Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and
in forecasting. Currently the package includes exponential smoothing models and
SARIMA in state-space form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Lancaster Centre for Marketing
Analytics and Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 2.2.0 dated 2017-10-27 and 2.2.1 dated 2017-11-15
DESCRIPTION | 16 +- MD5 | 86 +++++++-------- NEWS | 12 ++ R/autoces.R | 36 +++--- R/autoges.R | 202 +++++++++++++++++++++--------------- R/autossarima.R | 36 +++--- R/ces.R | 23 +--- R/es.R | 35 +++--- R/ges.R | 68 ++++++++---- R/iss.R | 22 ++-- R/methods.R | 16 +- R/sma.R | 6 - R/ssarima.R | 25 +--- R/ssfunctions.R | 149 +++++++++++++++++---------- R/ves.R | 2 inst/doc/ces.html | 28 ++--- inst/doc/es.R | 2 inst/doc/es.Rmd | 2 inst/doc/es.html | 86 +++++++-------- inst/doc/ges.html | 48 ++++---- inst/doc/simulate.html | 74 ++++++------- inst/doc/sma.html | 8 - inst/doc/smooth.html | 4 inst/doc/ssarima.html | 30 ++--- inst/doc/ves.html | 16 +- man/auto.ces.Rd | 23 ++-- man/auto.ges.Rd | 28 +++-- man/auto.ssarima.Rd | 31 +++-- man/ces.Rd | 22 ++-- man/es.Rd | 41 ++++--- man/ges.Rd | 32 +++-- man/iss.Rd | 9 + man/sma.Rd | 6 - man/smooth.Rd | 3 man/ssarima.Rd | 30 ++--- man/ves.Rd | 5 src/ssgeneralfun.cpp | 230 ++++++++++++++++++++++++++++-------------- src/vssGeneral.cpp | 2 tests/testthat/test_ces.R | 2 tests/testthat/test_es.R | 2 tests/testthat/test_ges.R | 2 tests/testthat/test_iss.R | 10 - tests/testthat/test_ssarima.R | 2 vignettes/es.Rmd | 2 44 files changed, 860 insertions(+), 654 deletions(-)
Title: Statistical Tools for Covariance Analysis
Description: Covariance is of universal prevalence across various disciplines within statistics.
We provide a rich collection of geometric and inferential tools for convenient analysis of
covariance structures, topics including distance measures, mean covariance estimator,
covariance hypothesis test for one-sample and two-sample cases, and covariance estimation.
For an introduction to covariance in multivariate statistical analysis,
see Schervish (1987) <doi:10.1214/ss/1177013111>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [ctb],
Kisung You [aut, cre]
Maintainer: Kisung You <kyou@nd.edu>
Diff between CovTools versions 0.2.0 dated 2017-11-08 and 0.2.1 dated 2017-11-15
CovTools-0.2.0/CovTools/src/rcpp_covest.cpp |only CovTools-0.2.1/CovTools/DESCRIPTION | 8 ++++---- CovTools-0.2.1/CovTools/MD5 | 9 ++++----- CovTools-0.2.1/CovTools/R/package-CovTools.R | 1 - CovTools-0.2.1/CovTools/src/rcpp_preest.cpp | 12 ++++++------ CovTools-0.2.1/CovTools/src/rcpp_test1.cpp | 3 ++- 6 files changed, 16 insertions(+), 17 deletions(-)
Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens <D.Lakens@tue.nl>
Maintainer: Daniel Lakens <D.Lakens@tue.nl>
Diff between TOSTER versions 0.2.4 dated 2017-09-02 and 0.3 dated 2017-11-15
DESCRIPTION | 14 - MD5 | 100 ++++----- NAMESPACE | 6 R/TOSTmeta.R | 35 ++- R/TOSTone.R | 30 +- R/TOSTone.raw.R | 26 +- R/TOSTpaired.R | 37 ++- R/TOSTpaired.raw.R | 37 ++- R/TOSTr.R | 31 ++ R/TOSTtwo.R | 17 + R/TOSTtwo.prop.R |only R/TOSTtwo.raw.R | 18 + R/datatostone.b.R | 25 +- R/datatostone.h.R | 355 +++++++++++++++++++++++---------- R/datatostpaired.b.R | 37 ++- R/datatostpaired.h.R | 393 ++++++++++++++++++++++++++---------- R/datatostr.h.R | 241 ++++++++++++++++------ R/datatosttwo.b.R | 38 ++- R/datatosttwo.h.R | 394 ++++++++++++++++++++++++++----------- R/powerTOSTone.R | 49 +++- R/powerTOSTone.raw.R | 49 ++++ R/powerTOSTpaired.R | 49 +++- R/powerTOSTpaired.raw.R | 43 +++- R/powerTOSTr.R | 49 +++- R/powerTOSTtwo.R | 47 +++- R/powerTOSTtwo.prop.R |only R/powerTOSTtwo.raw.R | 48 +++- build/vignette.rds |binary inst/doc/IntroductionToTOSTER.R | 3 inst/doc/IntroductionToTOSTER.Rmd | 9 inst/doc/IntroductionToTOSTER.html | 36 +-- man/TOSTmeta.Rd | 4 man/TOSTone.Rd | 4 man/TOSTone.raw.Rd | 4 man/TOSTpaired.Rd | 5 man/TOSTpaired.raw.Rd | 7 man/TOSTr.Rd | 4 man/TOSTtwo.Rd | 4 man/TOSTtwo.prop.Rd |only man/TOSTtwo.raw.Rd | 4 man/dataTOSTone.Rd | 41 ++- man/dataTOSTpaired.Rd | 42 +++ man/dataTOSTr.Rd | 23 +- man/dataTOSTtwo.Rd | 43 +++- man/powerTOSTone.Rd | 23 +- man/powerTOSTone.raw.Rd | 23 +- man/powerTOSTpaired.Rd | 21 + man/powerTOSTpaired.raw.Rd | 24 +- man/powerTOSTr.Rd | 25 +- man/powerTOSTtwo.Rd | 21 + man/powerTOSTtwo.prop.Rd |only man/powerTOSTtwo.raw.Rd | 24 +- vignettes/IntroductionToTOSTER.Rmd | 9 53 files changed, 1856 insertions(+), 715 deletions(-)
Title: R Bindings for the 'PicoSAT' SAT Solver
Description: Bindings for the 'PicoSAT' solver to solve Boolean satisfiability problems (SAT).
The boolean satisfiability problem asks the question if a given boolean formula can be TRUE;
i.e. does there exist an assignment of TRUE/FALSE for each variable such that the whole formula is TRUE?
The package bundles 'PicoSAT' solver release 965 <http://www.fmv.jku.at/picosat/>.
Author: Dirk Schumacher [aut, cre],
Armin Biere [ctb, cph] (Author and copyright holder of included PicoSAT
code)
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Diff between rpicosat versions 1.0.0 dated 2017-11-14 and 1.0.1 dated 2017-11-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++-- README.md | 12 ++++++++++-- src/r_picosat.c | 43 ++++++++++++++----------------------------- 5 files changed, 36 insertions(+), 40 deletions(-)
Title: EBGM Scores for Mining Large Contingency Tables
Description: An implementation of DuMouchel's (1999)
<doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the
market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and
quantile scores from the posterior distribution using the Gamma-Poisson
Shrinker (GPS) model to find unusually large cell counts in large, sparse
contingency tables. Can be used to find unusually high reporting rates of
adverse events associated with products. In general, can be used to mine any
database where the co-occurrence of two variables or items is of interest.
Also calculates relative and proportional reporting ratios. Builds on the work
of the 'PhViD' package, from which much of the code is derived. Some of the
added features include stratification to adjust for confounding variables and
data squashing to improve computational efficiency.
