Sat, 30 Jun 2018

Package GuardianR updated to version 0.9 with previous version 0.8 dated 2016-10-18

Title: The Guardian API Wrapper
Description: Provides an interface to the Open Platform's Content API of the Guardian Media Group. It retrieves content from news outlets The Observer, The Guardian, and guardian.co.uk from 1999 to current day.
Author: Marco Bastos [aut, cre], Cornelius Puschmann [aut], Mark Johnman [ctb]
Maintainer: Marco Bastos <marco@toledobastos.com>

Diff between GuardianR versions 0.8 dated 2016-10-18 and 0.9 dated 2018-06-30

 ChangeLog                |   63 +++++++++++++++++++++++------------------------
 DESCRIPTION              |    8 ++---
 MD5                      |   11 ++++----
 R/guardianr.R            |    4 +-
 README.md                |only
 man/GuardianR-package.Rd |    6 ++--
 man/get_guardian.Rd      |    2 -
 7 files changed, 48 insertions(+), 46 deletions(-)

More information about GuardianR at CRAN
Permanent link

Package BART updated to version 1.8 with previous version 1.7 dated 2018-06-08

Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut], Rodney Sparapani [aut, cre], Robert Gramacy [aut], Charles Spanbauer [aut], Matthew Pratola [aut], Bill Venables [ctb], Brian Ripley [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>

Diff between BART versions 1.7 dated 2018-06-08 and 1.8 dated 2018-06-30

 BART-1.7/BART/R/predict.crskmbart.R      |only
 BART-1.7/BART/R/r_lefttruncnorm.R        |only
 BART-1.7/BART/R/rs.wbart.R               |only
 BART-1.7/BART/inst/include               |only
 BART-1.7/BART/src/rn.h.bad               |only
 BART-1.8/BART/DESCRIPTION                |    8 ++---
 BART-1.8/BART/MD5                        |   43 +++++++++----------------------
 BART-1.8/BART/NAMESPACE                  |    6 ----
 BART-1.8/BART/NEWS                       |    6 ++++
 BART-1.8/BART/R/mc.recur.pwbart.R        |    2 -
 BART-1.8/BART/cleanup                    |    3 +-
 BART-1.8/BART/cleanup.win                |    3 +-
 BART-1.8/BART/inst/doc/bincat.pdf        |binary
 BART-1.8/BART/inst/doc/computing.pdf     |binary
 BART-1.8/BART/inst/doc/cont1.pdf         |binary
 BART-1.8/BART/inst/doc/cont2.pdf         |binary
 BART-1.8/BART/inst/doc/hwbart.pdf        |binary
 BART-1.8/BART/inst/doc/time-to-event.pdf |binary
 BART-1.8/BART/src/init.c                 |   10 ++++---
 19 files changed, 35 insertions(+), 46 deletions(-)

More information about BART at CRAN
Permanent link

Package TSA updated to version 1.2 with previous version 1.01 dated 2012-11-13

Title: Time Series Analysis
Description: Contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.
Author: Kung-Sik Chan, Brian Ripley
Maintainer: Kung-Sik Chan <kungsik.chan@gmail.com>

