Title: Regression Spline Functions and Classes Too
Description: A complementary package on splines providing functions
constructing B-splines, monotone splines (M-splines) and its integral
(I-splines), convex splines (C-splines), and integral of B-splines.
Piecewise constant basis is allowed for B-spline and M-spline basis.
Author: Wenjie Wang [aut, cre],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between splines2 versions 0.1.0 dated 2016-09-06 and 0.2.1 dated 2016-10-07
splines2-0.1.0/splines2/R/splines-package.R |only splines2-0.2.1/splines2/DESCRIPTION | 16 +++- splines2-0.2.1/splines2/MD5 | 39 ++++++++---- splines2-0.2.1/splines2/NAMESPACE | 11 +++ splines2-0.2.1/splines2/NEWS.md |only splines2-0.2.1/splines2/R/bSpline.R |only splines2-0.2.1/splines2/R/cSpline.R |only splines2-0.2.1/splines2/R/iSpline.R | 87 ++++++++++++++++++--------- splines2-0.2.1/splines2/R/ibs.R | 34 +++++----- splines2-0.2.1/splines2/R/mSpline.R | 39 ++++++------ splines2-0.2.1/splines2/R/predict.R | 65 +++++++++++++++----- splines2-0.2.1/splines2/R/print.R |only splines2-0.2.1/splines2/R/splines2-package.R |only splines2-0.2.1/splines2/README.md |only splines2-0.2.1/splines2/build |only splines2-0.2.1/splines2/inst |only splines2-0.2.1/splines2/man/bSpline.Rd |only splines2-0.2.1/splines2/man/cSpline.Rd |only splines2-0.2.1/splines2/man/iSpline.Rd | 30 +++++---- splines2-0.2.1/splines2/man/ibs.Rd | 23 +++---- splines2-0.2.1/splines2/man/mSpline.Rd | 32 +++++---- splines2-0.2.1/splines2/man/predict.Rd | 36 ++++++++--- splines2-0.2.1/splines2/man/print.Rd |only splines2-0.2.1/splines2/man/splines2.Rd | 8 +- splines2-0.2.1/splines2/vignettes |only 25 files changed, 273 insertions(+), 147 deletions(-)
Title: Render R Markdown Outputs Lazily
Description: An R Markdown html document format that provides the ability to lazily
load plot outputs as the user scrolls over them. This is useful for large R
Markdown documents with many plots, as it allows for a fast initial page load and
defers loading of individual graphics to the time that the user navigates near them.
Author: Ryan Hafen [aut, cre],
Barret Schloerke [aut],
jQuery Foundation [cph] (jQuery.js library),
Sourcey [cph] (recliner.js library)
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between lazyrmd versions 0.1.0 dated 2016-08-01 and 0.2.0 dated 2016-10-07
lazyrmd-0.1.0/lazyrmd/NEWS.md |only lazyrmd-0.1.0/lazyrmd/inst/doc/bc5930df80ffdf606fde3da6ebf158b5.html |only lazyrmd-0.1.0/lazyrmd/inst/doc/d3-3.5.2 |only lazyrmd-0.1.0/lazyrmd/inst/doc/d3.min.js |only lazyrmd-0.1.0/lazyrmd/inst/doc/htmlwidgets-0.6 |only lazyrmd-0.1.0/lazyrmd/inst/doc/htmlwidgets.js |only lazyrmd-0.1.0/lazyrmd/inst/doc/lazy_example.R |only lazyrmd-0.1.0/lazyrmd/inst/doc/lazy_widgets |only lazyrmd-0.1.0/lazyrmd/inst/doc/lib |only lazyrmd-0.1.0/lazyrmd/inst/doc/simpleNetwork-binding-0.2.12 |only lazyrmd-0.1.0/lazyrmd/inst/doc/simpleNetwork.js |only lazyrmd-0.1.0/lazyrmd/man/lazyhtml_document.Rd |only lazyrmd-0.1.0/lazyrmd/vignettes/.install_extras |only lazyrmd-0.1.0/lazyrmd/vignettes/lazy_widgets |only lazyrmd-0.2.0/lazyrmd/DESCRIPTION | 18 - lazyrmd-0.2.0/lazyrmd/MD5 | 41 --- lazyrmd-0.2.0/lazyrmd/NAMESPACE | 5 lazyrmd-0.2.0/lazyrmd/NEWS |only lazyrmd-0.2.0/lazyrmd/R/lazyhtml_document.R | 20 + lazyrmd-0.2.0/lazyrmd/R/print_lazy_widget.R | 7 lazyrmd-0.2.0/lazyrmd/README.md | 6 lazyrmd-0.2.0/lazyrmd/build/vignette.rds |binary lazyrmd-0.2.0/lazyrmd/inst/doc/lazy_example.Rmd | 34 -- lazyrmd-0.2.0/lazyrmd/inst/doc/lazy_example.html | 135 ---------- lazyrmd-0.2.0/lazyrmd/man/lazy_render.Rd |only lazyrmd-0.2.0/lazyrmd/vignettes/lazy_example.Rmd | 34 -- 26 files changed, 67 insertions(+), 233 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 1.07 dated 2015-09-11 and 2.0 dated 2016-10-07
irace-1.07/irace/inst/examples/acotsp/hook-run |only irace-1.07/irace/inst/examples/acotsp/tune-conf |only irace-1.07/irace/inst/examples/hook-run-python |only irace-1.07/irace/inst/examples/hypervolume/hook-evaluate |only irace-1.07/irace/inst/examples/hypervolume/hook-run |only irace-1.07/irace/inst/examples/moaco/hook-evaluate |only irace-1.07/irace/inst/examples/moaco/hook-run |only irace-1.07/irace/inst/examples/moaco/tune-conf |only irace-1.07/irace/inst/examples/mpi |only irace-1.07/irace/inst/examples/sge-cluster/hook-evaluate |only irace-1.07/irace/inst/examples/sge-cluster/hook-run |only irace-1.07/irace/inst/examples/sge-cluster/tune-main |only irace-1.07/irace/inst/examples/tune-main-cluster |only irace-1.07/irace/inst/examples/tune-main-tmp |only irace-1.07/irace/inst/templates/candidates.tmpl |only irace-1.07/irace/inst/templates/forbidden.tmpl |only irace-1.07/irace/inst/templates/hook-evaluate.tmpl |only irace-1.07/irace/inst/templates/hook-run.tmpl |only irace-1.07/irace/inst/templates/instances-list.tmpl |only irace-1.07/irace/inst/templates/parameters.tmpl |only irace-1.07/irace/inst/templates/tune-conf.tmpl |only irace-1.07/irace/inst/templates/tune-main.tmpl |only irace-1.07/irace/man/candidates.print.Rd |only irace-1.07/irace/man/candidates.print.command.Rd |only irace-1.07/irace/man/checkConfiguration.Rd |only irace-1.07/irace/man/defaultConfiguration.Rd |only irace-1.07/irace/man/hook.evaluate.default.Rd |only irace-1.07/irace/man/hook.run.default.Rd |only irace-1.07/irace/man/printConfiguration.Rd |only irace-1.07/irace/man/readConfiguration.Rd |only irace-1.07/irace/man/removeCandidatesMetaData.Rd |only irace-2.0/irace/BUGS |only irace-2.0/irace/DESCRIPTION | 24 irace-2.0/irace/MD5 | 154 + irace-2.0/irace/NAMESPACE | 14 irace-2.0/irace/NEWS | 103 + irace-2.0/irace/R/cluster.R | 130 - irace-2.0/irace/R/generation.R | 146 - irace-2.0/irace/R/irace.R | 1033 +++++++----- irace-2.0/irace/R/main.R | 430 ++-- irace-2.0/irace/R/model.R | 131 - irace-2.0/irace/R/parameterAnalysis.R |only irace-2.0/irace/R/race-wrapper.R | 551 +++--- irace-2.0/irace/R/race.R | 839 +++++---- irace-2.0/irace/R/readConfiguration.R | 688 ++++--- irace-2.0/irace/R/readParameters.R | 127 - irace-2.0/irace/R/testing.R | 75 irace-2.0/irace/R/tnorm.R | 18 irace-2.0/irace/R/utils.R | 391 +++- irace-2.0/irace/R/version.R | 2 irace-2.0/irace/README.md | 195 +- irace-2.0/irace/build |only