Author: John Ihrie [cre, aut],
Travis Canida [aut],
Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)),
Antoine Poncet [ctb] (author of 'PhViD' package (derived code))
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between openEBGM versions 0.2.0 dated 2017-07-31 and 0.3.0 dated 2017-11-15
DESCRIPTION | 6 - MD5 | 52 ++++---- NAMESPACE | 2 NEWS | 12 ++ R/f_checkInputs.R | 30 ++--- R/f_hyperEstimation.R | 151 ++++++++++++++++++++++---- R/f_transformInput.R | 7 - build/vignette.rds |binary inst/doc/x1_introAndDataPrepVignette.html | 38 +++--- inst/doc/x2_rawDataProcessingVignette.html | 4 inst/doc/x3_hyperParameterVignette.R | 5 inst/doc/x3_hyperParameterVignette.Rmd | 12 +- inst/doc/x3_hyperParameterVignette.html | 41 ++++--- inst/doc/x4_posteriorCalculationVignette.R | 19 +-- inst/doc/x4_posteriorCalculationVignette.Rmd | 19 +-- inst/doc/x4_posteriorCalculationVignette.html | 71 +++++------- inst/doc/x5_openEBGMObjectVignette.R | 12 +- inst/doc/x5_openEBGMObjectVignette.Rmd | 12 +- inst/doc/x5_openEBGMObjectVignette.html | 18 +-- man/autoHyper.Rd | 24 +++- man/exploreHypers.Rd | 20 ++- man/processRaw.Rd | 4 tests/testthat/testA_Counts.R | 6 - tests/testthat/testHypers.R | 33 +++-- vignettes/x3_hyperParameterVignette.Rmd | 12 +- vignettes/x4_posteriorCalculationVignette.Rmd | 19 +-- vignettes/x5_openEBGMObjectVignette.Rmd | 12 +- 27 files changed, 408 insertions(+), 233 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape.
Author: Miquel De Cáceres [aut, cre],
Nicolas Martin [aut],
Víctor Granda [aut],
Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between meteoland versions 0.6.4 dated 2017-09-05 and 0.6.7 dated 2017-11-15
meteoland-0.6.4/meteoland/vignettes/Meteorology-002.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-003.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-004.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-005.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-006.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-007.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-009.pdf |only meteoland-0.6.4/meteoland/vignettes/Meteorology-018.pdf |only meteoland-0.6.7/meteoland/DESCRIPTION | 23 +- meteoland-0.6.7/meteoland/MD5 | 75 +++---- meteoland-0.6.7/meteoland/NAMESPACE | 2 meteoland-0.6.7/meteoland/NEWS |only meteoland-0.6.7/meteoland/R/DefineProcedureClasses.R | 35 +++ meteoland-0.6.7/meteoland/R/RcppExports.R | 4 meteoland-0.6.7/meteoland/R/correctionpoints.R | 105 ++++++---- meteoland-0.6.7/meteoland/R/correctionpoints.errors.R | 52 +++- meteoland-0.6.7/meteoland/R/defaultCorrectionParams.R | 6 meteoland-0.6.7/meteoland/R/extractNetCDF.R | 9 meteoland-0.6.7/meteoland/R/extractpointdates.R | 6 meteoland-0.6.7/meteoland/R/interpolation.cv.R | 28 +- meteoland-0.6.7/meteoland/R/interpolationpoints.R | 10 meteoland-0.6.7/meteoland/R/meteoplot.R | 6 meteoland-0.6.7/meteoland/R/readmeteorologypoints.R | 28 ++ meteoland-0.6.7/meteoland/R/summarypoints.R | 11 - meteoland-0.6.7/meteoland/R/writemeteorologypoints.R | 88 ++++---- meteoland-0.6.7/meteoland/build/vignette.rds |binary meteoland-0.6.7/meteoland/inst/doc/Meteorology.Rnw | 10 meteoland-0.6.7/meteoland/inst/doc/Meteorology.pdf |binary meteoland-0.6.7/meteoland/inst/include/meteoland_RcppExports.h | 19 + meteoland-0.6.7/meteoland/man/correctionpoints.Rd | 8 meteoland-0.6.7/meteoland/man/defaultCorrectionParams.Rd | 8 meteoland-0.6.7/meteoland/man/extractNetCDF.Rd | 4 meteoland-0.6.7/meteoland/man/extractpointdates.Rd | 2 meteoland-0.6.7/meteoland/man/interpolationpoints.Rd | 6 meteoland-0.6.7/meteoland/man/meteoplot.Rd | 2 meteoland-0.6.7/meteoland/man/radiation.Rd | 7 meteoland-0.6.7/meteoland/man/readmeteorologypoint.Rd | 15 - meteoland-0.6.7/meteoland/man/summarypoints.Rd | 2 meteoland-0.6.7/meteoland/man/writemeteorologypoint.Rd | 70 +++--- meteoland-0.6.7/meteoland/src/RcppExports.cpp | 35 +++ meteoland-0.6.7/meteoland/src/radiation.cpp | 22 ++ meteoland-0.6.7/meteoland/src/radiation.h | 2 meteoland-0.6.7/meteoland/vignettes/Meteorology.Rnw | 10 43 files changed, 478 insertions(+), 232 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of matrix classes, including triangular,
symmetric, and diagonal matrices, both dense and sparse and with
pattern, logical and numeric entries. Numerous methods for and
operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Author: Douglas Bates [aut],
Martin Maechler [aut, cre],
Timothy A. Davis [ctb] (SuiteSparse and 'cs' C libraries, notably
CHOLMOD, AMD; collaborators listed in dir(pattern =
'^[A-Z]+[.]txt$', full.names=TRUE, system.file('doc',
'SuiteSparse', package='Matrix'))),
Jens Oehlschlägel [ctb] (initial nearPD()),
Jason Riedy [ctb] (condest() and onenormest() for octave, Copyright:
Regents of the University of California),
R Core Team [ctb] (base R matrix implementation)
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-11 dated 2017-08-16 and 1.2-12 dated 2017-11-15
DESCRIPTION | 41 +++++++++++++++++++++----- MD5 | 62 ++++++++++++++++++++-------------------- R/Auxiliaries.R | 17 +++++++--- R/Ops.R | 7 +++- R/indMatrix.R | 35 +++++++++++++--------- TODO | 9 +++-- build/vignette.rds |binary inst/NEWS.Rd | 25 +++++++++++++++- inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/Matrix.h | 1 inst/include/cholmod.h | 1 man/indMatrix-class.Rd | 9 +++-- man/kronecker-methods.Rd | 7 ++-- man/matrix-products.Rd | 5 +-- man/qr-methods.Rd | 4 +- man/symmetricMatrix-class.Rd | 5 +-- src/AMD/Source/Makefile | 2 - src/CHMfactor.c | 8 +++-- src/CHOLMOD/Lib/Makefile | 1 src/COLAMD/Source/Makefile | 2 - src/Makevars | 2 - src/SuiteSparse_config/Makefile | 1 src/chm_common.c | 26 +++++++++++++--- src/chm_common.h | 6 +++ src/init.c | 1 tests/group-methods.R | 18 +++++++++++ tests/matprod.R | 2 - tests/validObj.R | 10 +++--- 32 files changed, 210 insertions(+), 97 deletions(-)
Title: Optimal Multilevel Matching using a Network Algorithm
Description: Performs multilevel matches for data with cluster-level treatments and individual-level outcomes using a network optimization algorithm. Functions for checking balance at the cluster and individual levels are also provided, as are methods for permutation-inference-based outcome analysis. Details in Pimentel et al. (2017+), forthcoming in the Annals of Applied Statistics.