Diff between TSA versions 1.01 dated 2012-11-13 and 1.2 dated 2018-06-30

 TSA-1.01/TSA/changes                |only
 TSA-1.2/TSA/ChangeLog               |only
 TSA-1.2/TSA/DESCRIPTION             |   18 
 TSA-1.2/TSA/MD5                     |   90 +-
 TSA-1.2/TSA/NAMESPACE               |  111 ++-
 TSA-1.2/TSA/R/ARMAspec.R            |    3 
 TSA-1.2/TSA/R/BoxCox.ar.R           |    3 
 TSA-1.2/TSA/R/Keenan.test.R         |    3 
 TSA-1.2/TSA/R/LB.test.R             |    3 
 TSA-1.2/TSA/R/McLeod.Li.test.R      |    3 
 TSA-1.2/TSA/R/Tsay.test.R           |    3 
 TSA-1.2/TSA/R/acf.R                 |   12 
 TSA-1.2/TSA/R/arima.R               | 1321 +++++++++++++++++-------------------
 TSA-1.2/TSA/R/arima.boot.R          |    7 
 TSA-1.2/TSA/R/arimax.R              | 1258 ++++++++++++++++------------------
 TSA-1.2/TSA/R/armasubsets.R         |    4 
 TSA-1.2/TSA/R/detectAO.R            |    5 
 TSA-1.2/TSA/R/detectIO.R            |    3 
 TSA-1.2/TSA/R/eacf.R                |    3 
 TSA-1.2/TSA/R/fitted.Arimax.R       |    3 
 TSA-1.2/TSA/R/gBox.R                |  190 ++---
 TSA-1.2/TSA/R/garch.sim.R           |    3 
 TSA-1.2/TSA/R/harmonic.R            |    3 
 TSA-1.2/TSA/R/kurtosis.R            |    3 
 TSA-1.2/TSA/R/lagplot.R             |    5 
 TSA-1.2/TSA/R/periodogram.R         |    3 
 TSA-1.2/TSA/R/plot.Arima.R          |    3 
 TSA-1.2/TSA/R/plot.armasubsets.R    |    3 
 TSA-1.2/TSA/R/predict.TAR.R         |    3 
 TSA-1.2/TSA/R/prewhiten.R           |   16 
 TSA-1.2/TSA/R/qar.sim.R             |    3 
 TSA-1.2/TSA/R/rstandard.Arima.R     |    9 
 TSA-1.2/TSA/R/runs.R                |    3 
 TSA-1.2/TSA/R/season.R              |    3 
 TSA-1.2/TSA/R/skewness.R            |    3 
 TSA-1.2/TSA/R/spec.R                |    3 
 TSA-1.2/TSA/R/summary.armasubsets.R |    1 
 TSA-1.2/TSA/R/tar.R                 |  357 ++++-----
 TSA-1.2/TSA/R/tar.sim.R             |    3 
 TSA-1.2/TSA/R/tar.skeleton.R        |    3 
 TSA-1.2/TSA/R/tlrt.R                |    3 
 TSA-1.2/TSA/R/tsdiag.Arima.R        |    3 
 TSA-1.2/TSA/R/tsdiag.TAR.R          |    1 
 TSA-1.2/TSA/R/zlag.R                |    3 
 TSA-1.2/TSA/man/ARMAspec.Rd         |    2 
 TSA-1.2/TSA/man/gBox.Rd             |    4 
 TSA-1.2/TSA/man/tsdiag.Arima.Rd     |   10 
 47 files changed, 1759 insertions(+), 1740 deletions(-)

More information about TSA at CRAN
Permanent link

Package tdthap updated to version 1.1-9 with previous version 1.1-7 dated 2013-12-10

Title: TDT Tests for Extended Haplotypes
Description: Functions and examples are provided for Transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". Amer. J. Hum. Genet., 65:1161-1169, <doi:10.1086/302566>.
Author: David Clayton
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>

Diff between tdthap versions 1.1-7 dated 2013-12-10 and 1.1-9 dated 2018-06-30

 tdthap-1.1-7/tdthap/inst/doc/tdthap-paper.R                            |only
 tdthap-1.1-9/tdthap/ChangeLog                                          |   12 ++++++
 tdthap-1.1-9/tdthap/DESCRIPTION                                        |   18 ++++++----
 tdthap-1.1-9/tdthap/MD5                                                |   16 +++++---
 tdthap-1.1-9/tdthap/NAMESPACE                                          |    1 
 tdthap-1.1-9/tdthap/build                                              |only
 tdthap-1.1-9/tdthap/inst/doc/tdthap-paper.Rnw                          |    1 
 tdthap-1.1-9/tdthap/inst/doc/tdthap-paper.pdf                          |binary
 tdthap-1.1-9/tdthap/inst/tests/references.txt                          |only
 tdthap-1.1-9/tdthap/src/package_native_routine_registration_skeleton.c |only
 tdthap-1.1-9/tdthap/vignettes/tdthap-paper.Rnw                         |    1 
 11 files changed, 33 insertions(+), 16 deletions(-)

More information about tdthap at CRAN
Permanent link

Package scrm updated to version 1.7.2-4 with previous version 1.7.2-3 dated 2018-06-18

Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cph, ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab <develop@paulstaab.de>