irace-2.0/irace/inst/CITATION | 26 irace-2.0/irace/inst/bin/irace.bat |only irace-2.0/irace/inst/bin/parallel-irace | 57 irace-2.0/irace/inst/bin/parallel-irace-mpi |only irace-2.0/irace/inst/bin/parallel-irace-qsub |only irace-2.0/irace/inst/doc |only irace-2.0/irace/inst/examples/acotsp/README | 3 irace-2.0/irace/inst/examples/acotsp/default.txt | 2 irace-2.0/irace/inst/examples/acotsp/forbidden.txt | 2 irace-2.0/irace/inst/examples/acotsp/parameters-acotsp.txt | 12 irace-2.0/irace/inst/examples/acotsp/scenario.txt |only irace-2.0/irace/inst/examples/acotsp/target-runner |only irace-2.0/irace/inst/examples/hypervolume/README | 10 irace-2.0/irace/inst/examples/hypervolume/target-evaluator |only irace-2.0/irace/inst/examples/hypervolume/target-runner |only irace-2.0/irace/inst/examples/matlab |only irace-2.0/irace/inst/examples/moaco/parameters.txt | 4 irace-2.0/irace/inst/examples/moaco/scenario.txt |only irace-2.0/irace/inst/examples/moaco/target-evaluator |only irace-2.0/irace/inst/examples/moaco/target-runner |only irace-2.0/irace/inst/examples/sge-cluster/README | 16 irace-2.0/irace/inst/examples/sge-cluster/irace-sge-cluster |only irace-2.0/irace/inst/examples/sge-cluster/target-evaluator |only irace-2.0/irace/inst/examples/sge-cluster/target-runner |only irace-2.0/irace/inst/examples/target-runner-python |only irace-2.0/irace/inst/templates/configurations.txt.tmpl |only irace-2.0/irace/inst/templates/forbidden.txt.tmpl |only irace-2.0/irace/inst/templates/instances-list.txt.tmpl |only irace-2.0/irace/inst/templates/parameters.txt.tmpl |only irace-2.0/irace/inst/templates/scenario.txt.tmpl |only irace-2.0/irace/inst/templates/target-evaluator.tmpl |only irace-2.0/irace/inst/templates/target-runner.tmpl |only irace-2.0/irace/man/buildCommandLine.Rd | 4 irace-2.0/irace/man/checkIraceScenario.Rd |only irace-2.0/irace/man/checkScenario.Rd |only irace-2.0/irace/man/configurations.print.Rd |only irace-2.0/irace/man/configurations.print.command.Rd |only irace-2.0/irace/man/defaultScenario.Rd |only irace-2.0/irace/man/getConfigurationById.Rd |only irace-2.0/irace/man/getConfigurationByIteration.Rd |only irace-2.0/irace/man/getFinalElites.Rd |only irace-2.0/irace/man/irace-package.Rd | 31 irace-2.0/irace/man/irace.Rd |only irace-2.0/irace/man/irace.cmdline.Rd | 10 irace-2.0/irace/man/irace.main.Rd | 13 irace-2.0/irace/man/irace.usage.Rd | 5 irace-2.0/irace/man/parallelCoordinatesPlot.Rd |only irace-2.0/irace/man/parameterFrequency.Rd |only irace-2.0/irace/man/printScenario.Rd |only irace-2.0/irace/man/readConfigurationsFile.Rd |only irace-2.0/irace/man/readParameters.Rd | 32 irace-2.0/irace/man/readScenario.Rd |only irace-2.0/irace/man/removeConfigurationsMetaData.Rd |only irace-2.0/irace/man/target.evaluator.default.Rd |only irace-2.0/irace/man/target.runner.default.Rd |only irace-2.0/irace/man/testing.main.Rd |only irace-2.0/irace/tests |only irace-2.0/irace/vignettes |only 110 files changed, 3071 insertions(+), 2207 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus genotype-by-environment) and
GGB (genotype plus genotype-by-block-of-environments) models.