Author: Luke Keele, Sam Pimentel, and Paul Rosenbaum
Maintainer: Sam Pimentel <spi@berkeley.edu>
Diff between matchMulti versions 1.1.5 dated 2016-08-26 and 1.1.6 dated 2017-11-15
DESCRIPTION | 14 +++++++------- LICENSE | 4 ++-- MD5 | 18 +++++++++--------- R/balanceMulti.R | 25 ++++++++++--------------- R/balanceTable.R | 12 ++++++------ build/partial.rdb |binary inst/doc/multiMatch_vignette.pdf |binary man/balanceMulti.Rd | 3 +-- man/matchMulti.Rd | 25 +++++++++++++++++++++++-- man/pairmatchelastic.Rd | 6 ++---- 10 files changed, 60 insertions(+), 47 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.8 dated 2017-09-07 and 0.8.1.6 dated 2017-11-15
DESCRIPTION | 8 - MD5 | 24 ++--- NAMESPACE | 2 R/analysis.R | 6 - R/array.R | 34 ++++--- R/cell.R | 5 - R/group.R | 7 + R/options.R | 6 + R/results.R | 18 ++- R/utils.R | 5 - inst/jamovi.proto | 224 ++---------------------------------------------- man/Cell.BEGIN_GROUP.Rd | 3 man/Options.Rd | 3 13 files changed, 90 insertions(+), 255 deletions(-)
Title: Improved Quality Control Charts
Description: Builds statistical control charts with exact limits for
univariate and multivariate cases.
Author: Flavio Barros [aut, cre],
Emanuel Barbosa [ctb],
Elias Goncalves [ctb],
Daniela Recchia [ctb]
Maintainer: Flavio Barros <flaviomargarito@gmail.com>
Diff between IQCC versions 0.6 dated 2014-04-22 and 0.7 dated 2017-11-15
DESCRIPTION | 33 +++- LICENSE |only MD5 | 105 +++++++-------- NAMESPACE | 52 +++---- R/T2.1.R | 75 +++++++--- R/T2.2.R | 61 ++++++-- R/add.data.R | 75 +++++++++- R/alpha.risk.R | 62 +++++--- R/binomdata.R |only R/c4.R | 27 +++ R/cchart.R.R | 53 +++++-- R/cchart.S.R | 58 ++++++-- R/cchart.T2.1.R | 74 +++++++--- R/cchart.T2.2.R | 149 ++++++++++++++------- R/cchart.Xbar1.R | 37 ++++- R/cchart.Xbar2.R | 30 +++- R/cchart.Xbar_R.R | 29 +++- R/cchart.p.R | 353 ++++++++++++++++++++++++++++----------------------- R/cchart.u.R | 352 ++++++++++++++++++++++++++++---------------------- R/d2.R | 35 +++-- R/d3.R | 37 +++-- R/data.1.R | 72 +++++++--- R/data.2.R | 35 ++++- R/moonroof.R |only R/pistonrings.R |only R/remove.data.R | 35 +++-- R/softdrink.R |only R/stats.R | 108 +++++++++------ R/table.const.R | 33 +++- R/table.qtukey.R | 68 ++++++--- man/T2.1.Rd | 89 +++++++----- man/T2.2.Rd | 94 +++++++------ man/add.data.Rd | 131 ++++++++++-------- man/alpha.risk.Rd | 59 ++++---- man/binomdata.Rd | 47 +++--- man/c4.Rd | 59 ++++---- man/cchart.R.Rd | 73 ++++++---- man/cchart.S.Rd | 71 +++++----- man/cchart.T2.1.Rd | 85 +++++++----- man/cchart.T2.2.Rd | 130 ++++++++++-------- man/cchart.Xbar1.Rd | 63 +++++---- man/cchart.Xbar2.Rd | 71 +++++----- man/cchart.Xbar_R.Rd | 54 ++++--- man/cchart.p.Rd | 68 ++++++--- man/cchart.u.Rd | 66 ++++++--- man/d2.Rd | 52 ++++--- man/d3.Rd | 53 ++++--- man/data.1.Rd | 72 ++++++---- man/data.2.Rd | 79 ++++++----- man/moonroof.Rd | 59 ++++---- man/pistonrings.Rd | 50 +++---- man/remove.data.Rd | 59 ++++---- man/softdrink.Rd | 63 ++++----- man/stats.Rd | 79 ++++++----- man/table.const.Rd | 59 ++++---- man/table.qtukey.Rd | 57 ++++---- 56 files changed, 2375 insertions(+), 1515 deletions(-)
Title: The Faster Hash Map
Description: Provides a hash table class for fast
key-value storage of atomic vector types.
Author: Nathan Russell [aut, cre]
Maintainer: Nathan Russell <russell.nr2012@gmail.com>
Diff between hashmap versions 0.2.0 dated 2017-03-05 and 0.2.1 dated 2017-11-15
hashmap-0.2.0/hashmap/inst/include/hashmap/as_character.hpp |only hashmap-0.2.0/hashmap/inst/include/hashmap/format_date.hpp |only hashmap-0.2.0/hashmap/inst/include/hashmap/format_posix.hpp |only hashmap-0.2.1/hashmap/DESCRIPTION | 13 +-- hashmap-0.2.1/hashmap/MD5 | 48 +++++++----- hashmap-0.2.1/hashmap/R/Hashmap-class.R | 2 hashmap-0.2.1/hashmap/R/RcppExports.R | 8 +- hashmap-0.2.1/hashmap/README.md | 4 - hashmap-0.2.1/hashmap/inst/include/hashmap/HashTemplate.hpp | 14 +++ hashmap-0.2.1/hashmap/inst/include/hashmap/sparsepp |only hashmap-0.2.1/hashmap/man/Hashmap-class.Rd | 5 - hashmap-0.2.1/hashmap/man/Rcpp_Hashmap-class.Rd | 3 hashmap-0.2.1/hashmap/man/clone.Rd | 1 hashmap-0.2.1/hashmap/man/hashmap.Rd | 1 hashmap-0.2.1/hashmap/man/internal-functions.Rd | 8 +- hashmap-0.2.1/hashmap/man/load_hashmap.Rd | 1 hashmap-0.2.1/hashmap/man/merge.Rcpp_Hashmap.Rd | 1 hashmap-0.2.1/hashmap/man/plot.Rcpp_Hashmap.Rd | 1 hashmap-0.2.1/hashmap/man/save_hashmap.Rd | 1 hashmap-0.2.1/hashmap/src/Makevars | 6 + hashmap-0.2.1/hashmap/src/RcppExports.cpp | 8 +- hashmap-0.2.1/hashmap/src/init.c | 20 ++--- hashmap-0.2.1/hashmap/tools |only 23 files changed, 78 insertions(+), 67 deletions(-)
Title: Rmetrics - Trading and Rebalancing Financial Instruments
Description: A collection of functions for trading and rebalancing financial
instruments. It implements various technical indicators to analyse time series such
as moving averages or stochastic oscillators.
Author: Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@live.com>
Diff between fTrading versions 3010.78 dated 2013-12-10 and 3042.79 dated 2017-11-15
DESCRIPTION | 30 +++++++------- MD5 | 15 +++---- NAMESPACE | 62 ++---------------------------- R/BenchmarkAnalysis.R | 12 ----- R/TechnicalAnalysis.R | 12 ----- R/rollFun.R | 12 ----- R/zzz.R | 93 +++++++++++++++++++--------------------------- inst/unitTests/Makefile | 2 man/00fTrading-package.Rd |only 9 files changed, 69 insertions(+), 169 deletions(-)
Title: Rmetrics - Regression Based Decision and Prediction
Description: A collection of functions for linear and non-linear regression modelling.
It implements a wrapper for several regression models available in the base and
contributed packages of R.