Diff between scrm versions 1.7.2-3 dated 2018-06-18 and 1.7.2-4 dated 2018-06-30

 DESCRIPTION                    |    6 +++---
 MD5                            |   12 ++++++------
 NEWS                           |    8 ++++++++
 inst/doc/scrm-Arguments.html   |    4 ++--
 inst/doc/scrm-TreesForApe.html |    4 ++--
 src/scrm/node_container.cc     |    3 +++
 tests/testthat/test-scrm.R     |    6 ++++++
 7 files changed, 30 insertions(+), 13 deletions(-)

More information about scrm at CRAN
Permanent link

Package rbcb updated to version 0.1.5 with previous version 0.1.4 dated 2018-06-01

Title: R Interface to Brazilian Central Bank Web Services
Description: The Brazilian Central Bank API delivers many datasets which regard economic activity, regional economy, international economy, public finances, credit indicators and many more. For more information please see <http://dadosabertos.bcb.gov.br/>. These datasets can be accessed through 'rbcb' functions and can be obtained in different data structures common to R ('tibble', 'data.frame', 'xts', ...).
Author: Wilson Freitas <wilson.freitas@gmail.com>
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>

Diff between rbcb versions 0.1.4 dated 2018-06-01 and 0.1.5 dated 2018-06-30

 DESCRIPTION                                     |    6 
 MD5                                             |   18 
 NAMESPACE                                       |    9 
 NEWS                                            |    6 
 R/currency_helpers.R                            |only
 R/rbcb_get_market_expectations.R                |  444 ++++++++++++++++++++----
 README.md                                       |  297 ++++++++--------
 man/get_annual_market_expectations.Rd           |    2 
 man/get_top5s_annual_market_expectations.Rd     |only
 man/get_top5s_monthly_market_expectations.Rd    |only
 man/get_twelve_months_inflation_expectations.Rd |only
 man/helpers.Rd                                  |only
 tests/testthat/test-12-months-inflation.R       |only
 13 files changed, 559 insertions(+), 223 deletions(-)

More information about rbcb at CRAN
Permanent link

Package rangeMapper updated to version 0.3-4 with previous version 0.3-3 dated 2018-05-17

Title: A Platform for the Study of Macro-Ecology of Life History Traits
Description: Tools for easy generation of (life-history) traits maps based on species range (extent-of-occurrence) maps.
Author: Mihai Valcu [aut, cre], James Dale [aut], Joan Maspons [ctb]
Maintainer: Mihai Valcu <valcu@orn.mpg.de>

Diff between rangeMapper versions 0.3-3 dated 2018-05-17 and 0.3-4 dated 2018-06-30

 DESCRIPTION                                |    6 ++--
 MD5                                        |   34 ++++++++++++------------
 NEWS                                       |    6 ++++
 R/MapPlot-methods.R                        |    5 ++-
 R/MapProcess-methods.R                     |    7 ++--
 R/MapSave-methods.R                        |   11 +++----
 R/assemblageFetch-methods.R                |    2 -
 R/rangeMapper-ramp.R                       |   41 ++++++++++++++---------------
 build/vignette.rds                         |binary
 inst/doc/Appendix_S2_Valcu_et_al_2012.html |   14 ++++-----
 inst/doc/Appendix_S3_Valcu_et_al_2012.html |   14 ++++-----
 inst/doc/Appendix_S4_Valcu_et_al_2012.html |    4 +-
 inst/doc/Appendix_S5_Valcu_et_al_2012.html |   14 ++++-----
 man/assemblageFetch.Rd                     |    2 -
 man/plot-rmap.frame-missing-method.Rd      |    5 ++-
 man/processRanges.Rd                       |    5 ++-
 man/ramp.Rd                                |    7 ++--
 man/rangeMap.save.Rd                       |    8 ++---
 18 files changed, 96 insertions(+), 89 deletions(-)

More information about rangeMapper at CRAN
Permanent link

Package lmm updated to version 1.2 with previous version 1.0 dated 2015-02-10

Title: Linear Mixed Models
Description: It implements Expectation/Conditional Maximization Either (ECME) and rapidly converging algorithms as well as Bayesian inference for linear mixed models, which is described in Schafer, J.L. (1998) "Some improved procedures for linear mixed models". Dept. of Statistics, The Pennsylvania State University.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao <jinghuazhao@hotmail.com>

