R | 6 - tests/globals,tricky.R |only 13 files changed, 240 insertions(+), 185 deletions(-)
Title: Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>
Diff between ClusterStability versions 1.0.1 dated 2015-09-15 and 1.0.2 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/ClusterStability.R | 4 ++-- man/ClusterStability-package.Rd | 4 ++-- man/ClusterStability.Rd | 4 ++-- man/ClusterStability_exact.Rd | 4 ++-- 7 files changed, 24 insertions(+), 18 deletions(-)
More information about ClusterStability at CRAN
Permanent link
Title: Applies Multiclass AdaBoost.M1, SAMME and Bagging
Description: It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging
algorithm using classification trees as individual classifiers. Once these classifiers have been
trained, they can be used to predict on new data. Also, cross validation estimation of the error can
be done. Since version 2.0 the function margins() is available to calculate the margins for these
classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument
of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu
et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as
a function of the number of iterations. In addition, the ensembles can be pruned using the option
'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probability of
each class for observations can be obtained. Version 3.1 modifies the relative importance measure
to take into account the gain of the Gini index given by a variable in each tree and the weights of
these trees. Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo
and Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover, three new plots are also
available importanceplot(), plot.errorevol() and plot.margins(). Version 4.1 allows to predict on
unlabeled data.
Author: Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from Li Guo
Maintainer: Esteban Alfaro <Esteban.Alfaro@uclm.es>
Diff between adabag versions 4.0 dated 2014-12-21 and 4.1 dated 2015-10-14
DESCRIPTION | 23 ++++++++++---------- MD5 | 38 ++++++++++++++++----------------- NAMESPACE | 4 +++ R/adaboost.M1.R | 28 ++++++++++++++++++------ R/bagging.R | 29 +++++++++++++++++++++---- R/errorevol.R | 8 ++++--- R/predict.bagging.R | 41 +++++++++++++++++++++--------------- R/predict.boosting.R | 30 ++++++++++++++++++++------ R/select.R | 8 +++---- man/MarginOrderedPruning.Bagging.rd | 3 +- man/adabag-internal.Rd | 2 - man/adabag-package.Rd | 39 ++++++++++++++++++++-------------- man/bagging.Rd | 5 ++-- man/boosting.Rd | 5 ++-- man/errorevol.rd | 2 - man/margins.Rd | 2 - man/plot.errorevol.rd | 2 - man/plot.margins.rd | 2 - man/predict.bagging.Rd | 4 +-- man/predict.boosting.Rd | 4 +-- 20 files changed, 176 insertions(+), 103 deletions(-)
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.3 dated 2015-06-26 and 2.4 dated 2015-10-14
DESCRIPTION | 12 ++- MD5 | 31 +++++---- NAMESPACE | 9 ++ NEWS | 7 ++ R/itreemap.R | 9 +- R/pkg.R | 4 - R/tmAggregate.R | 32 +++++++-- R/tmColorsLegend.R | 6 - R/tmGenerateRect.R | 6 - R/treemap.R | 160 ++++++++++++++++++++++++++++++++++++------------- R/value2col.R | 71 +++++++++++++-------- build |only inst |only man/itreemap.Rd | 5 + man/treemap-package.Rd | 4 - man/treemap.Rd | 41 +++++++++--- vignettes |only 17 files changed, 277 insertions(+), 120 deletions(-)
Title: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Description: Interface to the API for 'TreeBASE' (http://treebase.org)
from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
trees (of species, population, or genes) and the data used to create
them.
