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 <https://r-nimble.org>.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-Bergman, Nick Michaud, Fritz Obermeyer, Claudia Wehrhahn Cortes, Abel Rodriguez, Duncan Temple Lang, and see AUTHORS file for additional contributors.
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6-12 dated 2018-07-27 and 0.6.13 dated 2019-01-25
DESCRIPTION | 12 INSTALL | 8 LICENSE | 4 MD5 | 138 NAMESPACE | 9 R/BNP_samplers.R | 1333 +++++-- R/BUGS_BUGSdecl.R | 2 R/BUGS_modelDef.R | 19 R/BUGS_utils.R | 2 R/CAR.R | 4 R/MCMC_build.R | 18 R/MCMC_configuration.R | 104 R/MCMC_conjugacy.R | 21 R/MCMC_samplers.R | 257 + R/MCMC_utils.R | 2 R/all_utils.R | 17 R/cppDefs_core.R | 4 R/cppDefs_cppProject.R | 39 R/cppDefs_nimbleList.R | 18 R/distributions_implementations.R | 78 R/distributions_inputList.R | 11 R/distributions_processInputList.R | 65 R/filtering_liuwest.R | 19 R/genCpp_sizeProcessing.R | 5 R/initializeModel.R | 99 R/nimbleFunction_Rexecution.R | 21 R/nimbleFunction_keywordProcessing.R | 13 R/nimbleFunction_nodeFunction.R | 4 R/nimbleProject.R | 20 inst/CITATION | 13 inst/CppCode/RcppNimbleUtils.cpp | 60 inst/CppCode/RcppUtils.cpp | 15 inst/CppCode/Utils.cpp | 6 inst/CppCode/accessorClasses.cpp | 42 inst/CppCode/dists.cpp | 236 + inst/CppCode/nimDists.cpp | 1 inst/CppCode/predefinedNimbleLists.cpp | 20 inst/NEWS | 66 inst/include/nimble/NimArr.h | 345 + inst/include/nimble/NimArrBase.h | 4 inst/include/nimble/dists.h | 9 inst/include/nimble/nimbleEigen.h | 8 inst/tests/dynamicIndexingTestLog_Correct.Rout | 1955 +++++++---- inst/tests/filteringTestLog_Correct.Rout | 18 inst/tests/mcmcTestLog_Correct.Rout | 1305 +++---- inst/tests/test-Filtering2.R | 5 inst/tests/test-Mcmc2.R | 4 inst/tests/test-bnp.R | 4414 +++++++++++++++++++------ inst/tests/test-coreR.R | 295 + inst/tests/test-distributions.R | 76 inst/tests/test-dynamicIndexing.R | 62 inst/tests/test-graphStructure.R | 25 inst/tests/test-initializeModel.R |only inst/tests/test-mcmc.R | 122 inst/tests/test-modelValuesInterface.R | 45 inst/tests/test-models.R | 54 inst/tests/test-size.R | 12 inst/tests/test-trunc.R | 18 inst/tests/test-user.R | 52 inst/tests/test_utils.R | 4 inst/tests/truncTestLog_Correct.Rout | 384 +- inst/tests/userTestLog_Correct.Rout | 4 man/Double-Exponential.Rd |only man/MCMCconf-class.Rd | 10 man/buildMCMC.Rd | 10 man/configureMCMC.Rd | 2 man/getSamplesDPmeasure.Rd | 26 man/is.na.vec.Rd |only man/nimble-R-functions.Rd | 7 man/printErrors.Rd |only man/samplers.Rd | 27 src/nimble.cpp | 4 72 files changed, 8735 insertions(+), 3376 deletions(-)
Title: Cholesky Decomposition of the Wishart Distribution
Description: Sampling from the Cholesky factorization of a Wishart random
variable, sampling from the inverse Wishart distribution, sampling from
the Cholesky factorization of an inverse Wishart random variable, sampling
from the pseudo Wishart distribution, sampling from the generalized
inverse Wishart distribution, computing densities for the Wishart
and inverse Wishart distributions, and computing the multivariate gamma
and digamma functions.
Author: Geoffrey Thompson [aut, cre],
R Core Team [ctb]
Maintainer: Geoffrey Thompson <gzthompson@gmail.com>
Diff between CholWishart versions 0.9.4 dated 2019-01-07 and 1.0.0 dated 2019-01-25
DESCRIPTION | 6 - MD5 | 28 +++---- NEWS.md | 5 + R/gammas.R | 2 R/wishart.R | 164 +++++++++++++++++++------------------------- README.md | 98 ++++++++------------------ build/partial.rdb |binary inst/doc/wishart.html | 24 +++--- man/lmvgamma.Rd | 2 man/rGenInvWishart.Rd | 13 +++ man/rPseudoWishart.Rd | 11 +- src/init.c | 2 src/rCholWishart.c | 75 ++++++++++++++++++++ tests/testthat/testinput.R | 18 ++++ tests/testthat/testoutput.R | 7 + 15 files changed, 258 insertions(+), 197 deletions(-)
Title: Exact Power of the Wilcoxon-Mann-Whitney Rank-Sum Test for a
Continuous Variable
Description: Power calculator for the two-sample Wilcoxon-Mann-Whitney rank-sum test for a continuous outcome (Mollan, Trumble, Reifeis et. al., Jan. 2019) <arXiv:1901.04597>, (Mann and Whitney 1947) <doi:10.1214/aoms/1177730491>, (Shieh, Jan, and Randles 2006) <doi:10.1080/10485250500473099>.
Author: Ilana Trumble, Orlando Ferrer, Camden Bay, Katie Mollan
Maintainer: Ilana Trumble <ilana.trumble@ucdenver.edu>
Diff between wmwpow versions 0.1.0 dated 2018-03-02 and 0.1.1 dated 2019-01-25
DESCRIPTION | 17 +++++++++-------- MD5 | 14 +++++++------- R/shiehpow.R | 26 ++++++++++++++++---------- R/wmwpowd.R | 28 ++++++++++++++++++---------- R/wmwpowp.R | 41 ++++++++++++++++++++++++++--------------- man/shiehpow.Rd | 18 ++++++++++++------ man/wmwpowd.Rd | 21 ++++++++++++++------- man/wmwpowp.Rd | 26 +++++++++++++++++--------- 8 files changed, 119 insertions(+), 72 deletions(-)
Title: Modeling Earthquake Data Using 'ETAS' Model
Description: Fits the space-time Epidemic Type Aftershock Sequence
('ETAS') model to earthquake catalogs using a stochastic 'declustering'
approach. The 'ETAS' model is a 'spatio-temporal' marked point process
model and a special case of the 'Hawkes' process. The package is based
on a Fortran program by 'Jiancang Zhuang'
(available at <http://bemlar.ism.ac.jp/zhuang/software.html>),
which is modified and translated into C++ and C such that it
can be called from R. Parallel computing with 'OpenMP' is possible
on supported platforms.