Diff between lmm versions 1.0 dated 2015-02-10 and 1.2 dated 2018-06-30

 ChangeLog                                          |    7 +++
 DESCRIPTION                                        |   19 ++++++---
 MD5                                                |   19 +++++----
 R/lmm.R                                            |    1 
 build/vignette.rds                                 |binary
 inst/doc/lmm-tr.Rnw                                |    3 -
 inst/doc/lmm-tr.pdf                                |binary
 man/example.Rd                                     |    2 -
 src/lmm.f                                          |   42 ++++++++++-----------
 src/package_native_routine_registration_skeleton.c |only
 vignettes/lmm-tr.Rnw                               |    3 -
 11 files changed, 54 insertions(+), 42 deletions(-)

More information about lmm at CRAN
Permanent link

Package biolink updated to version 0.1.6 with previous version 0.1.5 dated 2018-05-23

Title: Create Hyperlinks to Biological Databases and Resources
Description: Generate urls and hyperlinks to commonly used biological databases and resources based on standard identifiers. This is primarily useful when writing dynamic reports that reference things like gene symbols in text or tables, allowing you to, for example, convert gene identifiers to hyperlinks pointing to their entry in the NCBI Gene database. Currently supports NCBI Gene, PubMed, Gene Ontology, CRAN and Bioconductor.
Author: Aaron Wolen [aut, cre]
Maintainer: Aaron Wolen <aaron@wolen.com>

Diff between biolink versions 0.1.5 dated 2018-05-23 and 0.1.6 dated 2018-06-30

 DESCRIPTION                        |    6 +++---
 MD5                                |   14 +++++++-------
 tests/testthat/test-links-bioc.r   |    1 +
 tests/testthat/test-links-cran.r   |    1 +
 tests/testthat/test-links-entrez.r |    1 +
 tests/testthat/test-links-go.r     |    1 +
 tests/testthat/test-links-kegg.r   |    1 +
 tests/testthat/test-links-pubmed.r |    1 +
 8 files changed, 16 insertions(+), 10 deletions(-)

More information about biolink at CRAN
Permanent link

Package clustree (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-06-24 0.2.0
2018-04-19 0.1.2
2018-03-27 0.1.1

Permanent link
Package unfoldr updated to version 0.6.5 with previous version 0.6.1 dated 2017-10-25

Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding the joint size-shape-orientation distribution of spheroidal shaped particles.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@uni-jena.de>

Diff between unfoldr versions 0.6.1 dated 2017-10-25 and 0.6.5 dated 2018-06-30

 DESCRIPTION                    |   13 -
 MD5                            |   55 +++----
 NAMESPACE                      |    6 
 R/cylinder.R                   |   71 +++++++--
 R/sphere.R                     |   12 +
 R/spheroid.R                   |   63 +++++---
 R/unfolding.R                  |   15 +-
 R/unfoldr-package.R            |    6 
 data/data15p.rda               |binary
 man/cylinderIntersection.Rd    |only
 man/data15p.Rd                 |    4 
 man/setupSpheroidSystem.Rd     |    8 -
 man/simCylinderIntersection.Rd |only
 man/simCylinderSystem.Rd       |   16 +-
 man/simSphereSystem.Rd         |    5 
 man/simSpheroidIntersection.Rd |only
 man/simSpheroidSystem.Rd       |   20 +-
 man/verticalSection.Rd         |    5 
 src/GeometricPrimitives.cpp    |    4 
 src/GeometricPrimitives.h      |   11 -
 src/Intersector.h              |    1 
 src/Makevars                   |    2 
 src/SimCylinder.cpp            |  307 ++++++++++++++++++++++++++++++++++-------
 src/SimCylinder.h              |   12 +
 src/SimEllipsoid.cpp           |  183 ++++++++++++------------
 src/SimEllipsoid.h             |   13 -
 src/SimSphere.cpp              |   14 -
 src/Utils.cpp                  |   23 ++-
 src/Utils.h                    |    7 
 src/unfold.cpp                 |    3 
 30 files changed, 608 insertions(+), 271 deletions(-)

More information about unfoldr at CRAN
Permanent link

Package svMisc updated to version 1.1.0 with previous version 1.0-2 dated 2018-02-21