Author: Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@live.com>
Diff between fRegression versions 3011.81 dated 2014-09-16 and 3042.82 dated 2017-11-15
DESCRIPTION | 29 +++++++---------- MD5 | 8 ++-- NAMESPACE | 13 ++++++- R/zzz.R | 80 ++++++++++++++++++++++++------------------------ inst/unitTests/Makefile | 2 - 5 files changed, 68 insertions(+), 64 deletions(-)
Title: Dynamic Model Averaging and Dynamic Model Selection for
Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between fDMA versions 2.1 dated 2017-10-13 and 2.2 dated 2017-11-15
DESCRIPTION | 15 ++++++++------- MD5 | 19 +++++++++++++------ NAMESPACE | 5 +++-- NEWS | 8 ++++++++ R/RcppExports.R |only R/fDMA.R | 1 + R/onUnload.R |only R/tvp.R | 40 ++++------------------------------------ inst/include |only man/tvp.Rd | 2 ++ src |only 11 files changed, 39 insertions(+), 51 deletions(-)
Title: Rmetrics - Pricing and Evaluating Bonds
Description: It implements the Nelson-Siegel and the Nelson-Siegel-Svensson
term structures.
Author: Diethelm Wuertz [aut],
Tobias Setz [cre]
Maintainer: Tobias Setz <tobias.setz@live.com>
Diff between fBonds versions 3010.77 dated 2013-12-17 and 3042.78 dated 2017-11-15
ChangeLog | 5 - DESCRIPTION | 26 ++--- MD5 | 13 +- NAMESPACE | 17 +-- R/TermStructure.R | 12 -- R/zzz.R | 93 ++++++++------------ man/00fBonds-package.Rd |only man/TermStructure.Rd | 216 ++++++++++++++++++++++++------------------------ 8 files changed, 174 insertions(+), 208 deletions(-)
Title: Quantification of Fate Bias in Multipotent Progenitors
Description: Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2017) <doi:10.1101/218115>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between FateID versions 0.0.9 dated 2017-11-15 and 0.1.0 dated 2017-11-15
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Bayesian Single Arm Sample Size Calculation Software
Description: Bayesian sample size calculation software and examples for EuroSARC
clinical trials which utilise Bayesian methodology. These trials rely on
binomial based endpoints so the majority of programs found here relate to this
sort of endpoint. Developed as part of the EuroSARC FP7 grant.
Author: Peter Dutton
Maintainer: Peter Dutton <dutton.peter@gmail.com>
Diff between EurosarcBayes versions 1.0 dated 2015-11-18 and 1.1 dated 2017-11-15
EurosarcBayes-1.0/EurosarcBayes/R/bayes_binom_one_postprob_onestage_v1.0.R |only EurosarcBayes-1.1/EurosarcBayes/DESCRIPTION | 19 ++++------ EurosarcBayes-1.1/EurosarcBayes/MD5 | 8 ++-- EurosarcBayes-1.1/EurosarcBayes/R/bayes_binom_one_postprob_onestage_v2.0.R |only EurosarcBayes-1.1/EurosarcBayes/R/freq_binom_two_bryantday_twostage_v1.0.R | 3 - EurosarcBayes-1.1/EurosarcBayes/R/print.trialDesign_binom_one_v1.0.R | 1 6 files changed, 15 insertions(+), 16 deletions(-)
Title: Area-Proportional Euler and Venn Diagrams with Circles or
Ellipses
Description: If possible, generates exactly area-proportional Euler diagrams
using numerical optimization. A Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Euler diagrams can be fit with both ellipses and circles from
a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre],
A. Jonathan R. Godfrey [ctb]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between eulerr versions 3.0.0 dated 2017-11-15 and 3.0.1 dated 2017-11-15
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 5 + README.md | 162 +++++++++++++++++++++---------------------- inst/doc/introduction.R | 103 ++++++++------------------- inst/doc/introduction.Rnw | 12 --- inst/doc/introduction.pdf |binary inst/doc/under-the-hood.R | 101 +++++--------------------- inst/doc/under-the-hood.Rnw | 6 - inst/doc/under-the-hood.pdf |binary vignettes/introduction.Rnw | 12 --- vignettes/under-the-hood.Rnw | 6 - 12 files changed, 163 insertions(+), 272 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<http://www-03.ibm.com/systems/spectrum-computing/products/lsf/>),
'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>),
'TORQUE/PBS'
(<http://www.adaptivecomputing.com/products/open-source/torque/>), or
'Docker Swarm' (<https://docs.docker.com/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] (0000-0001-9754-0393),
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.6 dated 2017-09-06 and 0.9.7 dated 2017-11-15
batchtools-0.9.6/batchtools/tests/testthat/test_Results.R |only batchtools-0.9.7/batchtools/DESCRIPTION | 22 - batchtools-0.9.7/batchtools/MD5 | 202 +++++----- batchtools-0.9.7/batchtools/NAMESPACE | 3 batchtools-0.9.7/batchtools/NEWS.md | 15 batchtools-0.9.7/batchtools/R/Algorithm.R | 27 - batchtools-0.9.7/batchtools/R/ExperimentRegistry.R | 21 - batchtools-0.9.7/batchtools/R/Job.R | 41 +- batchtools-0.9.7/batchtools/R/JobCollection.R | 6 batchtools-0.9.7/batchtools/R/JobTables.R | 69 --- batchtools-0.9.7/batchtools/R/Problem.R | 28 - batchtools-0.9.7/batchtools/R/RDSReader.R | 4 batchtools-0.9.7/batchtools/R/Registry.R | 14 batchtools-0.9.7/batchtools/R/addExperiments.R | 36 - batchtools-0.9.7/batchtools/R/batchMap.R | 12 batchtools-0.9.7/batchtools/R/batchMapResults.R | 4 batchtools-0.9.7/batchtools/R/clusterFunctionsSlurm.R | 36 - batchtools-0.9.7/batchtools/R/clusterFunctionsTORQUE.R | 23 - batchtools-0.9.7/batchtools/R/doJobCollection.R | 29 + batchtools-0.9.7/batchtools/R/estimateRuntimes.R | 2 batchtools-0.9.7/batchtools/R/execJob.R | 2 batchtools-0.9.7/batchtools/R/findJobs.R | 18 batchtools-0.9.7/batchtools/R/flatten.R |only batchtools-0.9.7/batchtools/R/getStatus.R | 14 batchtools-0.9.7/batchtools/R/helpers.R | 13 batchtools-0.9.7/batchtools/R/loadRegistry.R | 2 batchtools-0.9.7/batchtools/R/reduceResults.R | 25 - batchtools-0.9.7/batchtools/R/sleep.R | 2 batchtools-0.9.7/batchtools/R/submitJobs.R | 57 +- batchtools-0.9.7/batchtools/R/summarizeExperiments.R | 5 batchtools-0.9.7/batchtools/R/updateRegisty.R | 21 + batchtools-0.9.7/batchtools/R/waitForFiles.R | 19 batchtools-0.9.7/batchtools/R/waitForJobs.R | 23 - batchtools-0.9.7/batchtools/R/zzz.R | 12 batchtools-0.9.7/batchtools/README.md | 11 batchtools-0.9.7/batchtools/build/vignette.rds |binary batchtools-0.9.7/batchtools/inst/doc/batchtools.R | 9 batchtools-0.9.7/batchtools/inst/doc/batchtools.Rmd | 22 - batchtools-0.9.7/batchtools/inst/doc/batchtools.pdf |binary batchtools-0.9.7/batchtools/man/addAlgorithm.Rd | 18 batchtools-0.9.7/batchtools/man/addExperiments.Rd | 2 batchtools-0.9.7/batchtools/man/addProblem.Rd | 20 batchtools-0.9.7/batchtools/man/batchMap.Rd | 4 batchtools-0.9.7/batchtools/man/batchMapResults.Rd | 4 batchtools-0.9.7/batchtools/man/batchtools-package.Rd | 2 batchtools-0.9.7/batchtools/man/estimateRuntimes.Rd | 2 batchtools-0.9.7/batchtools/man/flatten.Rd |only batchtools-0.9.7/batchtools/man/getJobTable.Rd | 28 - batchtools-0.9.7/batchtools/man/makeExperimentRegistry.Rd | 10 batchtools-0.9.7/batchtools/man/makeRegistry.Rd | 10 batchtools-0.9.7/batchtools/man/reduceResultsList.Rd | 14 batchtools-0.9.7/batchtools/man/submitJobs.Rd | 50 +- batchtools-0.9.7/batchtools/man/waitForJobs.Rd | 9 batchtools-0.9.7/batchtools/tests/testthat/helper.R | 32 + batchtools-0.9.7/batchtools/tests/testthat/test_ClusterFunctions.R | 12 batchtools-0.9.7/batchtools/tests/testthat/test_ClusterFunctionsMulticore.R | 21 - batchtools-0.9.7/batchtools/tests/testthat/test_ClusterFunctionsSSH.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_ClusterFunctionsSocket.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_ExperimentRegistry.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_Job.R | 10 batchtools-0.9.7/batchtools/tests/testthat/test_JobCollection.R | 15 batchtools-0.9.7/batchtools/tests/testthat/test_JobNames.