Author: Kevin Wright [aut, cre],
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.0 dated 2015-12-14 and 1.1 dated 2016-10-07
gge-1.0/gge/R/gge.r |only gge-1.1/gge/DESCRIPTION | 10 +-- gge-1.1/gge/MD5 | 19 +++--- gge-1.1/gge/R/gge.R |only gge-1.1/gge/build/vignette.rds |binary gge-1.1/gge/inst/doc/gge.R | 17 ++++- gge-1.1/gge/inst/doc/gge.Rmd | 25 ++++++-- gge-1.1/gge/inst/doc/gge.html | 128 +++++++++++++++++++++++++++++++++-------- gge-1.1/gge/man/RedGrayBlue.Rd | 12 --- gge-1.1/gge/man/gge.Rd | 18 ++++- gge-1.1/gge/tests |only gge-1.1/gge/vignettes/gge.Rmd | 25 ++++++-- 12 files changed, 192 insertions(+), 62 deletions(-)
Title: Simulation of Fatigue Lifetimes
Description: Provides methods for simulation and analysis of a very general fatigue
lifetime model for (metal matrix) composite materials.
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between simLife versions 0.2.3 dated 2016-06-26 and 0.3 dated 2016-10-07
DESCRIPTION | 10 MD5 | 64 ++-- R/densify.R | 240 ++++++++-------- R/rsaSpheroids.r | 99 +++--- R/simLife.R | 611 +++++++++++++++++++++++-------------------- R/times.R | 216 ++++++++------- man/CLF.Rd | 2 man/SF.Rd | 2 man/areaCrit.Rd | 6 man/densifyCluster.Rd | 15 - man/drawDefectProjections.Rd | 6 man/getCrackTime.Rd | 16 - man/getCylinderProjection.Rd | 4 man/getDelamTime.Rd | 16 - man/getSpheroidProjection.Rd | 2 man/plotDefectAcc.Rd | 24 - man/rsa.Rd | 8 man/showDensity.Rd | 29 +- man/simCluster.Rd | 6 man/simCrackTime.Rd | 23 - man/simDefect.Rd | 14 man/simFerrit.Rd | 4 man/simFracture.Rd | 77 +++-- man/simParticle.Rd | 6 man/simTimes.Rd | 25 - man/woehler.Rd | 66 ++-- man/woehlerDiagram.Rd | 22 - src/GeometricPrimitives.cpp | 2 src/GeometricPrimitives.h | 2 src/Vector.h | 2 src/convert.cpp | 2 src/sim2Life.cpp | 88 ++---- src/sim2Life.h | 9 33 files changed, 903 insertions(+), 815 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 0.2.0 dated 2016-07-19 and 0.2.1 dated 2016-10-07
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only R/input-time.R | 13 +++++-------- inst/www/input_binding_time.js | 32 +++++++++++++++++++++++++++++++- 5 files changed, 43 insertions(+), 15 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 3.3-1 dated 2016-09-06 and 3.3-2 dated 2016-10-07
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- data/SEQINR.UTIL.RData |binary data/sysdata.rda |binary man/SEQINR.UTIL.Rd | 4 ++-- man/translate.Rd | 7 +++++-- 6 files changed, 18 insertions(+), 15 deletions(-)
Title: Robust Rank Correlation Coefficient and Test
Description: The 'rococo' package provides a robust gamma rank correlation
coefficient along with a permutation-based rank correlation test.