Author: Carl Boettiger [aut, cre],
Duncan Temple Lang [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between treebase versions 0.1.1 dated 2015-06-16 and 0.1.2 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 4 +--- NEWS | 6 ++++++ R/metadata.R | 4 +++- man/cache_treebase.Rd | 2 +- man/clean_data.Rd | 2 +- man/download_metadata.Rd | 2 +- man/drop_nonascii.Rd | 2 +- man/drop_nontrees.Rd | 2 +- man/dryad_metadata.Rd | 2 +- man/get_nex.Rd | 2 +- man/get_study.Rd | 2 +- man/get_study_id.Rd | 2 +- man/have_branchlength.Rd | 2 +- man/metadata.Rd | 3 ++- man/metadata_from_oai.Rd | 2 +- man/oai_metadata.Rd | 2 +- man/phylo_metadata.Rd | 2 +- man/search_treebase.Rd | 2 +- man/show_metadata.Rd | 2 +- man/treebase.Rd | 2 +- tests/testthat/test_basic.R | 4 ++-- 23 files changed, 56 insertions(+), 49 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.5 dated 2014-12-09 and 0.6 dated 2015-10-14
GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetOptimizerMTK.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetOptimizerPIC.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetterCombinedMTK.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetterCombinedPIC.R |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetOptimizerMTK.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetOptimizerPIC.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetterCombinedMTK.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetterCombinedPIC.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/DESCRIPTION | 10 +- GeneticSubsetter-0.6/GeneticSubsetter/MD5 | 34 +++++----- GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetOptimizer.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetter.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetterCombined.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/HET.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/MTK.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/SubsetterMTK.R | 2 GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetOptimizer.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetter.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetterCombined.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/GeneticSubsetter.Rd | 10 +- GeneticSubsetter-0.6/GeneticSubsetter/man/MTK.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/MtkCalc.Rd | 6 - GeneticSubsetter-0.6/GeneticSubsetter/man/PIC.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/PicCalc.Rd | 12 +-- GeneticSubsetter-0.6/GeneticSubsetter/man/SubsetterMTK.Rd | 8 -- GeneticSubsetter-0.6/GeneticSubsetter/man/SubsetterPIC.Rd | 5 - GeneticSubsetter-0.6/GeneticSubsetter/man/genotypes.Rd | 2 27 files changed, 40 insertions(+), 49 deletions(-)
More information about GeneticSubsetter at CRAN
Permanent link
Title: Statistical Comparisons with Distance-Function Based Permutation
Tests
Description: Provides tools for making statistical comparisons with distance-function based permutation tests developed by P. W. Mielke, Jr. and colleagues at Colorado State University (Mielke, P. W. & Berry, K. J. Permutation Methods: A Distance Function Approach (Springer, New York, 2001)) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U. S. Geological Survey.
Author: Marian Talbert, Jon Richards, Paul Mielke, and Brian Cade
Maintainer: Marian Talbert <mtalbert@usgs.gov>
Diff between Blossom versions 1.2 dated 2015-10-14 and 1.3 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/InternalFcts.f90 | 11 ++++++----- 3 files changed, 13 insertions(+), 12 deletions(-)
Title: Easier cluster computing (based on snow).
Description: Usability wrapper around snow for easier development of
parallel R programs. This package offers e.g. extended error
checks, and additional functions. All functions work in
sequential mode, too, if no cluster is present or wished.
Package is also designed as connector to the cluster management
tool sfCluster, but can also used without it.