Author: Abdollah Jalilian [aut, cre] (<https://orcid.org/0000-0002-6573-0069>),
Jiancang Zhuang [ctb] (<https://orcid.org/0000-0002-9708-3871>)
Maintainer: Abdollah Jalilian <jalilian@razi.ac.ir>
Diff between ETAS versions 0.4.5 dated 2018-11-28 and 0.4.6 dated 2019-01-25
DESCRIPTION | 9 +++++---- MD5 | 11 ++++++----- README.md | 22 +++++----------------- data/iran.quakes.rda |binary data/italy.quakes.rda |binary data/japan.quakes.rda |binary inst |only 7 files changed, 16 insertions(+), 26 deletions(-)
Title: Ensemble Learning Algorithms Based on Support Vector Machines
Description: Three ensemble learning algorithms based on support vector machines.
They all train support vector machines on subset of data and combine the result.
Author: Tong He <hetong007@gmail.com>, Aydin Demircioglu <aydin.demircioglu@ini.ruhr-uni-bochum.de>
Maintainer: Tong He <hetong007@gmail.com>
Diff between SwarmSVM versions 0.1-4 dated 2018-04-18 and 0.1-5 dated 2019-01-25
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- R/alphasvm.R | 2 - build/vignette.rds |binary inst/doc/SwarmSVM.html | 68 ++++++++++++++++++++++++------------------------- src/svm.cpp | 3 +- src/svm.h | 2 - 7 files changed, 48 insertions(+), 47 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <http://data.neonscience.org>
or through the NEON Data API (see <http://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Christine Laney <claney@battelleecology.org>, Claire Lunch <clunch@battelleecology.org>
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.0.1 dated 2018-11-13 and 1.2.0 dated 2019-01-25
DESCRIPTION | 12 +++++------ MD5 | 28 ++++++++++++++++----------- NAMESPACE | 8 +++++++ R/cleanUp.R | 3 ++ R/getDatatable.R |only R/getTaxonTable.R |only R/loadByProduct.R |only R/stackByTable.R | 40 +++++++++++++++++++++++++++++++++------ R/stackDataFiles.R | 10 ++++----- R/sysdata.rda |binary R/unzipZipfile.R | 6 ++--- R/zipsByProduct.R | 52 ++++++++++++++++++++++++++++++++++++--------------- README.md | 39 +++++++++++++++++++++++++++++++++++--- man/getDatatable.Rd |only man/getTaxonTable.Rd |only man/loadByProduct.Rd |only man/stackByTable.Rd | 4 +-- man/zipsByProduct.Rd | 4 ++- 18 files changed, 154 insertions(+), 52 deletions(-)
Title: Zhang + Yue-Pilon Trends Package
Description: Contains an efficient implementation of Sen's slope method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and Yue-Pilon's (Yue, 2002) prewhitening approaches to determining trends in climate data.
Author: David Bronaugh <bronaugh@uvic.ca>, Arelia Werner <wernera@uvic.ca> for the Pacific Climate Impacts Consortium
Maintainer: David Bronaugh <bronaugh@uvic.ca>
Diff between zyp versions 0.10-1 dated 2013-09-19 and 0.10-1.1 dated 2019-01-25
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NAMESPACE | 6 ++++++ 3 files changed, 14 insertions(+), 8 deletions(-)
Title: Create Time Series BUGS Models
Description: Contains a collection of R functions
that can be used to create time series BUGS models of various
order. Included are function to create BUGS with non-constant
variance such stochastic volatility models and random variance
shift models.
Author: Guy J. Abel
Maintainer: "Guy J. Abel" <g.j.abel@gmail.com>
Diff between tsbugs versions 1.2 dated 2013-02-25 and 1.2.1 dated 2019-01-25
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 ++ data/ew.rda |binary data/svpdx.rda |binary 5 files changed, 11 insertions(+), 9 deletions(-)
Title: Scaled Sparse Linear Regression
Description: Algorithms for fitting scaled sparse linear regression and estimating precision matrices.
Author: Tingni Sun
Maintainer: Tingni Sun <tingni@wharton.upenn.edu>
Diff between scalreg versions 1.0 dated 2013-12-17 and 1.0.1 dated 2019-01-25
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 6 ++++++ data/sp500.RData |binary 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Parallelised Estimation of Prediction Error
Description: Designed for prediction error estimation
through resampling techniques, possibly accelerated by parallel
execution on a compute cluster. Newly developed model fitting
routines can be easily incorporated.
Author: Christine Porzelius, Harald Binder
Maintainer: Christine Porzelius <cp@imbi.uni-freiburg.de>
Diff between peperr versions 1.1-7 dated 2013-04-08 and 1.1-7.1 dated 2019-01-25
peperr-1.1-7.1/peperr/ChangeLog |only peperr-1.1-7.1/peperr/DESCRIPTION | 9 ++++----- peperr-1.1-7.1/peperr/MD5 | 18 +++++++++--------- peperr-1.1-7.1/peperr/NAMESPACE | 11 +++++++++++ peperr-1.1-7.1/peperr/R/aggregation.pmpec.R | 1 - peperr-1.1-7.1/peperr/R/complexity.ipec.CoxBoost.R | 1 - peperr-1.1-7.1/peperr/R/complexity.ripec.CoxBoost.R | 1 - peperr-1.1-7.1/peperr/R/fit.coxph.R | 1 - peperr-1.1-7.1/peperr/R/pmpec.R | 1 - peperr-1.1-7.1/peperr/R/predictProb.coxph.R | 3 +-- peperr-1.1-7/peperr/changeLog |only 11 files changed, 25 insertions(+), 21 deletions(-)
Title: Package for Nonparametric Statistical Methods using R
Description: Functions and datasets used in the book Nonparametric Statistical Methods Using R.
Author: John Kloke, Joseph McKean
Maintainer: John Kloke <kloke@biostat.wisc.edu>
Diff between npsm versions 0.5 dated 2014-11-06 and 0.5.1 dated 2019-01-25
npsm-0.5.1/npsm/DESCRIPTION | 8 ++--- npsm-0.5.1/npsm/MD5 | 51 ++++++++++++++++------------------ npsm-0.5.1/npsm/NAMESPACE | 9 ++++++ npsm-0.5.1/npsm/data/SCUD.rda |binary npsm-0.5.1/npsm/data/bb2010.rda |binary npsm-0.5.1/npsm/data/blood.plasma.rda |binary npsm-0.5.1/npsm/data/cancertrt.rda |binary npsm-0.5.1/npsm/data/cloud.rda |binary npsm-0.5.1/npsm/data/energy.rda |binary npsm-0.5.1/npsm/data/firstbase.rda |binary npsm-0.5.1/npsm/data/hemorrhage.rda |binary npsm-0.5.1/npsm/data/hodgkins.rda |binary npsm-0.5.1/npsm/data/huitema496.rda |binary npsm-0.5.1/npsm/data/insulation.rda |binary npsm-0.5.1/npsm/data/latour.rda |binary npsm-0.5.1/npsm/data/plank.rda |binary npsm-0.5.1/npsm/data/poly.rda |binary npsm-0.5.1/npsm/data/prostate.rda |binary npsm-0.5.1/npsm/data/qhic.rda |binary npsm-0.5.1/npsm/data/quail2.rda |binary npsm-0.5.1/npsm/data/rs.rda |binary npsm-0.5.1/npsm/data/sievers.rda |binary npsm-0.5.1/npsm/data/simon.rda |binary npsm-0.5.1/npsm/data/sincos.rda |binary npsm-0.5.1/npsm/data/speed.rda |binary npsm-0.5.1/npsm/data/weather.rda |binary npsm-0.5/npsm/README.md |only 27 files changed, 38 insertions(+), 30 deletions(-)
Title: Joint Estimation in Linear Quantile Regression
Description: Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.