The rank correlation coefficient and the test are explicitly
designed for dealing with noisy numerical data.
Author: Martin Krone, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between rococo versions 1.1.3 dated 2016-04-18 and 1.1.4 dated 2016-10-07
DESCRIPTION | 8 +-- MD5 | 20 ++++---- R/rococo.R | 76 +++++++++++++++++++++++++++--- R/rococo.test-methods.R | 112 ++++++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/NEWS | 5 ++ inst/doc/rococo.Rnw | 6 ++ inst/doc/rococo.pdf |binary man/rococo.Rd | 5 +- man/rococo.test-methods.Rd | 7 ++ vignettes/rococo.Rnw | 6 ++ 11 files changed, 211 insertions(+), 34 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-8 dated 2016-05-09 and 0.1-9 dated 2016-10-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/xml1.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional
data. Ensembles of classification, regression, survival and probability prediction
trees are supported. Data from genome-wide association studies can be analyzed
efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package
'GenABEL') can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between ranger versions 0.5.0 dated 2016-06-24 and 0.6.0 dated 2016-10-07
DESCRIPTION | 17 ++-- MD5 | 80 ++++++++++----------- NEWS | 8 ++ R/RcppExports.R | 6 - R/csrf.R | 4 - R/getTerminalNodeIDs.R | 49 ++----------- R/importance.R | 32 ++++---- R/predict.R | 115 +++++++++++++++++++------------ R/ranger.R | 61 +++++++++------- man/getTerminalNodeIDs.Rd | 6 + man/importance_pvalues.Rd | 10 +- man/predict.ranger.Rd | 12 ++- man/predict.ranger.forest.Rd | 14 +++ man/ranger.Rd | 35 ++++----- src/Forest.cpp | 17 ++-- src/Forest.h | 9 +- src/ForestClassification.cpp | 13 ++- src/ForestProbability.cpp | 38 +++++++--- src/ForestRegression.cpp | 17 +++- src/ForestSurvival.cpp | 24 ++++-- src/RcppExports.cpp | 15 ++-- src/TreeClassification.h | 6 + src/TreeProbability.h | 18 ++-- src/TreeRegression.h | 4 + src/TreeSurvival.cpp | 20 ++++- src/TreeSurvival.h | 9 +- src/globals.h | 8 ++ src/rangerCpp.cpp | 9 +- src/utility.cpp | 4 + src/utility.h | 7 + src/version.h | 2 tests/testthat/test_classification.R | 24 ++++-- tests/testthat/test_importance.R | 5 + tests/testthat/test_importance_pvalues.R | 12 ++- tests/testthat/test_predict.R | 76 ++++++++++++++++++++ tests/testthat/test_print.R | 2 tests/testthat/test_probability.R | 36 +++++++++ tests/testthat/test_ranger.R | 33 ++++++++ tests/testthat/test_regression.R | 2 tests/testthat/test_survival.R | 4 - tests/testthat/test_unordered.R | 50 +++++++++++++ 41 files changed, 628 insertions(+), 285 deletions(-)
Title: Collection of Tools for Genomic Data Analysis
Description: A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools versions 0.2 dated 2016-09-06 and 0.2.1 dated 2016-10-07
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 2 +- R/importGFF3.R | 17 ++++++++++++++++- build/vignette.rds |binary data/annotTrack.rda |binary data/geneEXP.rda |binary data/genotData.rda |binary data/mdrExample.rda |binary data/phenoData.rda |binary inst/ChangeLog | 4 ++++ inst/doc/GenomicTools-Vignette.pdf |binary man/GenomicTools-package.Rd | 4 ++-- man/importGFF3.Rd |only 14 files changed, 40 insertions(+), 20 deletions(-)
Title: Data for "GAMs: An Introduction with R"