Title: SciViews - Miscellaneous Functions
Description: Miscellaneous functions for SciViews or general use: manage a temporary environment attached to the search path for temporary variables you do not want to save() or load(), test if Aqua, Mac, Win, ... Show progress bar, etc.
Author: Philippe Grosjean [aut, cre], Romain Francois [ctb], Kamil Barton [ctb]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>

Diff between svMisc versions 1.0-2 dated 2018-02-21 and 1.1.0 dated 2018-06-30

 DESCRIPTION                         |    8 ++++----
 MD5                                 |   14 +++++++++-----
 NAMESPACE                           |    8 ++++++++
 R/about.R                           |only
 R/subsettable.R                     |only
 R/svMisc-package.R                  |    3 ++-
 build/vignette.rds                  |binary
 inst/doc/temporary_environment.html |    4 ++--
 man/about.Rd                        |only
 man/subsettable.Rd                  |only
 10 files changed, 25 insertions(+), 12 deletions(-)

More information about svMisc at CRAN
Permanent link

Package RcppAlgos updated to version 2.0.3 with previous version 2.0.2 dated 2018-06-14

Title: Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp' for solving problems in combinatorics and computational mathematics. There are combination/permutations function that are both flexible as well as efficient with respect to speed and memory. There are optional constraint parameters that when utilized, generate all combinations/ permutations of a vector meeting specific criteria (e.g. finding all combinations such that the sum is less than a bound). These functions are capable of generating specific combinations/permutations (e.g. retrieve only the 50th lexicographical permutation of 5 elements choose 3) by utilizing the bounds arguments. This sets up nicely for parallelization and allows for fast generation of combinations/ permutations beyond 2^31 - 1 results as chunks are generated independently. All combinatorial functions are capable of handling multisets as well. Additionally, there are several highly efficient number theoretic functions that are useful for problems common in computational mathematics. These include various sieving functions that can quickly generate the following: prime numbers, number of coprime elements, number of divisors, prime factorizations, and complete factorizations. Some of these functions make use of the fast integer division library 'libdivide' by <http://ridiculousfish.com>. The primeSieve function is based on the segmented sieve of Eratosthenes implementation by Kim Walisch. It is capable of generating all primes less than a billion in just over 1 second. It can also quickly generate prime numbers over a range (e.g. primeSieve(10^13, 10^13+10^9)). There are stand-alone vectorized functions for general factoring (e.g. all divisors of number), primality testing, as well as prime factoring via Pollard's rho algorithm. Finally, there is a prime counting function that implements a simple variation of Legendre's formula based on the algorithm by Kim Walisch. It is capable of returning the number of primes below a trillion in under 0.5 seconds.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>

Diff between RcppAlgos versions 2.0.2 dated 2018-06-14 and 2.0.3 dated 2018-06-30

 DESCRIPTION                         |    9 ++++-----
 MD5                                 |   12 ++++++------
 NEWS                                |    6 +++++-
 src/Combinatorics.cpp               |   20 ++++++++++----------
 src/ConstraintsUtils.cpp            |    6 +++---
 tests/testthat/testComboGeneral.R   |    2 +-
 tests/testthat/testPermuteGeneral.R |    2 +-
 7 files changed, 30 insertions(+), 27 deletions(-)