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_Registry.R | 50 +- batchtools-0.9.7/batchtools/tests/testthat/test_addAlgorithm.R | 10 batchtools-0.9.7/batchtools/tests/testthat/test_addExperiments.R | 22 - batchtools-0.9.7/batchtools/tests/testthat/test_addProblem.R | 7 batchtools-0.9.7/batchtools/tests/testthat/test_batchMap.R | 20 batchtools-0.9.7/batchtools/tests/testthat/test_batchReduce.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_btlapply.R | 8 batchtools-0.9.7/batchtools/tests/testthat/test_chunk.R | 9 batchtools-0.9.7/batchtools/tests/testthat/test_chunkIds.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_convertIds.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_doJobCollection.R | 10 batchtools-0.9.7/batchtools/tests/testthat/test_estimateRuntimes.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_export.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_findConfFile.R | 1 batchtools-0.9.7/batchtools/tests/testthat/test_findJobs.R | 10 batchtools-0.9.7/batchtools/tests/testthat/test_flatten.R |only batchtools-0.9.7/batchtools/tests/testthat/test_foreach.R |only batchtools-0.9.7/batchtools/tests/testthat/test_future.R |only batchtools-0.9.7/batchtools/tests/testthat/test_getErrorMessages.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_getJobTable.R | 128 ++---- batchtools-0.9.7/batchtools/tests/testthat/test_getStatus.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_grepLogs.R | 11 batchtools-0.9.7/batchtools/tests/testthat/test_hooks.R | 3 batchtools-0.9.7/batchtools/tests/testthat/test_joins.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_killJobs.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_manual.R | 5 batchtools-0.9.7/batchtools/tests/testthat/test_memory.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_mergeRegistries.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_parallelMap.R | 17 batchtools-0.9.7/batchtools/tests/testthat/test_reduceResults.R |only batchtools-0.9.7/batchtools/tests/testthat/test_removeExperiments.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_removeRegistry.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_resetJobs.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_runOSCommand.R | 1 batchtools-0.9.7/batchtools/tests/testthat/test_seed.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_showLog.R | 4 batchtools-0.9.7/batchtools/tests/testthat/test_sleep.R |only batchtools-0.9.7/batchtools/tests/testthat/test_submitJobs.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_summarizeExperiments.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_sweepRegistry.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_tags.R | 2 batchtools-0.9.7/batchtools/tests/testthat/test_testJob.R | 6 batchtools-0.9.7/batchtools/tests/testthat/test_waitForJobs.R | 13 batchtools-0.9.7/batchtools/vignettes/batchtools.Rmd | 22 - 106 files changed, 835 insertions(+), 718 deletions(-)
Title: Artificial Neural Networks for Anomaly Detection
Description: Training of general classification and regression neural networks using
gradient descent. Special features include a function for training replicator
neural networks and a function for training autoencoders. Multiple activation and
cost functions (including Huber and pseudo-Huber) are supported, as well as L1
and L2 regularization, momentum, early stopping and the possibility to specify
a learning rate schedule. The package contains a vectorized gradient descent
implementation which facilitates faster training through batch learning.
Author: Bart Lammers
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>
Diff between ANN2 versions 1.1 dated 2017-10-23 and 1.2 dated 2017-11-15
DESCRIPTION | 6 MD5 | 16 +- R/RcppExports.R | 8 - R/callable.R | 315 ++++++++++++++++++------------------------------- R/required-functions.R | 117 +++++++++++++----- man/autoencoder.Rd | 10 - man/replicator.Rd | 12 - src/RcppExports.cpp | 28 ---- src/rcpp-nn.cpp | 79 +++++++----- 9 files changed, 278 insertions(+), 313 deletions(-)
Title: Association Rule Classification
Description: Implements the Classification-based on
Association Rules (CBA) algorithm for association rule classification (ARC).
The package also contains several convenience methods that allow to automatically
set CBA parameters (minimum confidence, minimum support) and it also natively
handles numeric attributes by integrating a pre-discretization step.
The rule generation phase is handled by the 'arules' package.
Author: Tomas Kliegr [aut, cre]
Maintainer: Tomas Kliegr <kliegr@gmail.com>
Diff between arc versions 1.1.2 dated 2017-08-24 and 1.1.3 dated 2017-11-15
DESCRIPTION | 7 ++++--- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/cba.R | 3 ++- R/m1prune.R | 2 +- R/toprules.R | 8 ++++---- man/predict.CBARuleModel.Rd | 2 +- man/topRules.Rd | 2 +- 8 files changed, 22 insertions(+), 19 deletions(-)
Title: Preprocessing Algorithms for Imbalanced Datasets
Description: Algorithms to treat imbalanced datasets. Imbalanced datasets usually damage
the performance of the classifiers. Thus, it is important to treat data before
applying a classifier algorithm. This package includes recent preprocessing algorithms
in the literature.
Author: Ignacio Cordón [aut, cre]
Maintainer: Ignacio Cordón <nacho.cordon.castillo@gmail.com>
Diff between imbalance versions 0.1.0 dated 2017-11-13 and 0.1.1 dated 2017-11-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/racog.R | 6 +++++- inst/doc/imbalance.pdf |binary man/racog.Rd | 6 +++++- src/pdfos.cpp | 2 +- 6 files changed, 20 insertions(+), 12 deletions(-)
Title: Random Ferns Classifier
Description: An R implementation of the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>
Diff between rFerns versions 2.0.2 dated 2016-07-22 and 2.0.3 dated 2017-11-15
DESCRIPTION | 12 +++++------- MD5 | 21 +++++++++++---------- NAMESPACE | 3 +-- R/ferns.R | 4 ++-- R/naivewrapper.R | 1 + inst/NEWS | 4 ++++ man/merge.rFerns.Rd | 1 - man/naiveWrapper.Rd | 4 +++- man/predict.rFerns.Rd | 1 - man/rFerns.Rd | 11 +++++------ src/Makevars |only src/ferns.c | 16 ++++++++++++++++ 12 files changed, 48 insertions(+), 30 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using 'gnm', with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Functions allow computing the intrinsic association coefficient
(and therefore the Altham index), including via the Bayes shrinkage
estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Author: Milan Bouchet-Valat [aut, cre],
Heather Turner [ctb],
Michael Friendly [ctb],
Jim Lemon [cph],
Gabor Csardi [cph]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between logmult versions 0.6.4 dated 2017-03-21 and 0.6.5 dated 2017-11-15
DESCRIPTION | 21 ++++++++++++++------- MD5 | 27 ++++++++++++++++----------- NAMESPACE | 1 + NEWS | 6 ++++++ R/iac.R |only R/maor.R | 8 -------- R/unidiff.R | 5 ++--- build/vignette.rds |binary data/hg16.RData |only inst/doc/logmult.Rmd | 9 ++++----- inst/doc/logmult.html | 8 ++++---- man/hg16.Rd |only man/iac.Rd |only man/maor.Rd | 26 +++++++++++++------------- tests/iac.R |only tests/maor.R | 6 ++++++ vignettes/logmult.Rmd | 9 ++++----- 17 files changed, 70 insertions(+), 56 deletions(-)
Title: Tumor Mutation Detection in Plasma
Description: Aims at detecting single nucleotide variation
(SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used
as a surrogate marker for tumor, at each base position of an Next Generation
Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele
frequency at each position to the measured PER in control samples.