Author: Surya Tokdar <surya.tokdar@duke.edu> and Erika Cunningham <erika.ball@duke.edu>
Maintainer: Surya Tokdar <surya.tokdar@duke.edu>
Diff between qrjoint versions 2.0-2 dated 2018-09-13 and 2.0-3 dated 2019-01-25
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- R/qrjoint.R | 17 ++++++++++------- data/redmaple.rda |only man/chull.center.Rd | 2 +- man/qrjoint.Rd | 2 +- man/redmaple.Rd |only man/summary.qde.Rd | 2 +- man/summary.qrjoint.Rd | 22 +++++++++++----------- src/qrjoint.c | 45 +++++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 82 insertions(+), 32 deletions(-)
Title: A Suite of Packages for Analysis of Big Genomic Data
Description: An umbrella package providing a phenotype/genotype data structure
and scalable and efficient computational methods for large genomic datasets
in combination with several other packages: 'BEDMatrix', 'LinkedMatrix',
and 'symDMatrix'.
Author: Gustavo de los Campos [aut],
Alexander Grueneberg [aut, cre],
Paulino Perez [ctb],
Ana Vazquez [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BGData versions 2.0.0 dated 2018-08-24 and 2.1.0 dated 2019-01-25
DESCRIPTION | 10 - MD5 | 34 +++-- NAMESPACE | 2 NEWS.md | 14 ++ R/BGData.R | 4 R/GWAS.R | 94 ++++++-------- R/chunkedApply.R | 100 +++++++++++---- R/getG.R | 20 +-- R/package.R | 1 R/summarize.R | 22 +-- man/GWAS.Rd | 5 man/chunkedMap.Rd |only man/examples/chunkedMap.R |only src |only tests/testthat/helper-utils.R |only tests/testthat/test-BGData.R | 16 +- tests/testthat/test-GWAS.R |only tests/testthat/test-chunkedApply.R |only tests/testthat/test-getG.R |only tests/testthat/test-summarize.R |only tests/testthat/test-utils.R | 235 ------------------------------------- 21 files changed, 189 insertions(+), 368 deletions(-)
Title: Functions for R Beginners
Description: Useful functions for R beginners, including hints for the arguments of the 'plot()' function, self-defined functions for error bars, user-customized pair plots and hist plots, enhanced linear regression figures, etc.. This package could be helpful to R experts as well.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between beginr versions 0.1.4 dated 2019-01-11 and 0.1.5 dated 2019-01-25
beginr-0.1.4/beginr/R/foo.R |only beginr-0.1.5/beginr/DESCRIPTION | 8 +-- beginr-0.1.5/beginr/MD5 | 69 +++++++++++++++++++------------- beginr-0.1.5/beginr/NAMESPACE | 2 beginr-0.1.5/beginr/R/beginr.R |only beginr-0.1.5/beginr/R/packr.R |only beginr-0.1.5/beginr/inst/skeleton |only beginr-0.1.5/beginr/man/bib.Rd | 2 beginr-0.1.5/beginr/man/dfplot.Rd | 2 beginr-0.1.5/beginr/man/dfplot2.Rd | 2 beginr-0.1.5/beginr/man/errorbar.Rd | 2 beginr-0.1.5/beginr/man/list2ascii.Rd | 2 beginr-0.1.5/beginr/man/lmdf.Rd | 2 beginr-0.1.5/beginr/man/mf_skewness.Rd | 2 beginr-0.1.5/beginr/man/name.Rd | 2 beginr-0.1.5/beginr/man/packr.Rd |only beginr-0.1.5/beginr/man/plotblank.Rd | 2 beginr-0.1.5/beginr/man/plotcolorbar.Rd | 2 beginr-0.1.5/beginr/man/plotcolors.Rd | 2 beginr-0.1.5/beginr/man/plothist.Rd | 2 beginr-0.1.5/beginr/man/plotlm.Rd | 2 beginr-0.1.5/beginr/man/plotlty.Rd | 2 beginr-0.1.5/beginr/man/plotpairs.Rd | 2 beginr-0.1.5/beginr/man/plotpairs2.Rd | 2 beginr-0.1.5/beginr/man/plotpch.Rd | 2 beginr-0.1.5/beginr/man/plotpkg.Rd | 2 beginr-0.1.5/beginr/man/plottype.Rd | 2 beginr-0.1.5/beginr/man/readdir.Rd | 2 beginr-0.1.5/beginr/man/rpkg.Rd | 2 beginr-0.1.5/beginr/man/rplc.Rd |only beginr-0.1.5/beginr/man/se.Rd | 2 beginr-0.1.5/beginr/man/tapplydf.Rd | 2 beginr-0.1.5/beginr/man/tapplydfv.Rd | 2 beginr-0.1.5/beginr/man/writefile.Rd | 2 34 files changed, 72 insertions(+), 57 deletions(-)
Title: Bayesian Analysis of Quantile Regression Models
Description: Bayesian estimation and variable selection for quantile regression models.
Author: Rahim Alhamzawi
Maintainer: Rahim Alhamzawi (University of Al-Qadisiyah) <rahim.alhamzawi@qu.edu.iq>
Diff between Brq versions 2.2 dated 2019-01-14 and 2.3 dated 2019-01-25
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/CITATION | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-18 1.2.2
2016-06-13 1.2.1
2016-05-03 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-09 1.2
2012-07-03 1.1
2012-06-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-03 1.0.1
2013-08-30 1.0.0
2013-01-30 0.8.1
2013-01-25 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-15 0.2
2014-10-15 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-16 0.6.2
2015-03-31 0.6.1
2013-12-14 0.6.0
2012-08-28 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-23 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-18 2.2
2017-08-13 2.1
2016-10-26 2.0
2015-07-14 1.5.1
2015-06-18 1.5
2014-05-06 1.4
2014-03-18 1.3
2013-12-25 1.2
2013-12-24 1.1
2013-08-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-21 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-05 0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-06 1.8.9
2018-10-19 1.8.8
2018-10-18 1.8.7
2018-09-25 1.8.6
2017-10-10 1.8.5
2017-07-23 1.8.4
2017-04-04 1.8.2
2017-02-21 1.8.1
2016-08-25 1.8
2016-06-14 1.7
2016-03-30 1.6
2016-03-19 1.5
2016-01-07 1.4
2015-10-03 1.3
2015-09-25 1.2
2015-06-16 1.1
2015-02-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-25 1.1.2
2017-11-14 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-28 1.0
Title: Strategy Estimation
Description: Variants of the strategy frequency estimation method by Dal Bo & Frechette (2011) <doi:10.1257/aer.101.1.411>, including the adaptation to estimate choice parameters of behavior strategies by Breitmoser (2015) <doi:10.1257/aer.20130675>, and the extension in the spirit of latent-class regression by Dvorak & Fehrler (2018) <doi:10.2139/ssrn.2986445>.