Author: Jochen Knaus
Maintainer: Jochen Knaus <jo@imbi.uni-freiburg.de>
Diff between snowfall versions 1.84-6 dated 2013-12-18 and 1.84-6.1 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/init.R | 10 +++++----- R/sysdata.rda |binary data/test.rda |binary 5 files changed, 13 insertions(+), 13 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.1.2 dated 2014-03-12 and 1.2.0 dated 2015-10-14
reportr-1.1.2/reportr/R/infix.R |only reportr-1.1.2/reportr/R/substitute.R |only reportr-1.1.2/reportr/man/infix.Rd |only reportr-1.1.2/reportr/man/substitute.Rd |only reportr-1.2.0/reportr/DESCRIPTION | 15 +- reportr-1.2.0/reportr/MD5 | 17 +- reportr-1.2.0/reportr/NAMESPACE | 13 + reportr-1.2.0/reportr/R/00_constants.R | 13 + reportr-1.2.0/reportr/R/reportr.R | 227 ++++++++++++++++++++++++++------ reportr-1.2.0/reportr/README.md |only reportr-1.2.0/reportr/man/reportr.Rd | 164 +++++++++++++++++------ reportr-1.2.0/reportr/tests |only 12 files changed, 348 insertions(+), 101 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.4.1 dated 2015-10-06 and 0.5.0 dated 2015-10-14
DESCRIPTION | 6 +- MD5 | 20 +++--- NEWS | 8 ++ R/Globals-class.R | 2 R/cleanup.R | 30 ++++++---- R/globalsOf.R | 20 +++++- R/utils.R | 20 ++++++ man/cleanup.Globals.Rd | 41 ++++++------- man/globalsOf.Rd | 144 ++++++++++++++++++++++++------------------------- tests/globalsOf.R | 69 +++++++++++++++++++++++ tests/utils.R | 57 +++++++++++++++++++ 11 files changed, 295 insertions(+), 122 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.3 dated 2015-10-06 and 1.1.4 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/GDM_Table_Funcs.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>
Diff between docopulae versions 0.3.1 dated 2015-09-30 and 0.3.2 dated 2015-10-14
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- R/examples/main.R | 17 +++++++----- R/main.R | 71 ++++++++++++++++++++++++++++++++-------------------- man/Defficiency.Rd | 6 ++-- man/Dsensitivity.Rd | 16 ++++++++--- man/FedorovWynn.Rd | 5 ++- man/design.Rd | 3 +- man/numDerivLogf.Rd | 16 +++++------ man/param.Rd | 17 +++++++----- man/plot.desigh.Rd | 10 +++++-- 11 files changed, 113 insertions(+), 74 deletions(-)
Title: Item Focused Trees for the Identification of Items in
Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of
items and variables that induce Differential Item Functioning (DIF) in Item Response models.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Diff between DIFtree versions 1.0.0 dated 2015-04-28 and 1.1.0 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/DIFtree.R | 52 +++++++++++++++++++++++++++++++++++++++++----------- R/plot.DIFtree.R | 8 +++----- man/DIFtree.Rd | 3 ++- 5 files changed, 54 insertions(+), 25 deletions(-)
Title: Tools for Structural Reliability Analysis
Description: A variety of tools useful for performing structural
reliability analysis, such as with structure function and
system signatures. Plans to expand more widely.
Author: Louis Aslett <aslett@stats.ox.ac.uk>
Maintainer: Louis Aslett <aslett@stats.ox.ac.uk>
Diff between ReliabilityTheory versions 0.1.4 dated 2014-06-12 and 0.1.5 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS | 5 +++++ R/MinimalVertexPairCutSets.R | 2 +- README.md |only man/ReliabilityTheory-package.Rd | 4 ++-- 7 files changed, 20 insertions(+), 13 deletions(-)
More information about ReliabilityTheory at CRAN
Permanent link
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test.