Author: Yves Rozenholc, Nicolas Pécuchet, Pierre Laurent-Puig
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between PlasmaMutationDetector versions 1.5.2 dated 2016-09-09 and 1.6.2 dated 2017-11-15
DESCRIPTION | 10 +++--- MD5 | 21 +++++++------ R/functions.R | 55 +++++++++++++++++++++-------------- inst/extdata/4test_only/case/Results |only man/BuildCtrlErrorRate.Rd | 7 +--- man/DetectPlasmaMutation.Rd | 7 +--- man/MAF_from_BAM.Rd | 7 +--- man/PrepareLibrary.Rd | 7 +--- man/background_error_rate.Rd | 7 +--- man/hotspot.Rd | 7 +--- man/positions_ranges.Rd | 13 +++----- 11 files changed, 74 insertions(+), 67 deletions(-)
More information about PlasmaMutationDetector at CRAN
Permanent link
Title: Area-Proportional Euler and Venn Diagrams with Circles or
Ellipses
Description: If possible, generates exactly area-proportional Euler diagrams
using numerical optimization. A Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Euler diagrams can be fit with both ellipses and circles from
a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre],
A. Jonathan R. Godfrey [ctb]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between eulerr versions 2.0.0 dated 2017-06-20 and 3.0.0 dated 2017-11-15
eulerr-2.0.0/eulerr/R/optimization.R |only eulerr-2.0.0/eulerr/inst/doc/Introduction.R |only eulerr-2.0.0/eulerr/inst/doc/Introduction.Rmd |only eulerr-2.0.0/eulerr/inst/doc/Introduction.html |only eulerr-2.0.0/eulerr/man/center_circles.Rd |only eulerr-2.0.0/eulerr/man/eulerr.Rd |only eulerr-2.0.0/eulerr/man/locate_centers.Rd |only eulerr-2.0.0/eulerr/src/Makevars.win |only eulerr-2.0.0/eulerr/tests/testthat/test_geometry.R |only eulerr-2.0.0/eulerr/vignettes/Introduction.Rmd |only eulerr-3.0.0/eulerr/DESCRIPTION | 25 eulerr-3.0.0/eulerr/MD5 | 103 - eulerr-3.0.0/eulerr/NAMESPACE | 37 eulerr-3.0.0/eulerr/NEWS.md | 215 +- eulerr-3.0.0/eulerr/R/RcppExports.R | 38 eulerr-3.0.0/eulerr/R/euler.R | 797 ++++++---- eulerr-3.0.0/eulerr/R/eulerr.R | 17 eulerr-3.0.0/eulerr/R/geometry.R | 46 eulerr-3.0.0/eulerr/R/label.R |only eulerr-3.0.0/eulerr/R/lattice-imports.R | 14 eulerr-3.0.0/eulerr/R/layout.R |only eulerr-3.0.0/eulerr/R/plot.euler.R | 1034 +++++++------- eulerr-3.0.0/eulerr/R/print.euler.R | 49 eulerr-3.0.0/eulerr/R/sysdata.rda |binary eulerr-3.0.0/eulerr/R/utils.R | 337 ++-- eulerr-3.0.0/eulerr/README.md | 33 eulerr-3.0.0/eulerr/build/vignette.rds |binary eulerr-3.0.0/eulerr/inst/doc/introduction.R |only eulerr-3.0.0/eulerr/inst/doc/introduction.Rnw |only eulerr-3.0.0/eulerr/inst/doc/introduction.pdf |only eulerr-3.0.0/eulerr/inst/doc/under-the-hood.R |only eulerr-3.0.0/eulerr/inst/doc/under-the-hood.Rnw |only eulerr-3.0.0/eulerr/inst/doc/under-the-hood.pdf |only eulerr-3.0.0/eulerr/man/bit_indexr.Rd |only eulerr-3.0.0/eulerr/man/center_layout.Rd |only eulerr-3.0.0/eulerr/man/compress_layout.Rd |only eulerr-3.0.0/eulerr/man/diagError.Rd |only eulerr-3.0.0/eulerr/man/euler.Rd | 45 eulerr-3.0.0/eulerr/man/eulerr-package.Rd |only eulerr-3.0.0/eulerr/man/get_bounding_box.Rd |only eulerr-3.0.0/eulerr/man/get_constraints.Rd |only eulerr-3.0.0/eulerr/man/label.Rd |only eulerr-3.0.0/eulerr/man/n_sets.Rd |only eulerr-3.0.0/eulerr/man/panel.euler.Rd | 40 eulerr-3.0.0/eulerr/man/panel.euler.circles.Rd | 10 eulerr-3.0.0/eulerr/man/panel.euler.ellipses.Rd |only eulerr-3.0.0/eulerr/man/panel.euler.labels.Rd | 31 eulerr-3.0.0/eulerr/man/plot.euler.Rd | 17 eulerr-3.0.0/eulerr/man/prepanel.euler.Rd | 13 eulerr-3.0.0/eulerr/man/print.euler.Rd | 2 eulerr-3.0.0/eulerr/man/regionError.Rd |only eulerr-3.0.0/eulerr/man/separate_two_discs.Rd |only eulerr-3.0.0/eulerr/man/shelf_pack.Rd |only eulerr-3.0.0/eulerr/man/skyline_pack.Rd |only eulerr-3.0.0/eulerr/src/Makevars | 2 eulerr-3.0.0/eulerr/src/RcppExports.cpp | 143 + eulerr-3.0.0/eulerr/src/areas.h |only eulerr-3.0.0/eulerr/src/constants.h |only eulerr-3.0.0/eulerr/src/conversions.h |only eulerr-3.0.0/eulerr/src/geometry.h |only eulerr-3.0.0/eulerr/src/helpers.h |only eulerr-3.0.0/eulerr/src/intersections.h |only eulerr-3.0.0/eulerr/src/neldermead.h |only eulerr-3.0.0/eulerr/src/optim_final.cpp | 331 +--- eulerr-3.0.0/eulerr/src/optim_init.cpp |only eulerr-3.0.0/eulerr/src/overlap_centers.cpp |only eulerr-3.0.0/eulerr/src/solver.h |only eulerr-3.0.0/eulerr/src/transformations.h |only eulerr-3.0.0/eulerr/src/utils.cpp | 64 eulerr-3.0.0/eulerr/tests/testthat/test_plotting.R | 82 - eulerr-3.0.0/eulerr/tests/testthat/test_reproducibility.R | 200 +- eulerr-3.0.0/eulerr/tools/README-plot_method-1.png |binary eulerr-3.0.0/eulerr/vignettes/eulerr.bib | 404 +++++ eulerr-3.0.0/eulerr/vignettes/introduction.Rnw |only eulerr-3.0.0/eulerr/vignettes/under-the-hood.Rnw |only 75 files changed, 2400 insertions(+), 1729 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, particle filtering, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <http://r-nimble.org>.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-Bergman, Nick Michaud, Fritz Obermeyer, Duncan Temple Lang, and see AUTHORS file for additional contributors.