Author: Fabian Dvorak
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Diff between stratEst versions 0.1.1 dated 2018-12-17 and 0.1.2 dated 2019-01-25
DESCRIPTION | 12 - MD5 | 23 +- R/RcppExports.R | 4 R/stratEst.R | 94 ++++++--- README.md | 48 +++- inst/stratEst_paper_181201.pdf |only man/stratEst.Rd | 36 ++- src/RcppExports.cpp | 9 src/stratEst.cpp | 377 +++++++++++++++++++------------------- tests/testthat/test.behavior.R | 1 tests/testthat/test.example1.R |only tests/testthat/test.example2.R |only tests/testthat/test.sfem.R | 1 tests/testthat/tests.systematic.R | 52 +++++ 14 files changed, 396 insertions(+), 261 deletions(-)
Title: Generalized Ensemble Methods
Description: Generalized ensemble methods allowing arbitrary underlying
models to be used. Currently only bagging is supported.
Author: Peter Werner, Eugene Dubossarsky
Maintainer: Peter Werner <gensemble.r@gmail.com>
Diff between gensemble versions 1.0 dated 2013-02-11 and 1.0.1 dated 2019-01-25
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- NAMESPACE | 4 ++++ 3 files changed, 11 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-09 1.2.3
2015-10-28 1.2.2
2015-05-23 1.2
2015-04-30 1.1.7
2015-01-27 1.1.5
2014-04-13 1.1.3
2014-02-19 1.0.3
2014-01-03 1.0.2
2013-09-28 1.0.1
2013-07-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-11 1.0.10
2014-05-05 1.0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-21 0.1.0
More information about provSummarizeR at CRAN
Permanent link
Title: Violin Plot
Description: A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Author: Daniel Adler <dadler@uni-goettingen.de>
Maintainer: Tom Kelly <tom.kelly@postgrad.otago.ac.nz>
Diff between vioplot versions 0.2 dated 2005-10-29 and 0.3.0 dated 2019-01-25
DESCRIPTION | 29 +- LICENSE | 34 --- MD5 |only NAMESPACE | 27 ++ NEWS.md |only R/vioplot.R | 590 +++++++++++++++++++++++++++++++++++++++------------------ build |only inst |only man/vioplot.Rd | 238 ++++++++++++++++------ tests |only vignettes |only 11 files changed, 628 insertions(+), 290 deletions(-)
Title: Generalized Autoregressive Score Models
Description: Simulate, estimate and forecast using univariate and multivariate GAS models
as described in Ardia et al. (2019) <doi:10.18637/jss.v088.i06>.
Author: Leopoldo Catania [aut,cre], Kris Boudt [ctb], David Ardia [ctb]
Maintainer: Leopoldo Catania <leopoldo.catania@econ.au.dk>
Diff between GAS versions 0.2.9 dated 2018-09-18 and 0.3.0 dated 2019-01-25
DESCRIPTION | 8 +++--- MD5 | 18 +++++++------- R/RcppExports.R | 16 ++++++------ README.md | 16 ++++++------ build/partial.rdb |binary inst/CITATION | 52 ++++++++++++++-------------------------- man/BacktestVaR.Rd | 36 ++++++++++++++-------------- man/GAS-package.Rd | 12 ++++----- man/PIT_test.Rd | 34 +++++++++++++------------- src/RcppExports.cpp | 66 ++++++++++++++++++++++++++-------------------------- 10 files changed, 121 insertions(+), 137 deletions(-)
Title: A Data-Driven Similarity Kernel on Probability Spaces
Description: We present a rank-based Mercer kernel to compute a pair-wise similarity metric corresponding to informative representation of data. We tailor the development of a kernel to encode our prior knowledge about the data distribution over a probability space. The philosophical concept behind our construction is that objects whose feature values fall on the extreme of that feature’s probability mass distribution are more similar to each other, than objects whose feature values lie closer to the mean. Semblance emphasizes features whose values lie far away from the mean of their probability distribution. The kernel relies on properties empirically determined from the data and does not assume an underlying distribution. The use of feature ranks on a probability space ensures that Semblance is computational efficacious, robust to outliers, and statistically stable, thus making it widely applicable algorithm for pattern analysis. The output from the kernel is a square, symmetric matrix that gives proximity values between pairs of observations.
Author: Divyansh Agarwal <divyansh@upenn.edu>
Nancy R. Zhang <nzh@wharton.upenn.edu>
Maintainer: Divyansh Agarwal <divyansh@upenn.edu>
Diff between Semblance versions 0.1.0 dated 2018-05-30 and 1.1.0 dated 2019-01-25
DESCRIPTION | 15 ++++--- MD5 | 10 +++-- NAMESPACE | 4 ++ R/semblance.R | 62 ++++++++++++++++++++++++++++++++- man/computeSemblanceOneFeature_Gini.Rd |only man/ranksem.Rd | 2 - man/ranksem_Gini.Rd |only 7 files changed, 80 insertions(+), 13 deletions(-)
Title: R Optimization Infrastructure: 'MIPLIB' 2010 Benchmark Instances
Description: The mixed integer programming library 'MIPLIB' (see <http://miplib.zib.de/>)
is commonly used to compare the performance of mixed integer optimization solvers.
This package provides functions to access 'MIPLIB' from the
'R' Optimization Infrastructure ('ROI'). More information about 'MIPLIB'
can be found in the paper by Koch et al. available at
<http://mpc.zib.de/index.php/MPC/article/viewFile/56/28>.
The 'README.md' file illustrates how to use this package.