Author: Michael Thrun, Onno Hansen-Goos, Rabea Griese, Catharina Lippmann, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between AdaptGauss versions 1.0 dated 2015-10-09 and 1.1.0 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 2 +- R/AdaptGauss.R | 6 +++--- R/Chi2testMixtures.R | 3 +++ R/KStestMixtures.R |only man/AdaptGauss-package.Rd | 4 ++-- man/AdaptGauss.Rd | 19 ++++++++++--------- man/BayesDecisionBoundaries.Rd | 2 +- man/BayesForMixes.Rd | 1 + man/CDFMixtures.Rd | 2 +- man/Chi2testMixtures.Rd | 9 +++++++-- man/EMGauss.Rd | 1 + man/KStestMixtures.Rd |only man/paretoDensityEstimationForGMM.Rd | 6 +++--- man/paretoRadiusForGMM.Rd | 4 ++-- man/qqplotGMM.Rd | 2 +- 17 files changed, 57 insertions(+), 44 deletions(-)
Title: Unit Testing for R
Description: A unit testing system designed to be fun, flexible and easy to
set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 0.10.0 dated 2015-05-22 and 0.11.0 dated 2015-10-14
DESCRIPTION | 13 ++-- MD5 | 103 ++++++++++++++++++------------------ NAMESPACE | 8 ++ R/auto-test.r | 27 +++++---- R/compare.r | 41 ++++++++------ R/expect-that.r | 17 +++-- R/expectation.r | 7 +- R/expectations-equality.R | 4 - R/expectations-matches.R | 48 ++++++++++++---- R/expectations-silent.R |only R/expectations.r | 67 ++++++++++++++++++++++- R/mock.r | 5 + R/praise.R |only R/reporter-stop.r | 2 R/reporter-summary.r | 24 +++----- R/reporter-tap.r | 2 R/reporter.r | 2 R/test-example.R | 2 R/test-files.r | 21 +++++-- R/test-package.r | 28 +++++---- R/test-results.r | 2 R/test-that.r | 15 ++--- R/utils.r | 38 ++++++++++++- R/watcher.r | 9 +-- README.md | 23 ++------ man/StopReporter-class.Rd | 2 man/compare.Rd | 2 man/equivalence.Rd | 10 ++- man/expect-compare.Rd | 15 ++++- man/expect_equal_to_reference.Rd | 8 +- man/expect_is.Rd | 6 +- man/expect_named.Rd | 6 +- man/expect_null.Rd | 6 +- man/expect_silent.Rd |only man/expect_true.Rd | 8 +- man/expectation.Rd | 6 +- man/find_test_scripts.Rd | 4 + man/matching-expectations.Rd | 21 ++++--- man/not.Rd | 4 + man/skip.Rd | 12 ++++ man/takes_less_than.Rd | 7 +- man/test_examples.Rd | 2 man/test_package.Rd | 21 +++---- man/test_that.Rd | 10 +-- man/with_mock.Rd | 3 + tests/testthat/test-bare.r | 4 + tests/testthat/test-compare.r | 26 +++++++++ tests/testthat/test-expectations.r | 13 ++++ tests/testthat/test-mock.r | 2 tests/testthat/test-reporter-list.r | 10 ++- tests/testthat/test-reporter-tap.r |only tests/testthat/test-silence.R | 2 tests/testthat/test-test_dir.r | 16 +++-- tests/testthat/test-watcher.r | 8 ++ tests/testthat/test_dir/test-skip.r |only 55 files changed, 500 insertions(+), 242 deletions(-)
Title: R Unit Test Framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools.
Author: Matthias Burger <burgerm@users.sourceforge.net>, Klaus
Juenemann <k.junemann@gmx.net>, Thomas Koenig
<thomas.koenig@epigenomics.com>
Maintainer: Roman Zenka <zenka.roman@mayo.edu>
Diff between RUnit versions 0.4.29 dated 2015-08-11 and 0.4.30 dated 2015-10-14
DESCRIPTION | 9 +++++---- MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS | 3 +++ R/junitProtocol.r |only build/RUnit.pdf |binary inst/doc/RUnit.pdf |binary inst/unitTests/runitJUnitProtocol.r |only man/textProtocol.Rd | 22 ++++++++++++++++++---- 9 files changed, 35 insertions(+), 14 deletions(-)
Title: Tools for Working with Rotation Data
Description: Tools for working with rotational data, including
simulation from the most commonly used distributions on SO(3),
methods for different Bayes, mean and median type estimators for
the central orientation of a sample, confidence/credible
regions for the central orientation based on those estimators and
a novel visualization technique for rotation data. Most recently,
functions to identify potentially discordant (outlying) values
have been added.