More information about RcppAlgos at CRAN
Permanent link

New package pgbart with initial version 0.6.10
Package: pgbart
Type: Package
Title: Bayesian Additive Regression Trees Using Particle Gibbs Sampler and Gibbs/Metropolis-Hastings Sampler
Version: 0.6.10
Authors@R: c(person("Pingyu","Wang", role = c("aut", "cre"),email = "applewangpingyu@gmail.com"), person("Dai","Feng", role = "aut",email = "dai_feng@merck.com"), person("Yang","Bai", role = "aut",email = "by0132@live.cn"), person("Qiuyue","Shi", role = "aut",email = "shiqiuyue@bupt.edu.cn"), person("Zhicheng","Zhao", role = "aut",email = "zhaozc@bupt.edu.cn"), person("Fei","Su", role = "aut",email = "sufei@bupt.edu.cn"), person("Hugh","Chipman", role = "aut",email = "hugh.chipman@gmail.com"), person("Robert","McCulloch", role = "aut",email = "robert.e.mcculloch@gmail.com"))
Author: Pingyu Wang [aut, cre], Dai Feng [aut], Yang Bai [aut], Qiuyue Shi [aut], Zhicheng Zhao [aut], Fei Su [aut], Hugh Chipman [aut], Robert McCulloch [aut]
Maintainer: Pingyu Wang <applewangpingyu@gmail.com>
Description: The Particle Gibbs sampler and Gibbs/Metropolis-Hastings sampler were implemented to fit Bayesian additive regression tree model. Construction of the model (training) and prediction for a new data set (testing) can be separated. Our reference paper is: Lakshminarayanan B, Roy D, Teh Y W. Particle Gibbs for Bayesian additive regression trees[C], Artificial Intelligence and Statistics. 2015: 553-561, <http://proceedings.mlr.press/v38/lakshminarayanan15.pdf>.
Depends: R (>= 3.2.2)
Imports: BayesTree (>= 0.3-1.4)
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2018-06-25 06:14:52 UTC; Lilac
Repository: CRAN
Date/Publication: 2018-06-30 17:04:14 UTC

More information about pgbart at CRAN
Permanent link

Package mosaic updated to version 1.3.0 with previous version 1.2.0 dated 2018-05-23

Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan <kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

Diff between mosaic versions 1.2.0 dated 2018-05-23 and 1.3.0 dated 2018-06-30

 mosaic-1.2.0/mosaic/inst/doc/MinimalR.R                                             |only
 mosaic-1.2.0/mosaic/inst/doc/MinimalR.Rnw                                           |only
 mosaic-1.2.0/mosaic/inst/doc/MinimalR.pdf                                           |only
 mosaic-1.2.0/mosaic/vignettes/MinimalR.Rnw                                          |only
 mosaic-1.3.0/mosaic/DESCRIPTION                                                     |    8 
 mosaic-1.3.0/mosaic/MD5                                                             |   62 +-
 mosaic-1.3.0/mosaic/NAMESPACE                                                       |    2 
 mosaic-1.3.0/mosaic/R/aggregatingAux.R                                              |    7 
 mosaic-1.3.0/mosaic/R/aggregatingMeta.R                                             |   12 
 mosaic-1.3.0/mosaic/R/interval.R                                                    |   15 
 mosaic-1.3.0/mosaic/R/mplot.R                                                       |   24 -
 mosaic-1.3.0/mosaic/README.md                                                       |    2 
 mosaic-1.3.0/mosaic/build/vignette.rds                                              |binary
 mosaic-1.3.0/mosaic/inst/doc/MinimalRgg.R                                           |    8 
 mosaic-1.3.0/mosaic/inst/doc/MinimalRgg.Rnw                                         |    8 
 mosaic-1.3.0/mosaic/inst/doc/MinimalRgg.pdf                                         |binary
 mosaic-1.3.0/mosaic/inst/doc/Resampling.R                                           |  165 ++++---
 mosaic-1.3.0/mosaic/inst/doc/Resampling.Rnw                                         |  207 +++++-----
 mosaic-1.3.0/mosaic/inst/doc/Resampling.pdf                                         |binary
 mosaic-1.3.0/mosaic/inst/doc/ggformula-lattice.R                                    |   18 
 mosaic-1.3.0/mosaic/inst/doc/ggformula-lattice.Rmd                                  |   34 +
 mosaic-1.3.0/mosaic/inst/doc/ggformula-lattice.pdf                                  |binary
 mosaic-1.3.0/mosaic/inst/doc/mosaic-resources.Rmd                                   |   33 -
 mosaic-1.3.0/mosaic/inst/doc/mosaic-resources.html                                  |   28 -
 mosaic-1.3.0/mosaic/inst/rmarkdown/templates/mosaic-fancy/skeleton/skeleton.Rmd     |    8 
 mosaic-1.3.0/mosaic/inst/rmarkdown/templates/mosaic-plain-pdf/skeleton/skeleton.Rmd |   10 
 mosaic-1.3.0/mosaic/inst/rmarkdown/templates/mosaic-plain/skeleton/skeleton.Rmd     |   10 
 mosaic-1.3.0/mosaic/inst/rmarkdown/templates/mosaic-shiny/skeleton/skeleton.Rmd     |  108 ++---
 mosaic-1.3.0/mosaic/man/interval.Rd                                                 |    3 
 mosaic-1.3.0/mosaic/man/mplot.Rd                                                    |    2 
 mosaic-1.3.0/mosaic/vignettes/MinimalRgg.Rnw                                        |    8 
 mosaic-1.3.0/mosaic/vignettes/Resampling.Rnw                                        |  207 +++++-----
 mosaic-1.3.0/mosaic/vignettes/ggformula-lattice.Rmd                                 |   34 +
 mosaic-1.3.0/mosaic/vignettes/mosaic-resources.Rmd                                  |   33 -
 34 files changed, 590 insertions(+), 466 deletions(-)