Author: Florian Schwendinger [aut, cre],
Stefan Theussl [aut]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.models.miplib versions 0.0-1 dated 2017-05-23 and 0.0-2 dated 2019-01-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/miplib.R | 33 ++++++++++++++++++++------------- README.md | 2 +- man/miplib_download.Rd | 9 +++++---- 5 files changed, 34 insertions(+), 26 deletions(-)
More information about ROI.models.miplib at CRAN
Permanent link
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 1.3.4 dated 2018-05-16 and 2.0.0 dated 2019-01-25
mvSLOUCH-1.3.4/mvSLOUCH/R/MVslouchSimulStudy.R |only mvSLOUCH-1.3.4/mvSLOUCH/R/grid.R |only mvSLOUCH-1.3.4/mvSLOUCH/R/ouch2slouch.mvsl.R |only mvSLOUCH-1.3.4/mvSLOUCH/R/sdemomentsphyl.R |only mvSLOUCH-1.3.4/mvSLOUCH/R/treeDists.R |only mvSLOUCH-2.0.0/mvSLOUCH/DESCRIPTION | 33 mvSLOUCH-2.0.0/mvSLOUCH/MD5 | 89 - mvSLOUCH-2.0.0/mvSLOUCH/NAMESPACE | 18 mvSLOUCH-2.0.0/mvSLOUCH/R/PhyloSDEestim.R | 834 ++++++++--- mvSLOUCH-2.0.0/mvSLOUCH/R/bootstrap.R |only mvSLOUCH-2.0.0/mvSLOUCH/R/ci.R | 348 ++-- mvSLOUCH-2.0.0/mvSLOUCH/R/estimBM.R | 282 +++- mvSLOUCH-2.0.0/mvSLOUCH/R/estimGLSGC.R | 226 +-- mvSLOUCH-2.0.0/mvSLOUCH/R/estimMAXLIK.R | 229 --- mvSLOUCH-2.0.0/mvSLOUCH/R/evolmodelest.R | 631 ++++++-- mvSLOUCH-2.0.0/mvSLOUCH/R/fitch.mvsl.R | 42 mvSLOUCH-2.0.0/mvSLOUCH/R/getESS.R | 339 +++- mvSLOUCH-2.0.0/mvSLOUCH/R/loglik.R | 407 ++++- mvSLOUCH-2.0.0/mvSLOUCH/R/make.states.mvsl.R | 9 mvSLOUCH-2.0.0/mvSLOUCH/R/matrixexps.R | 50 mvSLOUCH-2.0.0/mvSLOUCH/R/matrixparametrizations.R | 68 mvSLOUCH-2.0.0/mvSLOUCH/R/modelparams.R | 191 +- mvSLOUCH-2.0.0/mvSLOUCH/R/modelparamssummary.R | 473 ++++-- mvSLOUCH-2.0.0/mvSLOUCH/R/modelparamstransform.R | 663 ++++++++- mvSLOUCH-2.0.0/mvSLOUCH/R/phylgls.R | 914 ++++++++----- mvSLOUCH-2.0.0/mvSLOUCH/R/phyltree_paths.R |only mvSLOUCH-2.0.0/mvSLOUCH/R/precalcs.R | 212 +-- mvSLOUCH-2.0.0/mvSLOUCH/R/regimes.R | 291 ++++ mvSLOUCH-2.0.0/mvSLOUCH/R/sdecovariancephyl.R |only mvSLOUCH-2.0.0/mvSLOUCH/R/sdemoments.R | 57 mvSLOUCH-2.0.0/mvSLOUCH/R/simulVasicekproc.R | 19 mvSLOUCH-2.0.0/mvSLOUCH/R/simulVasicekprocphyl.R | 213 +-- mvSLOUCH-2.0.0/mvSLOUCH/R/trees2slouch.mvsl.R |only mvSLOUCH-2.0.0/mvSLOUCH/R/wrappers.R | 172 ++ mvSLOUCH-2.0.0/mvSLOUCH/man/BrownianMotionModel.Rd | 138 + mvSLOUCH-2.0.0/mvSLOUCH/man/SummarizeBM.Rd | 116 - mvSLOUCH-2.0.0/mvSLOUCH/man/SummarizeMVSLOUCH.Rd | 172 +- mvSLOUCH-2.0.0/mvSLOUCH/man/SummarizeOUCH.Rd | 159 +- mvSLOUCH-2.0.0/mvSLOUCH/man/drawPhylProcess.Rd | 35 mvSLOUCH-2.0.0/mvSLOUCH/man/estimate.evolutionary.model.Rd | 294 +++- mvSLOUCH-2.0.0/mvSLOUCH/man/fitch.mvsl.Rd | 47 mvSLOUCH-2.0.0/mvSLOUCH/man/generate.model.setups.Rd | 14 mvSLOUCH-2.0.0/mvSLOUCH/man/mvSLOUCH-internal.Rd | 275 ++- mvSLOUCH-2.0.0/mvSLOUCH/man/mvSLOUCH-package.Rd | 99 - mvSLOUCH-2.0.0/mvSLOUCH/man/mvslouchModel.Rd | 356 +++-- mvSLOUCH-2.0.0/mvSLOUCH/man/ouchModel.Rd | 292 ++-- mvSLOUCH-2.0.0/mvSLOUCH/man/parametric.bootstrap.Rd |only mvSLOUCH-2.0.0/mvSLOUCH/man/phyltree_paths.Rd |only mvSLOUCH-2.0.0/mvSLOUCH/man/simulBMProcPhylTree.Rd | 84 - mvSLOUCH-2.0.0/mvSLOUCH/man/simulMVSLOUCHProcPhylTree.Rd | 83 - mvSLOUCH-2.0.0/mvSLOUCH/man/simulOUCHProcPhylTree.Rd | 82 - 51 files changed, 6035 insertions(+), 3021 deletions(-)
Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into mindmap widgets or files ('.mm'), and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between mindr versions 1.1.9 dated 2018-12-16 and 1.2.0 dated 2019-01-25
DESCRIPTION | 12 - MD5 | 35 ++- NAMESPACE | 3 R/internal.R | 222 ++++++++++++++++++++++ R/mindr.R | 451 ++++++++++++++++++++++++++++++++++++---------- inst/examples/r/rmd2r.Rmd | 1 inst/examples/xuer |only inst/resource |only man/count_space.Rd |only man/dir2.Rd | 22 +- man/dir4.Rd |only man/get_filename_ext.Rd |only man/markmap.Rd | 7 man/md2mm.Rd | 6 man/mm.Rd |only man/mm2r.Rd | 6 man/r2mm.Rd | 6 man/r2rmd.Rd | 4 man/rmd2r.Rd | 6 man/tree.Rd |only man/tree2mm.Rd | 4 21 files changed, 656 insertions(+), 129 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 1.2 dated 2017-09-14 and 1.3 dated 2019-01-25
DESCRIPTION | 7 - MD5 | 20 ++-- inst/CITATION | 30 +++--- inst/NEWS | 5 + man/mams.Rd | 225 ++++++++++++++++++++++++------------------------- man/mams.sim.Rd | 183 ++++++++++++++++++++------------------- man/new.bounds.Rd | 178 ++++++++++++++++++++------------------ man/ordinal.mams.Rd | 158 +++++++++++++++++----------------- man/stepdown.mams.Rd | 147 ++++++++++++++++---------------- man/stepdown.update.Rd | 181 ++++++++++++++++++++------------------- man/tite.mams.Rd | 147 ++++++++++++++++---------------- 11 files changed, 658 insertions(+), 623 deletions(-)
Title: Generate Assorted Books and Documents with R 'bookdown' Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in 'YAML' and 'LaTeX'.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between bookdownplus versions 1.5.4 dated 2018-12-16 and 1.5.5 dated 2019-01-25
DESCRIPTION | 8 +++---- MD5 | 10 ++++----- R/fun.R | 53 +++++++++++++++++++++++----------------------------- R/internal.R | 2 - man/bd.Rd | 4 ++- man/bookdownplus.Rd | 11 +++++++++- 6 files changed, 47 insertions(+), 41 deletions(-)
Title: Download and Manage Data from Tehran Stock Exchange
Description: Tools for downloading and organizing data from Tehran Stock Exchange (TSE) <http://new.tse.ir/en/>. It also performs some descriptive data analysis for assets.