Author: Bryan Stanfill <bstanfill2003@gmail.com>, Heike Hofmann
<hofmann@iastate.edu>, Ulrike Genschel <ulrike@iastate.edu>
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between rotations versions 1.3 dated 2014-12-16 and 1.4 dated 2015-10-14
DESCRIPTION | 12 LICENSE | 2 MD5 | 164 +-- NAMESPACE | 234 ++-- NEWS | 270 ++--- R/RcppExports.R | 362 +++--- R/bayes.R | 534 ++++----- R/distributions.R | 1131 +++++++++++---------- R/estimators.R | 592 +++++------ R/grid-search.R | 200 +-- R/help.R | 20 R/kappa.R | 233 ++-- R/parameterizations.R | 1002 +++++++++--------- R/plot.R | 1060 ++++++++++--------- R/preliminary.R | 1423 +++++++++++++------------- R/primatives.R | 670 ++++++------ R/regions.R | 1076 ++++++++++---------- R/robust.R | 188 +-- build/vignette.rds |binary data/datalist | 4 inst/CITATION | 32 inst/REFERENCES.bib | 367 +++--- inst/doc/rotations-intro.R | 156 +- inst/doc/rotations-intro.Rnw | 732 ++++++------- inst/doc/rotations-intro.pdf |binary inst/include/rotations.h | 18 inst/include/rotations_RcppExports.h | 1713 ++++++++++++++++---------------- man/Angular-distributions.Rd | 40 man/Arithmetic.Rd | 155 +- man/Cayley.Rd | 164 +-- man/Fisher.Rd | 154 +- man/Haar.Rd | 142 +- man/MCMCSO3.Rd | 166 +-- man/Maxwell.Rd |only man/Mises.Rd | 142 +- man/Q4-class.Rd | 20 man/Q4.Rd | 212 +-- man/SO3-class.Rd | 22 man/SO3.Rd | 218 ++-- man/UARS.Rd | 172 +-- man/bayes.mean.Rd | 188 +-- man/bayesCR.Rd | 186 +-- man/cayley.kappa.Rd | 84 - man/center.Rd | 88 - man/chang.Rd | 122 +- man/discord.Rd | 104 - man/drill.Rd | 114 +- man/fisher.kappa.Rd | 85 - man/fisheretal.Rd | 134 +- man/genR.Rd | 92 - man/gradient.search.Rd | 98 - man/log.SO3.Rd | 86 - man/maxwell.kappa.Rd |only man/mean.SO3.Rd | 166 +-- man/median.SO3.Rd | 152 +- man/mis.angle.Rd | 108 +- man/mis.axis.Rd | 116 +- man/nickel.Rd | 120 +- man/plot.SO3.Rd | 182 +-- man/pointsXYZ.Rd | 68 - man/prentice.Rd | 118 +- man/project.SO3.Rd | 88 - man/region.Rd | 140 +- man/rot.dist.Rd | 132 +- man/rotations.Rd | 30 man/rotdist.sum.Rd | 130 +- man/skew.exp.Rd | 68 - man/vmises.kappa.Rd | 85 - man/weighted.mean.SO3.Rd | 168 +-- man/zhang.Rd | 122 +- src/CppBayesFunctions.cpp | 106 + src/Makevars.win | 12 src/RcppExports.cpp | 649 ++++-------- src/basics.cpp | 1 tests/test-all.R | 2 tests/testthat/test_arithmetic.R | 78 - tests/testthat/test_basics.R | 90 - tests/testthat/test_conversions.R | 40 tests/testthat/test_discord.R | 28 tests/testthat/test_estimators.R | 60 - tests/testthat/test_metrics.R | 24 vignettes/RJournal_edited.sty | 670 ++++++------ vignettes/rotations-intro.Rnw | 732 ++++++------- vignettes/stanfill-hofmann-genschel.bib | 754 +++++++------- 84 files changed, 10304 insertions(+), 10118 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in NeXML format. The
package should add new functionality to R such as the possibility to
manipulate NeXML objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.0.3 dated 2015-05-26 and 2.0.4 dated 2015-10-14
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++++ NEWS | 5 +++++ R/add_basic_meta.R | 2 ++ R/classes.R | 3 ++- R/get_characters.R | 11 ++++++----- R/simmap.R | 4 ++++ build/vignette.rds |binary tests/testthat/test_publish.R | 7 ++++++- tests/testthat/test_rdf.R | 2 ++ 11 files changed, 44 insertions(+), 20 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.4 dated 2015-10-01 and 0.0.5 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Aggregate.R | 2 +- R/create_infotables.R | 1 + inst/doc/Information-vignette.html | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Interactive Dendrograms
Description: Interactive dendrogram that enables the user to select and
color clusters, to zoom and pan the dendrogram, and to visualize
the clustered data not only in a built-in heat map, but also in
'GGobi' interactive plots and user-supplied plots.