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6-6 dated 2017-07-28 and 0.6-7 dated 2017-11-15
nimble-0.6-6/nimble/inst/tests/test-types.R |only nimble-0.6-6/nimble/man/toEigenCalls.Rd |only nimble-0.6-7/nimble/DESCRIPTION | 63 nimble-0.6-7/nimble/INSTALL | 6 nimble-0.6-7/nimble/MD5 | 374 - nimble-0.6-7/nimble/NAMESPACE | 26 nimble-0.6-7/nimble/NEWS | 70 nimble-0.6-7/nimble/R/BUGS_BUGSdecl.R | 1309 ++++- nimble-0.6-7/nimble/R/BUGS_macros.R |only nimble-0.6-7/nimble/R/BUGS_model.R | 254 - nimble-0.6-7/nimble/R/BUGS_modelDef.R | 204 nimble-0.6-7/nimble/R/BUGS_nimbleGraph.R | 6 nimble-0.6-7/nimble/R/BUGS_readBUGS.R | 117 nimble-0.6-7/nimble/R/BUGS_testBUGS.R | 8 nimble-0.6-7/nimble/R/BUGS_utils.R | 33 nimble-0.6-7/nimble/R/CAR.R | 495 +- nimble-0.6-7/nimble/R/MCEM_build.R | 24 nimble-0.6-7/nimble/R/MCMC_autoBlock.R | 2 nimble-0.6-7/nimble/R/MCMC_build.R | 83 nimble-0.6-7/nimble/R/MCMC_comparisons.R | 30 nimble-0.6-7/nimble/R/MCMC_configuration.R | 55 nimble-0.6-7/nimble/R/MCMC_conjugacy.R | 343 - nimble-0.6-7/nimble/R/MCMC_run.R | 222 nimble-0.6-7/nimble/R/MCMC_samplers.R | 145 nimble-0.6-7/nimble/R/MCMC_suite.R | 1 nimble-0.6-7/nimble/R/RCfunction_compile.R | 770 ++- nimble-0.6-7/nimble/R/RCfunction_core.R | 247 - 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Title: In-Process Version of 'MonetDB'
Description: An in-process version of 'MonetDB', a SQL database designed for analytical tasks. Similar to 'SQLite', the database runs entirely inside the 'R' shell.
Author: Hannes Muehleisen [aut, cre], Anthony Damico [ctb], Mark Raasveldt [ctb], Thomas Lumley [ctb], MonetDB B.V. [cph], CWI [cph], The Regents of the University of California [cph], Kungliga Tekniska Hogskolan [cph], Free Software Foundation, Inc. [cph]
Maintainer: Hannes Muehleisen <hannes@cwi.nl>
Diff between MonetDBLite versions 0.4.1 dated 2017-08-02 and 0.5.0 dated 2017-11-15
MonetDBLite-0.4.1/MonetDBLite/cleanup |only MonetDBLite-0.4.1/MonetDBLite/configure |only MonetDBLite-0.4.1/MonetDBLite/configure.win |only MonetDBLite-0.4.1/MonetDBLite/src/Makefile.am |only MonetDBLite-0.4.1/MonetDBLite/src/Makefile.in |only MonetDBLite-0.4.1/MonetDBLite/src/aclocal.m4 |only MonetDBLite-0.4.1/MonetDBLite/src/acout |only MonetDBLite-0.4.1/MonetDBLite/src/acout.in |only MonetDBLite-0.4.1/MonetDBLite/src/bootstrap |only MonetDBLite-0.4.1/MonetDBLite/src/buildtools |only MonetDBLite-0.4.1/MonetDBLite/src/common |only MonetDBLite-0.4.1/MonetDBLite/src/configure |only MonetDBLite-0.4.1/MonetDBLite/src/configure.ac |only MonetDBLite-0.4.1/MonetDBLite/src/doc.lst |only MonetDBLite-0.4.1/MonetDBLite/src/embedded |only MonetDBLite-0.4.1/MonetDBLite/src/gdk |only MonetDBLite-0.4.1/MonetDBLite/src/install.lst |only MonetDBLite-0.4.1/MonetDBLite/src/libversions |only MonetDBLite-0.4.1/MonetDBLite/src/mal |only MonetDBLite-0.4.1/MonetDBLite/src/mapisplit |only MonetDBLite-0.4.1/MonetDBLite/src/monetdb_config.h.in |only MonetDBLite-0.4.1/MonetDBLite/src/sql |only MonetDBLite-0.5.0/MonetDBLite/DESCRIPTION | 16 MonetDBLite-0.5.0/MonetDBLite/MD5 | 858 ++++------ MonetDBLite-0.5.0/MonetDBLite/NAMESPACE | 2 MonetDBLite-0.5.0/MonetDBLite/R/dbi.R | 8 MonetDBLite-0.5.0/MonetDBLite/R/embedded.R | 30 MonetDBLite-0.5.0/MonetDBLite/README.md | 17 MonetDBLite-0.5.0/MonetDBLite/src/Makevars |only MonetDBLite-0.5.0/MonetDBLite/src/dummy.c |only MonetDBLite-0.5.0/MonetDBLite/src/embeddedr |only MonetDBLite-0.5.0/MonetDBLite/src/monetdblite |only MonetDBLite-0.5.0/MonetDBLite/tests/testthat.R | 3 MonetDBLite-0.5.0/MonetDBLite/tests/testthat/test_01_lowlevel.R | 36 MonetDBLite-0.5.0/MonetDBLite/tests/testthat/test_02_dbi.R | 53 MonetDBLite-0.5.0/MonetDBLite/tests/testthat/test_03_dbitest.R | 15 MonetDBLite-0.5.0/MonetDBLite/tests/testthat/test_04_dplyr.R | 23 MonetDBLite-0.5.0/MonetDBLite/tests/testthat/test_05_survey.R | 18 38 files changed, 535 insertions(+), 544 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between asnipe versions 1.1.4 dated 2017-07-24 and 1.1.5 dated 2017-11-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/get_network.R | 25 ++++++++++++++++++++++++- man/asnipe-package.Rd | 2 +- man/get_network.Rd | 7 +++++-- man/network_permutation.Rd | 3 +++ man/network_swap.Rd | 3 +++ 7 files changed, 46 insertions(+), 14 deletions(-)
Title: Model Response Styles in Partial Credit Models
Description: Implementation of PCMRS (Partial Credit Model with Response Styles) as proposed in by Tutz, Schauberger and Berger (2016) <https://epub.ub.uni-muenchen.de/29373/> . PCMRS is an extension of the regular partial credit model. PCMRS allows for an additional person parameter that characterizes the response style of the person. By taking the response style into account, the estimates of the item parameters are less biased than in partial credit models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between PCMRS versions 0.0-1 dated 2017-11-07 and 0.0-2 dated 2017-11-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/PCMRS.R | 2 +- R/RcppExports.R | 4 ++-- man/PCMRS.Rd | 2 +- src/RcppExports.cpp | 15 +++++++++++++-- src/cppEPCM.cpp | 6 +----- 7 files changed, 28 insertions(+), 21 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: An R package for feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Michail Tsagris [aut, cre], Ioannis Tsamardinos [aut], Vincenzo Lagani [aut], Giorgos Athineou [aut], Giorgos Borboudakis [ctb], Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 1.2 dated 2017-10-10 and 1.2.5 dated 2017-11-15