Author: Ali Saeb
Maintainer: Ali Saeb <ali.saeb@gmail.com>
Diff between TSEtools versions 0.1.1 dated 2018-04-21 and 0.1.2 dated 2019-01-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/mcPrt.R | 19 ++++++++++++++----- README.md | 4 ++++ man/mcPrt.Rd | 8 ++++---- 6 files changed, 32 insertions(+), 18 deletions(-)
Title: 'optimx' Plug-in for the 'R' Optimization Infrastructure
Description: Enhances the R Optimization Infrastructure ('ROI') package
with the 'optimx' package.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.optimx versions 0.3-0 dated 2017-10-22 and 0.3-2 dated 2019-01-25
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/zzz.R | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-)
More information about ROI.plugin.optimx at CRAN
Permanent link
Title: Plot Publication-Grade Gene and Genome Maps
Description: Draws gene or genome maps and comparisons between these, in a
publication-grade manner. Starting from simple, common files, it will
draw postscript or PDF files that can be sent as such to journals.
Author: Lionel Guy <lionel.guy@imbim.uu.se>
Maintainer: Lionel Guy <lionel.guy@imbim.uu.se>
Diff between genoPlotR versions 0.8.7 dated 2017-11-06 and 0.8.9 dated 2019-01-25
DESCRIPTION | 13 +++++-------- MD5 | 29 +++++++++++++++-------------- NEWS | 11 +++++++++++ R/annotation.R | 2 +- R/dna_seg.R | 2 +- R/grobs.R | 2 +- build/partial.rdb |only build/vignette.rds |binary data/barto.RData |binary data/chrY_subseg.RData |binary data/mauve_bbone.RData |binary data/three_genes.RData |binary inst/doc/genoPlotR.pdf |binary man/dna_seg.Rd | 6 ++---- man/gene_types.Rd | 4 ++-- man/genoPlotR-package.Rd | 28 +++++++++++----------------- 16 files changed, 49 insertions(+), 48 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 0.3.0 dated 2018-11-05 and 0.4.0 dated 2019-01-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/visvow.R | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Permutation Tests for Regression, (Repeated Measures)
ANOVA/ANCOVA and Comparison of Signals
Description: Functions to compute p-values based on permutation tests. Regression, ANOVA and ANCOVA, omnibus F-tests, marginal unilateral and bilateral t-tests are available. Several methods to handle nuisance variables are implemented (Kherad-Pajouh, S., & Renaud, O. (2010) <doi:10.1016/j.csda.2010.02.015> ; Kherad-Pajouh, S., & Renaud, O. (2014) <doi:10.1007/s00362-014-0617-3> ; Winkler, A. M., Ridgway, G. R., Webster, M. A., Smith, S. M., & Nichols, T. E. (2014) <doi:10.1016/j.neuroimage.2014.01.060>). An extension for the comparison of signals issued from experimental conditions (e.g. EEG/ERP signals) is provided. Several corrections for multiple testing are possible, including the cluster-mass statistic (Maris, E., & Oostenveld, R. (2007) <doi:10.1016/j.jneumeth.2007.03.024>) and the threshold-free cluster enhancement (Smith, S. M., & Nichols, T. E. (2009) <doi:10.1016/j.neuroimage.2008.03.061>).
Author: Jaromil Frossard [aut, cre],
Olivier Renaud [aut]
Maintainer: Jaromil Frossard <jaromil.frossard@unige.ch>
Diff between permuco versions 1.0.1 dated 2018-02-14 and 1.0.2 dated 2019-01-25
DESCRIPTION | 12 ++--- MD5 | 46 ++++++++++----------- NAMESPACE | 1 NEWS | 14 +++++- R/aovperm_fix.R | 2 R/aovperm_rnd.R | 2 R/cluster_fit_model.R | 19 +++++---- R/cluster_methods.R | 88 ++++++++++++++++++++++-------------------- R/cluster_private.R | 42 ++++++++++---------- R/clusterlm_fix.R | 88 ++++++++++++++++++++++++------------------ R/clusterlm_rnd.R | 9 ++-- R/fit_model.R | 12 ++--- R/lmperm_fix.R | 6 +- R/methods.R | 40 ------------------- R/private.R | 20 ++++----- README.md | 20 ++++++--- build/vignette.rds |binary inst/doc/permuco_tutorial.pdf |binary man/aovperm.Rd | 2 man/clusterlm.Rd | 19 +++++---- man/lmperm.Rd | 10 ++-- man/plot.clusterlm.Rd | 14 ++++-- man/print.clusterlm.Rd | 6 +- man/summary.clusterlm.Rd | 4 - 24 files changed, 245 insertions(+), 231 deletions(-)
Title: Modified Versions of Mann Kendall and Spearman's Rho Trend Tests
Description: Power of non-parametric Mann-Kendall test and Spearman’s Rho test is highly influenced by serially correlated data. To address this issue, trend tests may applied on the modified versions of the time series data by Block Bootstrapping (BBS), Prewhitening (PW) , Trend Free Prewhitening (TFPW), Bias Corrected Prewhitening and Variance Correction Approach by calculating effective sample size.
Mann, H. B. (1945).<doi:10.1017/CBO9781107415324.004>.
Kendall, M. (1975). Multivariate analysis. Charles Griffin&Company Ltd,.
sen, P. K. (1968).<doi:10.2307/2285891>.
Önöz, B., & Bayazit, M. (2012) <doi:10.1002/hyp.8438>.
Hamed, K. H. (2009).<doi:10.1016/j.jhydrol.2009.01.040>.
Yue, S., & Wang, C. Y. (2002) <doi:10.1029/2001WR000861>.
Yue, S., Pilon, P., Phinney, B., & Cavadias, G. (2002) <doi:10.1002/hyp.1095>.
Hamed, K. H., & Ramachandra Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>.
Yue, S., & Wang, C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>.
Author: Sandeep Kumar Patakamuri [aut, cre],
Nicole O'Brien [aut, ctb]
Maintainer: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>
Diff between modifiedmk versions 1.2.0 dated 2018-11-06 and 1.3.0 dated 2019-01-25
modifiedmk-1.2.0/modifiedmk/man/bbsmK.Rd |only modifiedmk-1.3.0/modifiedmk/DESCRIPTION | 8 modifiedmk-1.3.0/modifiedmk/MD5 | 20 - modifiedmk-1.3.0/modifiedmk/NAMESPACE | 3 modifiedmk-1.3.0/modifiedmk/R/bbsmk.R | 37 +- modifiedmk-1.3.0/modifiedmk/R/bbssr.R | 22 - modifiedmk-1.3.0/modifiedmk/R/bcpw.R | 14 modifiedmk-1.3.0/modifiedmk/R/pbmk.R |only modifiedmk-1.3.0/modifiedmk/README.md | 15 modifiedmk-1.3.0/modifiedmk/inst/doc/my-vignette.html | 272 +++++++++++++++++- modifiedmk-1.3.0/modifiedmk/man/bbsmk.Rd |only modifiedmk-1.3.0/modifiedmk/man/bbssr.Rd | 4 modifiedmk-1.3.0/modifiedmk/man/pbmk.Rd |only 13 files changed, 334 insertions(+), 61 deletions(-)
Title: Variable Selection for Heterogeneous Populations
Description: Provides variable selection and estimation routines for models
with main effects stratified on multiple binary factors. The 'vennLasso' package
is an implementation of the method introduced in Huling, et al. (2017) <doi:10.1111/biom.12769>.