This is a backport of Qt-based 'idendro'
(https://github.com/tsieger/idendro) to base R graphics and Tcl/Tk GUI.
Author: Tomas Sieger
Maintainer: Tomas Sieger <tomas.sieger@seznam.cz>
Diff between idendr0 versions 1.5.0 dated 2015-10-07 and 1.5.1 dated 2015-10-14
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS | 11 +++++++++-- R/idendro.R | 40 ++++++++++++++++++++++++++++++---------- README.md | 4 ++-- demo/idendroWithGgobi.R | 1 - man/idendr0-package.Rd | 7 ++++--- man/idendro.Rd | 3 +-- 8 files changed, 59 insertions(+), 32 deletions(-)
Title: Study Design and Data Analysis in the Presence of Error-Prone
Diagnostic Tests and Self-Reported Outcomes
Description: We consider studies in which information from error-prone
diagnostic tests or self-reports are gathered sequentially to determine the
occurrence of a silent event. Using a likelihood-based approach
incorporating the proportional hazards assumption, we provide functions to
estimate the survival distribution and covariate effects. We also provide
functions for power and sample size calculations for this setting.
Author: Xiangdong Gu and Raji Balasubramanian
Maintainer: Xiangdong Gu <ustcgxd@gmail.com>
Diff between icensmis versions 1.2.1 dated 2014-06-27 and 1.3.0 dated 2015-10-14
DESCRIPTION | 15 MD5 | 30 + NAMESPACE | 11 R/HighDimCR.R | 20 - R/RcppExports.R | 16 R/datasim.R | 27 + R/icpower.R | 221 +++++-------- README.md |only man/datasim.Rd | 11 man/icmis.Rd | 3 man/icpower.Rd | 10 man/icpower.val.Rd | 3 man/icpowerpf.Rd | 3 src/HighDimCR.cpp | 24 - src/RcppExports.cpp | 878 +++++++++++++++++++++++----------------------------- src/powerfuncs.cpp |only tests |only 17 files changed, 594 insertions(+), 678 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Author: John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.2 dated 2015-05-11 and 1.3 dated 2015-10-14
DESCRIPTION | 9 ++-- MD5 | 74 +++++++++++++++++----------------- NAMESPACE | 6 ++ R/Calc_Hepatic_Clearance.r | 2 R/Calc_ratioblood2plasma.R | 2 R/Calc_volume_of_distribution.R | 59 ++++++++++++++++++++------- R/Export_PBTK_Jarnac.R | 26 +++++------ R/Export_PBTK_SBML.R | 24 +++++------ R/Get_lumped_tissues.R | 32 +++++++++----- R/Parameterize_PBTK.r | 44 ++++++-------------- R/Predict_partitioning_Schmitt.R | 17 +++---- R/add_chemtable.R | 6 +- R/calc_analytic_css.R | 14 +++--- R/calc_css.R | 47 +++++++++++++-------- R/get_Wetmore_Css.R | 17 +++++-- R/get_Wetmore_Oral_Equiv.R | 5 +- R/get_chem_id.R | 1 R/get_cheminfo.R | 1 R/in.list.R |only R/ionization_functions.R | 17 +++++-- R/solve_3comp.R | 7 +-- R/solve_pbtk.R | 5 +- data/Tables.RData |binary man/Parameterize_PBTK.Rd | 12 ++--- man/Wetmore.data.Rd | 2 man/Wetmore_Css.Rd | 2 man/Wetmore_Oral_Equiv.Rd | 9 ++++ man/calc_analytic_css.Rd | 2 man/calc_css.Rd | 10 ++-- man/calc_ionization.Rd |only man/chem.lists.Rd |only man/chem_physical_and_invitro_data.Rd | 3 + man/get_cheminfo.Rd | 29 +++++++++++++ man/get_wetmore_cheminfo.Rd | 7 +++ man/in_list.Rd |only man/parameterize_3comp.Rd | 8 +-- man/solve_3comp_pbpk.Rd | 2 man/solve_pbtk.Rd | 2 tests/cheminfo_test.Rout.save | 22 +++++----- tests/other_tests.Rout.save | 64 ++++++++++++++--------------- 40 files changed, 352 insertions(+), 237 deletions(-)
Title: Foreach Parallel Adaptor for the 'snow' Package
Description: Provides a parallel backend for the %dopar% function using
Luke Tierney's snow package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Stephen Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doSNOW versions 1.0.12 dated 2014-03-13 and 1.0.14 dated 2015-10-14
DESCRIPTION | 22 ++++++---- MD5 | 8 +-- NAMESPACE | 1 R/doSNOW.R | 102 +++++++++++++++++++++++++++++++++++++++++++++----- man/registerDoSNOW.Rd | 1 5 files changed, 113 insertions(+), 21 deletions(-)
Title: Foreach Parallel Adaptor for the 'parallel' Package
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut],
Dan Tenenbaum [ctb]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doParallel versions 1.0.8 dated 2014-02-28 and 1.0.10 dated 2015-10-14
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 4 +++- R/doParallel.R | 9 ++++++--- build/vignette.rds |binary inst/doc/gettingstartedParallel.pdf |binary 7 files changed, 31 insertions(+), 18 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Chris H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.2.8 dated 2015-08-26 and 0.2.9 dated 2015-10-14
DESCRIPTION | 12 - MD5 | 68 +++++---- NAMESPACE | 1 NEWS | 20 ++ R/generic.R | 72 ++++++++++ R/kde.R | 331 +++++++++++++++++++++++++++++++++++------------- R/krige.R | 151 +++++++++++++++++++++ R/likelihood.R | 95 +++++++++---- R/periodogram.R | 186 ++++++++++++++++++++++++-- R/telemetry.R | 116 ++++++++++++---- R/variogram.R | 124 ++++++++++++----- TODO | 27 ++- build/vignette.rds |binary data/gazelle.rda |only inst/doc/akde.html | 14 +- inst/doc/variogram.R | 50 +++++-- inst/doc/variogram.Rmd | 63 ++++++--- inst/doc/variogram.html | 83 +++++++----- man/akde.Rd | 20 +- man/akde.bandwidth.Rd | 7 - man/as.telemetry.Rd | 3 man/buffalo.Rd | 4 man/ctmm-package.Rd | 4 man/ctmm.fit.Rd | 7 - man/ctmm.loglike.Rd | 2 man/export.Rd | 6 man/gazelle.Rd |only man/mean.variogram.Rd | 6 man/periodogram.Rd | 25 ++- man/plot.variogram.Rd | 4 man/simulate.ctmm.Rd | 2 man/summary.akde.Rd | 8 - man/summary.ctmm.Rd | 2 man/variogram.Rd | 14 +- man/variogram.fit.Rd | 6 vignettes/variogram.Rmd | 63 ++++++--- 36 files changed, 1196 insertions(+), 400 deletions(-)