DESCRIPTION | 13 MD5 | 324 ++++++++------ NAMESPACE | 14 R/InternalMMPC.R | 12 R/InternalMMPC.temporal.R | 12 R/InternalSES.R | 15 R/InternalSES.temporal.R | 16 R/Internalmases.R | 6 R/MMPC.R | 23 - R/MMPC.temporal.R | 6 R/SES.R | 12 R/SES.temporal.R | 6 R/auc.R | 24 - R/beta.bsreg.R | 25 - R/beta.fsreg.R | 3 R/beta.fsreg_2.R | 56 -- R/bic.betafsreg.R | 2 R/bic.clogit.fsreg.R |only R/bic.fsreg.R | 24 - R/bic.gammafsreg.R | 27 - R/bic.glm.fsreg.R | 69 +-- R/bic.normlog.fsreg.R | 27 - R/bic.tobit.fsreg.R | 30 - R/bic.zipfsreg.R | 2 R/bn.skel.utils.R |only R/bs.reg.R | 40 + R/cat_condis.R |only R/clogit.bsreg.R |only R/clogit.fsreg.R |only R/clogit.fsreg_2.R |only R/comb_condis.R |only R/condi.R | 4 R/condis.R |only R/distcor_condis.R |only R/ebic.beta.bsreg.R | 10 R/ebic.bsreg.R | 3 R/ebic.clogit.bsreg.R |only R/ebic.cr.bsreg.R | 12 R/ebic.fbed.beta.R | 2 R/ebic.fbed.clogit.R |only R/ebic.fbed.cr.R | 2 R/ebic.fbed.glm.R | 2 R/ebic.fbed.glmm.R |only R/ebic.fbed.lm.R | 2 R/ebic.fbed.lmm.R |only R/ebic.fbed.mmreg.R | 2 R/ebic.fbed.multinom.R | 2 R/ebic.fbed.nb.R | 2 R/ebic.fbed.ordinal.R | 2 R/ebic.fbed.tobit.R | 2 R/ebic.fbed.wr.R | 2 R/ebic.fbed.zip.R | 2 R/ebic.glm.bsreg.R | 12 R/ebic.glmm.bsreg.R |only R/ebic.lm.bsreg.R | 12 R/ebic.lmm.bsreg.R |only R/ebic.mm.bsreg.R | 12 R/ebic.multinom.bsreg.R | 12 R/ebic.nb.bsreg.R | 12 R/ebic.ordinal.bsreg.R | 12 R/ebic.tobit.bsreg.R | 12 R/ebic.wr.bsreg.R | 12 R/ebic.zip.bsreg.R | 12 R/fbed.clogit.R |only R/fbed.glm.R | 32 - R/fbed.glmm.R |only R/fbed.glmm.reg.R |only R/fbed.lm.R | 24 - R/fbed.lmm.R |only R/fbed.multinom.R | 36 - R/fbed.nb.R | 14 R/fbed.reg.R | 7 R/fs.reg.R | 25 - R/fs.reg_2.R | 109 ++-- R/gammabsreg.R | 30 - R/gammafsreg.R | 35 - R/gammafsreg_2.R | 67 +-- R/glm.bsreg.R | 102 ++-- R/glm.fsreg.R | 105 ++-- R/glm.fsreg_2.R | 11 R/glmm.bsreg.R |only R/glmm.ci.mm.R |only R/glmm.pc.skel.R |only R/iamb.R | 4 R/iamb.betabs.R | 26 - R/iamb.bs.R | 10 R/iamb.gammabs.R | 23 - R/iamb.glmbs.R | 25 - R/iamb.normlogbs.R | 25 - R/iamb.tobitbs.R | 27 - R/iamb.zipbs.R | 32 - R/internaliamb.betabs.R | 14 R/internaliamb.binombs.R | 30 - R/internaliamb.bs.R | 18 R/internaliamb.gammabs.R | 30 - R/internaliamb.lmbs.R | 40 - R/internaliamb.normlogbs.R | 30 - R/internaliamb.poisbs.R | 28 - R/internaliamb.tobitbs.R | 22 R/internaliamb.zipbs.R | 8 R/lm.fsreg.R | 2 R/lm.fsreg_2.R | 159 +++---- R/lm.fsreg_2.heavy.R | 77 +-- R/lmm.bsreg.R |only R/local.mmhc.skel.R |only R/ma.mmpc.R | 2 R/mmhc.skel.R | 229 +++++----- R/mmmb.R | 58 -- R/mmpc.or.R |only R/mmpcbackphase.R | 17 R/normlog.bsreg.R | 30 - R/normlog.fsreg.R | 7 R/normlog.fsreg_2.R | 76 +-- R/pc.or.R | 243 +++++------ R/pc.skel.R | 107 ++-- R/pc.skel.boot.R |only R/pearson_condis.R |only R/pearson_condis.rob.R |only R/perm.Internalmmpc.R | 2 R/perm.Internalses.R | 3 R/perm.mmpc.R | 4 R/perm.univregs.R | 7 R/permClogit.R | 138 +++--- R/permDcor.R | 5 R/rdag.R | 6 R/rdag2.R | 9 R/reg.fit.R | 67 +-- R/ridge.plot.R | 8 R/ridge.reg.R | 41 - R/ridgereg.cv.R | 40 - R/rint.regs.R | 134 ++++-- R/rmdag.R | 10 R/ses.model.R | 11 R/testIndClogit.R | 5 R/testIndFisher.R | 2 R/testIndGLMM.R | 13 R/testIndGamma.R | 10 R/testIndNormLog.R | 11 R/testIndRQ.R | 10 R/testIndReg.R | 17 R/testIndSpearman.R | 9 R/tobit.bsreg.R | 61 +- R/tobit.fsreg.R | 3 R/tobit.fsreg_2.R | 10 R/topological_sort.R | 26 - R/univregs.R | 8 R/wald.Internalmmpc.R | 2 R/wald.Internalses.R | 3 R/wald.mmpc.R | 1 R/waldMMreg.R | 1 R/zip.bsreg.R | 31 - R/zip.fsreg.R | 2 R/zip.fsreg_2.R | 68 +-- inst/doc/article.pdf |binary inst/doc/guide.pdf |binary man/MXM-internal.Rd | 26 + man/MXM-package.Rd | 6 man/MXMCondIndTests.Rd | 7 man/SES.Rd | 31 - man/SES.temporal.Rd | 12 man/auc.Rd | 8 man/bn.skel.utils.Rd |only man/bs.reg.Rd | 4 man/censIndCR.Rd | 17 man/condis.Rd |only man/ebic.bsreg.Rd | 2 man/ebic.glmm.bsreg.Rd |only man/fbed.glmm.reg.Rd |only man/fbed.reg.Rd | 2 man/glmm.bsreg.Rd |only man/glmm.ci.mm.Rd |only man/local.mmhc.skel.Rd |only man/mmhc.skel.Rd | 26 - man/mmpc.or.Rd |only man/mmpcbackphase.Rd | 3 man/pc.or.Rd | 11 man/pc.skel.Rd | 82 ++- man/testIndClogit.Rd | 5 man/testIndGamma.Rd | 12 man/topological_sort.Rd | 7 vignettes/biblio.bib | 992 ++++++++++++++++++++++----------------------- 181 files changed, 2467 insertions(+), 2507 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.5 dated 2017-09-25 and 1.5-1 dated 2017-11-15
laGP-1.5-1/laGP/ChangeLog | 5 +++ laGP-1.5-1/laGP/DESCRIPTION | 8 ++--- laGP-1.5-1/laGP/MD5 | 17 +++++----- laGP-1.5-1/laGP/R/blhs.R | 2 + laGP-1.5-1/laGP/R/laGP_sep.R | 2 - laGP-1.5-1/laGP/build/vignette.rds |binary laGP-1.5-1/laGP/inst/doc/laGP.pdf |binary laGP-1.5-1/laGP/src/laGP.c | 58 ++++++++++++++++++------------------- laGP-1.5-1/laGP/src/laGP_sep.c | 52 ++++++++++++++++----------------- laGP-1.5/laGP/src/symbols.rds |only 10 files changed, 75 insertions(+), 69 deletions(-)
Title: Easy Nonlinear Model
Description: Fit and plot some nonlinear models.
Author: Emmanuel Arnhold
Maintainer: Emmanuel Arnhold <emmanuelarnhold@yahoo.com.br>
Diff between easynls versions 4.0 dated 2014-02-06 and 5.0 dated 2017-11-15
DESCRIPTION | 13 ++++++----- MD5 | 14 ++++++------ NAMESPACE | 6 ++++- R/nlsfit.R | 52 +++++++++++++++++++++++++++++++---------------- R/nlsplot.R | 15 ++++--------- man/easynls-package.Rd | 54 ++++++------------------------------------------- man/nlsfit.Rd | 27 +++++------------------- man/nlsplot.Rd | 34 +++++++++--------------------- 8 files changed, 82 insertions(+), 133 deletions(-)