Description: Data sets and scripts used in the book "Generalized
Additive Models: An Introduction with R", Wood (2006) CRC.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between gamair versions 0.0-9 dated 2015-07-22 and 1.0-0 dated 2016-10-07
ChangeLog | 7 ++++++ DESCRIPTION | 7 +++--- MD5 | 55 ++++++++++++++++++++++++++++++++++++++++++-------- data/aral.bnd.rda |only data/aral.rda |only data/bone.rda |only data/canWeather.rda |only data/datalist | 14 ++++++++++++ data/gas.rda |only data/german.polys.rda |only data/larynx.rda |only data/med.rda |only data/meh.rda |only data/mpg.rda |only data/prostate.rda |only data/sitka.rda |only data/swer.rda |only data/wesdr.rda |only man/aral.Rd |only man/bird.Rd | 3 +- man/bone.Rd |only man/canWeather.Rd |only man/ch1.Rd |only man/ch1.solutions.Rd |only man/ch2.Rd |only man/ch2.solutions.Rd |only man/ch3.Rd |only man/ch3.solutions.Rd |only man/ch4.Rd |only man/ch4.solutions.Rd |only man/ch5.Rd |only man/ch5.solutions.Rd |only man/ch6.Rd |only man/ch6.solutions.Rd |only man/ch7.Rd |only man/ch7.solutions.Rd |only man/chicago.Rd | 1 man/coast.Rd | 4 +-- man/gamair-package.Rd | 24 ++++++++++++++++----- man/gas.Rd |only man/larynx.Rd |only man/meh.Rd |only man/mpg.Rd |only man/prostate.Rd |only man/sitka.Rd |only man/sole.Rd | 24 ++++++++++++++++++++- man/swer.Rd |only man/wesdr.Rd |only 48 files changed, 116 insertions(+), 23 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, an algorithm for transportability from multiple domains with limited experiments by Elias Bareinboim and Judea Pearl and a selection bias recovery algorithm by Elias Bareinboim and Jin Tian. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.2.4 dated 2016-02-23 and 1.3.0 dated 2016-10-07
causaleffect-1.2.4/causaleffect/R/getNonIgnorableNodes.R |only causaleffect-1.2.4/causaleffect/R/perm.R |only causaleffect-1.2.4/causaleffect/R/sid.R |only causaleffect-1.2.4/causaleffect/R/simplify.meta.expression.R |only causaleffect-1.2.4/causaleffect/R/trz.R |only causaleffect-1.2.4/causaleffect/R/usid.R |only causaleffect-1.2.4/causaleffect/R/zid.R |only causaleffect-1.2.4/causaleffect/inst/doc/causaleffect.tex.rsp |only causaleffect-1.2.4/causaleffect/vignettes/causaleffect.tex.rsp |only causaleffect-1.3.0/causaleffect/DESCRIPTION | 10 causaleffect-1.3.0/causaleffect/MD5 | 94 +++--- causaleffect-1.3.0/causaleffect/NAMESPACE | 5 causaleffect-1.3.0/causaleffect/NEWS | 8 causaleffect-1.3.0/causaleffect/R/activate.interventions.R | 31 + causaleffect-1.3.0/causaleffect/R/cancel.R |only causaleffect-1.3.0/causaleffect/R/cancel.rc.R |only causaleffect-1.3.0/causaleffect/R/causal.effect.R | 61 +-- causaleffect-1.3.0/causaleffect/R/compute.q.R |only causaleffect-1.3.0/causaleffect/R/deconstruct.R | 156 ++++++++-- causaleffect-1.3.0/causaleffect/R/factorize.R | 21 - causaleffect-1.3.0/causaleffect/R/generalize.R |only causaleffect-1.3.0/causaleffect/R/get.expression.R | 54 ++- causaleffect-1.3.0/causaleffect/R/id.R | 138 +++++--- causaleffect-1.3.0/causaleffect/R/idc.R | 19 + causaleffect-1.3.0/causaleffect/R/identify.R |only causaleffect-1.3.0/causaleffect/R/insert.R |only causaleffect-1.3.0/causaleffect/R/join.R | 51 +-- causaleffect-1.3.0/causaleffect/R/meta.transport.R | 30 - causaleffect-1.3.0/causaleffect/R/organize.terms.R | 26 - causaleffect-1.3.0/causaleffect/R/parse.deconstruct.R | 48 +-- causaleffect-1.3.0/causaleffect/R/parse.expression.R | 72 ++-- causaleffect-1.3.0/causaleffect/R/parse.joint.R | 12 causaleffect-1.3.0/causaleffect/R/parse.layout.R |only causaleffect-1.3.0/causaleffect/R/probability.R | 8 causaleffect-1.3.0/causaleffect/R/rc.R |only causaleffect-1.3.0/causaleffect/R/recover.R |only causaleffect-1.3.0/causaleffect/R/simplify.R | 53 +-- causaleffect-1.3.0/causaleffect/R/simplify.causal.R |only causaleffect-1.3.0/causaleffect/R/simplify.expression.R | 99 +++--- causaleffect-1.3.0/causaleffect/R/simplify.rc.R |only causaleffect-1.3.0/causaleffect/R/simplify.trmz.R |only causaleffect-1.3.0/causaleffect/R/transport.R | 29 - causaleffect-1.3.0/causaleffect/R/trmz.R |only causaleffect-1.3.0/causaleffect/R/zzaux.effect.R | 26 - causaleffect-1.3.0/causaleffect/build/vignette.rds |binary causaleffect-1.3.0/causaleffect/inst/doc/causaleffect.ltx |only causaleffect-1.3.0/causaleffect/inst/doc/causaleffect.pdf |binary causaleffect-1.3.0/causaleffect/inst/doc/simplification.ltx |only causaleffect-1.3.0/causaleffect/inst/doc/simplification.pdf |only causaleffect-1.3.0/causaleffect/man/causal.effect.Rd | 19 - causaleffect-1.3.0/causaleffect/man/causaleffect-package.Rd | 17 - causaleffect-1.3.0/causaleffect/man/generalize.Rd |only causaleffect-1.3.0/causaleffect/man/get.expression.Rd | 4 causaleffect-1.3.0/causaleffect/man/meta.transport.Rd | 38 +- causaleffect-1.3.0/causaleffect/man/parse.graphml.Rd | 12 causaleffect-1.3.0/causaleffect/man/recover.Rd |only causaleffect-1.3.0/causaleffect/man/transport.Rd | 24 - causaleffect-1.3.0/causaleffect/man/zzaux.effect.Rd | 15 causaleffect-1.3.0/causaleffect/vignettes/causaleffect.ltx |only causaleffect-1.3.0/causaleffect/vignettes/giden.pdf |only causaleffect-1.3.0/causaleffect/vignettes/ginsert.pdf |only causaleffect-1.3.0/causaleffect/vignettes/gtian.pdf |only causaleffect-1.3.0/causaleffect/vignettes/jmlr2e.sty |only causaleffect-1.3.0/causaleffect/vignettes/simplification.bib |only causaleffect-1.3.0/causaleffect/vignettes/simplification.ltx |only 65 files changed, 702 insertions(+), 478 deletions(-)
Title: Transcriptome Overlap Measure
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette.
Author: Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Maintainer: Jingyi Jessica Li <jli@stat.ucla.edu>
Diff between TROM versions 1.1 dated 2015-06-26 and 1.2 dated 2016-10-07
DESCRIPTION | 11 - MD5 | 38 ++--- NAMESPACE | 8 + R/TROM-internal.R | 250 ++++++++++++++++++------------------- R/choose.z.R | 27 ++- R/sp.associated.idx.R | 2 R/sp.ortholog.z.R | 2 R/sp.std.R |only R/ws.trom.two.R | 5 inst/doc/TROM-manual.pdf |only inst/doc/TROM_Vignette.pdf |binary man/TROM-package.Rd | 16 +- man/bs.trom.Rd | 2 man/choose.z.Rd | 18 ++ man/find.top.GO.slim.terms.Rd | 2 man/find.top.GO.terms.Rd | 2 man/heatmap.3.Rd | 2 man/select.associated.genes.Rd | 2 man/select.associated.orthologs.Rd | 2 man/ws.trom.Rd | 2 man/ws.trom.orthologs.Rd | 2 21 files changed, 219 insertions(+), 174 deletions(-)
Title: Borenstein Analysis
Description: An implementation of the analysis about seed components from Borenstein et.al. 2008.