Author: Jared Huling [aut, cre] (<https://orcid.org/0000-0003-0670-4845>),
Muxuan Liang [ctb],
Yixuan Qiu [cph],
Gael Guennebaud [cph],
Ray Gardner [cph],
Jitse Niesen [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between vennLasso versions 0.1.4 dated 2019-01-10 and 0.1.5 dated 2019-01-25
DESCRIPTION | 6 +- MD5 | 24 ++++----- R/cv_vennLasso.R | 2 R/vennLasso.R | 2 inst/doc/using_the_vennLasso_package.pdf |binary man/cv.vennLasso.Rd | 2 man/vennLasso.Rd | 2 src/ADMMogLassoCoxPHTall.h | 8 ++- src/ADMMogLassoLogisticTall.h | 8 ++- src/ADMMogLassoLogisticWide.h | 8 ++- src/ADMMogLassoTall.h | 68 +++++++++++++++++++++++--- src/ADMMogLassoWide.h | 1 src/FADMMBase.h | 79 ++++++++++++++++++------------- 13 files changed, 151 insertions(+), 59 deletions(-)
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd
Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The
Statistical Sleuth: A Course in Methods of Data Analysis (3rd
ed)", Cengage Learning.
Author: Original by F.L. Ramsey and D.W. Schafer;
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin
A. Turlach; vignettes contributed by Nicholas Horton, Linda Loi,
Kate Aloisio and Ruobing Zhang, with corrections by Randall Pruim
Maintainer: Berwin A Turlach <Berwin.Turlach@gmail.com>
Diff between Sleuth3 versions 1.0-2.1 dated 2019-01-23 and 1.0-3 dated 2019-01-25
DESCRIPTION | 20 - MD5 | 394 +++++++++++++++++------------------ data/case0101.rda |binary data/case0102.rda |binary data/case0201.rda |binary data/case0202.rda |binary data/case0301.rda |binary data/case0302.rda |binary data/case0401.rda |binary data/case0402.rda |binary data/case0501.rda |binary data/case0502.rda |binary data/case0601.rda |binary data/case0602.rda |binary data/case0701.rda |binary data/case0702.rda |binary data/case0801.rda |binary data/case0802.rda |binary data/case0901.rda |binary data/case0902.rda |binary data/case1001.rda |binary data/case1002.rda |binary data/case1101.rda |binary data/case1102.rda |binary data/case1201.rda |binary data/case1202.rda |binary data/case1301.rda |binary data/case1302.rda |binary data/case1401.rda |binary data/case1402.rda |binary data/case1501.rda |binary data/case1502.rda |binary data/case1601.rda |binary data/case1602.rda |binary data/case1701.rda |binary data/case1702.rda |binary data/case1801.rda |binary data/case1802.rda |binary data/case1803.rda |binary data/case1901.rda |binary data/case1902.rda |binary data/case2001.rda |binary data/case2002.rda |binary data/case2101.rda |binary data/case2102.rda |binary data/case2201.rda |binary data/case2202.rda |binary data/ex0112.rda |binary data/ex0116.rda |binary data/ex0125.rda |binary data/ex0126.rda |binary data/ex0127.rda |binary data/ex0211.rda |binary data/ex0218.rda |binary data/ex0221.rda |binary data/ex0222.rda |binary data/ex0223.rda |binary data/ex0321.rda |binary data/ex0323.rda |binary data/ex0327.rda |binary data/ex0330.rda |binary data/ex0331.rda |binary data/ex0332.rda |binary data/ex0333.rda |binary data/ex0428.rda |binary data/ex0429.rda |binary data/ex0430.rda |binary data/ex0431.rda |binary data/ex0432.rda |binary data/ex0518.rda |binary data/ex0523.rda |binary data/ex0524.rda |binary data/ex0525.rda |binary data/ex0623.rda |binary data/ex0624.rda |binary data/ex0721.rda |binary data/ex0722.rda |binary data/ex0724.rda |binary data/ex0725.rda |binary data/ex0726.rda |binary data/ex0727.rda |binary data/ex0728.rda |binary data/ex0729.rda |binary data/ex0730.rda |binary data/ex0816.rda |binary data/ex0817.rda |binary data/ex0820.rda |binary data/ex0822.rda |binary data/ex0823.rda |binary data/ex0824.rda |binary data/ex0825.rda |binary data/ex0826.rda |binary data/ex0828.rda |binary data/ex0829.rda |binary data/ex0914.rda |binary data/ex0915.rda |binary data/ex0918.rda |binary data/ex0920.rda |binary data/ex0921.rda |binary data/ex0923.rda |binary data/ex1014.rda |binary data/ex1026.rda |binary data/ex1027.rda |binary data/ex1028.rda |binary data/ex1029.rda |binary data/ex1030.rda |binary data/ex1031.rda |binary data/ex1033.rda |binary data/ex1111.rda |binary data/ex1120.rda |binary data/ex1122.rda |binary data/ex1123.rda |binary data/ex1124.rda |binary data/ex1125.rda |binary data/ex1217.rda |binary data/ex1220.rda |binary data/ex1221.rda |binary data/ex1222.rda |binary data/ex1223.rda |binary data/ex1225.rda |binary data/ex1317.rda |binary data/ex1319.rda |binary data/ex1320.rda |binary data/ex1321.rda |binary data/ex1416.rda |binary data/ex1417.rda |binary data/ex1419.rda |binary data/ex1420.rda |binary data/ex1507.rda |binary data/ex1509.rda |binary data/ex1514.rda |binary data/ex1515.rda |binary data/ex1516.rda |binary data/ex1517.rda |binary data/ex1518.rda |binary data/ex1519.rda |binary data/ex1605.rda |binary data/ex1611.rda |binary data/ex1612.rda |binary data/ex1613.rda |binary data/ex1614.rda |binary data/ex1615.rda |binary data/ex1620.rda |binary data/ex1708.rda |binary data/ex1715.rda |binary data/ex1716.rda |binary data/ex1914.rda |binary data/ex1916.rda |binary data/ex1917.rda |binary data/ex1918.rda |binary data/ex1919.rda |binary data/ex1921.rda |binary data/ex1922.rda |binary data/ex1923.rda |binary data/ex2011.rda |binary data/ex2012.rda |binary data/ex2015.rda |binary data/ex2016.rda |binary data/ex2017.rda |binary data/ex2018.rda |binary data/ex2019.rda |binary data/ex2113.rda |binary data/ex2115.rda |binary data/ex2116.rda |binary data/ex2117.rda |binary data/ex2118.rda |binary data/ex2119.rda |binary data/ex2120.rda |binary data/ex2216.rda |binary data/ex2220.rda |binary data/ex2222.rda |binary data/ex2223.rda |binary data/ex2224.rda |binary data/ex2225.rda |binary data/ex2226.rda |binary data/ex2414.rda |binary inst/doc/Sleuth3-manual.pdf |binary inst/doc/chapter01-HortonMosaic.pdf |binary inst/doc/chapter02-HortonMosaic.pdf |binary inst/doc/chapter03-HortonMosaic.pdf |binary inst/doc/chapter04-HortonMosaic.pdf |binary inst/doc/chapter05-HortonMosaic.pdf |binary inst/doc/chapter06-HortonMosaic.pdf |binary inst/doc/chapter07-HortonMosaic.pdf |binary inst/doc/chapter08-HortonMosaic.pdf |binary inst/doc/chapter09-HortonMosaic.pdf |binary inst/doc/chapter10-HortonMosaic.pdf |binary inst/doc/chapter11-HortonMosaic.Rnw | 20 - inst/doc/chapter11-HortonMosaic.pdf |binary inst/doc/chapter12-HortonMosaic.R | 2 inst/doc/chapter12-HortonMosaic.Rnw | 2 inst/doc/chapter12-HortonMosaic.pdf |binary inst/doc/chapter13-HortonMosaic.pdf |binary man/ex0820.Rd | 2 man/ex1028.Rd | 2 man/ex1029.Rd | 8 vignettes/chapter11-HortonMosaic.Rnw | 20 - vignettes/chapter12-HortonMosaic.Rnw | 2 198 files changed, 234 insertions(+), 238 deletions(-)
Title: Generate PMML for Various Models
Description: The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms. The package isofor (used for anomaly detection) can be installed with devtools::install_github("Zelazny7/isofor").