Author: Claus Jonathan Fritzemeier
Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between RSeed versions 0.1.31 dated 2012-05-04 and 0.1.60 dated 2016-10-07
DESCRIPTION | 17 ++++++-------- MD5 | 6 ++--- NAMESPACE | 7 ++++-- R/borenstein.R | 66 +++++++++++++++++++++------------------------------------ 4 files changed, 41 insertions(+), 55 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Education Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 1.0.1 dated 2016-09-12 and 1.1.0 dated 2016-10-07
DESCRIPTION | 14 +++++++------- MD5 | 18 ++++++++++++------ NAMESPACE | 3 +++ R/cldList.r |only R/pairwisePermutationMatrix.r | 6 ++---- R/pairwisePermutationSymmetry.r |only R/pairwisePermutationSymmetryMatrix.r |only R/pairwisePermutationTest.r | 8 +++----- man/cldList.Rd |only man/pairwisePermutationMatrix.Rd | 2 +- man/pairwisePermutationSymmetry.Rd |only man/pairwisePermutationSymmetryMatrix.Rd |only man/pairwisePermutationTest.Rd | 2 +- 13 files changed, 29 insertions(+), 24 deletions(-)
Title: Power Estimates for ANOVA Designs
Description: Functions for bootstrapping the power of ANOVA designs
based on estimated means and standard deviations of the conditions.
Please refer to the documentation of the boot.power.anova() function
for further details.
Author: Frank Papenmeier [aut, cre]
Maintainer: Frank Papenmeier <frank.papenmeier@uni-tuebingen.de>
Diff between powerbydesign versions 1.0.2 dated 2016-04-05 and 1.0.3 dated 2016-10-07
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS |only R/boot.power.anova.R | 8 +++++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database (<https://
www.pangaea.de>), including functions for searching for data, fetching 'datasets'
by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre],
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pangaear versions 0.2.0 dated 2016-05-06 and 0.2.4 dated 2016-10-07
DESCRIPTION | 12 +- MD5 | 34 ++--- NAMESPACE | 2 NEWS.md | 19 +++ R/pangaear-package.R | 2 R/pg_data.R | 70 +++++++---- R/pg_list_identifiers.R | 11 - R/pg_list_records.R | 54 ++++----- R/pg_search.R | 112 +++++++++++++----- R/zzz.R | 25 ++-- README.md | 216 +++++++++++++++--------------------- man/pg_data.Rd | 35 +++-- man/pg_list_identifiers.Rd | 40 +++--- man/pg_list_records.Rd | 58 +++++---- man/pg_search.Rd | 41 +++++- tests/testthat/test-oai_functions.R | 38 +++--- tests/testthat/test-pg_data.R | 6 + tests/testthat/test-pg_search.r | 10 + 18 files changed, 447 insertions(+), 338 deletions(-)
Title: Machina Time Series Generation and Backtesting
Description: Connects to <https://machi.na/> and allows the creation
of time series, and running backtests on selected strategy if requested.
Author: Nelson Mark [aut],
Gursky Michael [aut],
Kamal Akram [ctb],
Norton Tim [cre]
Maintainer: Norton Tim <tnorton@machi.na>
Diff between machina versions 0.1.5 dated 2016-08-03 and 0.1.6 dated 2016-10-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/machinaWS.functions.R | 2 +- R/versions.R | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)