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler
(arules), Software AG, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha,
Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@softwareag.com>
Diff between pmml versions 1.5.6 dated 2018-10-08 and 1.5.7 dated 2019-01-25
DESCRIPTION | 10 MD5 | 20 - NAMESPACE | 1 R/functionToPMML.R | 3 R/pmml.R | 331 +++++++++++++++++++++- R/pmml.iForest.R |only R/pmml.svm.R | 748 ++++++++++++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/ChangeLog | 5 man/functionToPMML.Rd | 3 man/pmml.iForest.Rd |only man/pmml.svm.Rd | 147 ++++++--- 12 files changed, 967 insertions(+), 301 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data.
Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.75 dated 2018-11-17 and 1.76 dated 2019-01-25
fungible-1.75/fungible/inst/doc |only fungible-1.76/fungible/DESCRIPTION | 29 +++++++++++++++++------------ fungible-1.76/fungible/MD5 | 27 +++++++++++++++++++++------ fungible-1.76/fungible/NAMESPACE | 2 +- fungible-1.76/fungible/R/Omega.R |only fungible-1.76/fungible/R/SLi.R |only fungible-1.76/fungible/R/SchmidLeiman.R |only fungible-1.76/fungible/R/cosMAT.R |only fungible-1.76/fungible/R/faAlign.R | 6 +++++- fungible-1.76/fungible/R/faX.R |only fungible-1.76/fungible/R/fals.R | 12 ++++++------ fungible-1.76/fungible/R/fapa.R |only fungible-1.76/fungible/R/promaxQ.R |only fungible-1.76/fungible/R/rotate.R |only fungible-1.76/fungible/inst/CITATION | 8 ++++---- fungible-1.76/fungible/man/Omega.Rd |only fungible-1.76/fungible/man/SLi.Rd |only fungible-1.76/fungible/man/SchmidLeiman.Rd |only fungible-1.76/fungible/man/cosMat.Rd |only fungible-1.76/fungible/man/faX.Rd |only fungible-1.76/fungible/man/fapa.Rd |only fungible-1.76/fungible/man/promaxQ.Rd |only fungible-1.76/fungible/man/rotate.Rd |only 23 files changed, 54 insertions(+), 30 deletions(-)
Title: 'ROI' Optimization Problems Based on 'NETLIB-LP'
Description: A collection of 'ROI' optimization problems based on the 'NETLIB-LP' collection.
'Netlib' is a software repository, which amongst many other software for scientific computing contains a collection of linear programming problems. The purpose of this package is to make
this problems easily accessible from 'R' as 'ROI' optimization problems.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.models.netlib versions 1.0 dated 2016-12-22 and 1.1 dated 2019-01-25
DESCRIPTION | 7 +++---- MD5 | 6 +++--- inst/roi_op/metainfo.rds |binary man/netlib.Rd | 6 +++--- 4 files changed, 9 insertions(+), 10 deletions(-)
More information about ROI.models.netlib at CRAN
Permanent link
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 3.1.8 dated 2018-11-19 and 3.2.0 dated 2019-01-25
DESCRIPTION | 8 - MD5 | 107 +++++++------- NAMESPACE | 14 + NEWS | 27 +++ R/Fewstervarn.R |only R/derivedMS.R | 143 +++++++++++++------ R/derivedStratified.R |only R/empirical.R | 320 ++++++++++++++++++------------------------- R/make.mask.R | 12 + R/methods.R | 85 +++++++---- R/pdot.R | 35 ++-- R/plot.popn.R | 5 R/plot.secr.R | 3 R/plot.traps.R | 59 ++++--- R/reduce.R | 48 +++--- R/secrloglik.R | 4 R/split.capthist.R | 41 ----- R/split.mask.R |only R/summary.secr.R | 4 R/trap.builder.R | 161 +++++++++++++-------- R/utility.R | 34 ++++ R/write.traps.R | 3 build/vignette.rds |binary data/OVpossum.RData |binary data/deermouse.RData |binary data/hornedlizard.RData |binary data/housemouse.RData |binary data/ovenbird.RData |binary data/ovensong.RData |binary data/possum.RData |binary data/secrdemo.RData |binary data/skink.RData |binary data/stoatDNA.RData |binary inst/doc/secr-datainput.R | 25 +-- inst/doc/secr-datainput.Rmd | 76 ++++------ inst/doc/secr-datainput.pdf |binary inst/doc/secr-overview.Rmd | 18 +- inst/doc/secr-overview.pdf |binary man/contour.Rd | 6 man/derivedMS.Rd | 12 + man/empirical.Rd | 118 +++++++++++---- man/esaplot.Rd | 6 man/esaplotsecr.Rd | 5 man/homerange.Rd | 11 + man/make.systematic.Rd | 20 ++ man/plot.popn.Rd | 2 man/plot.traps.Rd | 2 man/secr-package.Rd | 4 man/subset.mask.Rd | 14 + man/summary.capthist.Rd | 8 - man/trap.builder.Rd | 36 +++- src/secr.c | 136 +++++++++++------- src/secr.h | 8 - src/sighting.c | 46 +++--- vignettes/secr-datainput.Rmd | 76 ++++------ vignettes/secr-overview.Rmd | 18 +- 56 files changed, 1028 insertions(+), 732 deletions(-)
Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with
'Socrata' open data portals <http://dev.socrata.com>.
Users can provide a 'Socrata' data set resource URL,
or a 'Socrata' Open Data API (SoDA) web query,
or a 'Socrata' "human-friendly" URL,
returns an R data frame. Converts dates to 'POSIX'
format and manages throttling by 'Socrata'.
Users can upload data to 'Socrata' portals directly
from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>
Diff between RSocrata versions 1.7.4-7 dated 2017-12-21 and 1.7.5-3 dated 2019-01-25
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/RSocrata.R | 1 + man/read.socrata.Rd | 1 + man/write.socrata.Rd | 4 ++-- tests/testthat/test-all.R | 4 ++-- 6 files changed, 16 insertions(+), 14 deletions(-)