More information about mosaic at CRAN
Permanent link

New package mgcViz with initial version 0.1.1
Package: mgcViz
Title: Visualisations for Generalized Additive Models
Version: 0.1.1
Authors@R: c(person("Matteo", "Fasiolo", email = "matteo.fasiolo@gmail.com", role = c("aut", "cre")), person("Raphael", "Nedellec", email = "raphael.nedellec@edf.fr", role = c("aut")))
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models (GAMs) that exploit the additive structure of GAMs, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Depends: R (>= 3.4), mgcv (>= 1.8-24), qgam (>= 1.2.2), ggplot2, rgl
Imports: shiny, matrixStats, viridis, colourpicker, miniUI, rstudioapi, plotly, GGally, KernSmooth, data.table, dplyr, gridExtra, mvnfast, plyr
Suggests: knitr, rmarkdown, testthat, MASS
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
URL: https://github.com/mfasiolo/mgcViz
BugReports: https://github.com/mfasiolo/mgcViz/issues
NeedsCompilation: no
Packaged: 2018-06-29 14:46:49 UTC; teo
Author: Matteo Fasiolo [aut, cre], Raphael Nedellec [aut]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Repository: CRAN
Date/Publication: 2018-06-30 17:19:38 UTC

More information about mgcViz at CRAN
Permanent link

Package MAINT.Data updated to version 1.2.2 with previous version 1.2.1 dated 2018-01-07

Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal and Skew-Normal distributions, considering appropriate parameterizations of the variance-covariance matrix that takes into account the intrinsic nature of interval data, and lead to four different possible configuration structures. The Skew-Normal parameters can be estimated by maximum likelihood, while Normal parameters may be estimated by maximum likelihood or robust trimmed maximum likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>

Diff between MAINT.Data versions 1.2.1 dated 2018-01-07 and 1.2.2 dated 2018-06-30

 CHANGELOG                 |    8 ++++++++
 DESCRIPTION               |    8 ++++----
 MD5                       |    8 ++++----
 R/fasttle.R               |    8 +++++++-
 man/MAINT.Data-package.Rd |    4 ++--
 5 files changed, 25 insertions(+), 11 deletions(-)

More information about MAINT.Data at CRAN
Permanent link

Package LaplacesDemon updated to version 16.1.1 with previous version 16.1.0 dated 2017-12-19

Title: Complete Environment for Bayesian Inference
Description: Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.
Author: Byron Hall [aut], Martina Hall [aut], Statisticat, LLC [aut], Eric Brown [ctb], Richard Hermanson [ctb], Emmanuel Charpentier [ctb], Daniel Heck [ctb], Stephane Laurent [ctb], Quentin F. Gronau [ctb], Henrik Singmann [cre]
Maintainer: Henrik Singmann <singmann+LaplacesDemon@gmail.com>

Diff between LaplacesDemon versions 16.1.0 dated 2017-12-19 and 16.1.1 dated 2018-06-30

 CHANGELOG                          |    1 
 DESCRIPTION                        |    6 
 MD5                                |   15 +-
 build/partial.rdb                  |only
 build/vignette.rds                 |binary
 inst/doc/BayesianInference.pdf     |binary
 inst/doc/Examples.pdf              |binary
 inst/doc/LaplacesDemonTutorial.pdf |binary
 man/LaplacesDemon-package.Rd       |  224 ++++++++++++++++++-------------------
 9 files changed, 125 insertions(+), 121 deletions(-)

More information about LaplacesDemon at CRAN
Permanent link

Package gimme updated to version 0.4-1 with previous version 0.4 dated 2018-05-20

Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and individual-level relations in time series data from within a structural equation modeling framework.
Author: Stephanie Lane [aut, cre, trl], Kathleen Gates [aut], Peter Molenaar [aut], Michael Hallquist [ctb], Hallie Pike [ctb], Zachary Fisher [ctb], Cara Arizmendi [ctb], Teague Henry [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>

Diff between gimme versions 0.4 dated 2018-05-20 and 0.4-1 dated 2018-06-30

 DESCRIPTION      |    8 +++----
 MD5              |    8 +++----
 R/new_funcs.R    |   61 ++++++++++++++++++++++++++++++++++++-------------------
 R/new_setup.R    |   16 +++++++++-----
 R/print.gimmep.R |    4 +--
 5 files changed, 61 insertions(+), 36 deletions(-)

More information about gimme at CRAN
Permanent link

Package CARRoT updated to version 1.0.0 with previous version 0.1.0 dated 2018-04-06

Title: Predicting Categorical and Continuous Outcomes Using One in Ten Rule
Description: Predicts categorical or continuous outcomes while concentrating on four key points. These are Cross-validation, Accuracy, Regression and Rule of Ten or "one in ten rule" (CARRoT). It performs the cross-validation specified number of times by partitioning the input into training and test set and fitting linear/multinomial/binary regression models to the training set. All regression models satisfying a rule of ten events per variable are fitted and the ones with the best predictive power are given as an output. Best predictive power is understood as highest accuracy in case of binary/multinomial outcomes, smallest absolute and relative errors in case of continuous outcomes. For binary case there is also an option of finding a regression model which gives the highest AUROC (Area Under Receiver Operating Curve) value. The option of parallel toolbox is also available. Methods are described in Peduzzi et al. (1996) <doi:10.1016/S0895-4356(96)00236-3> and Rhemtulla et al. (2012) <doi:10.1037/a0029315>.
Author: Alina Bazarova [aut, cre], Marko Raseta [aut]
Maintainer: Alina Bazarova <a.bazarova@bham.ac.uk>

Diff between CARRoT versions 0.1.0 dated 2018-04-06 and 1.0.0 dated 2018-06-30

 DESCRIPTION                |   15 
 MD5                        |   20 
 R/carrot_functions.R       | 1039 +++++++++++++++++++++++++--------------------
 build/partial.rdb          |binary
 man/compute_max_length.Rd  |    6 
 man/cross_val.Rd           |   19 
 man/get_predictions_lin.Rd |    2 
 man/make_numeric.Rd        |    3 
 man/make_numeric_sets.Rd   |    4 
 man/regr_ind.Rd            |   15 
 man/regr_whole.Rd          |   17 
 11 files changed, 649 insertions(+), 491 deletions(-)

More information about CARRoT at CRAN
Permanent link

New package anomaly with initial version 1.0.0
Package: anomaly
Type: Package
Title: Detecting Anomalies in Data
Version: 1.0.0
Date: 2018-06-20
Authors@R: c(person("Alex","Fisch",email="a.t.fisch@lancaster.ac.uk",role=c("aut")), person("Daniel","Grose",email="dan.grose@lancaster.ac.uk",role=c("ctb","cre")), person("Idris","Eckley",email="i.eckley@lancaster.ac.uk",role=c("ths")), person("Paul","Fearnhead",email="p.fearnhead@lancaster.ac.uk",role=c("ths")))
Description: An implementation of CAPA (Collective And Point Anomaly) by Fisch, Eckley and Fearnhead (2018) <arXiv:1806.01947> for the detection of anomalies in time series data. The package also contains Kepler lightcurve data and shows how CAPA can be applied to detect exoplanets.
License: GPL
Imports: dplyr,rlang,Rdpack
NeedsCompilation: yes
RoxygenNote: 6.0.1
RdMacros: Rdpack
Packaged: 2018-06-25 11:58:18 UTC; grosedj1
Author: Alex Fisch [aut], Daniel Grose [ctb, cre], Idris Eckley [ths], Paul Fearnhead [ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-06-30 17:04:20 UTC

More information about anomaly at CRAN
Permanent link

Package seplyr updated to version 0.5.8 with previous version 0.5.7 dated 2018-06-30

Title: Improved Standard Evaluation Interfaces for Common Data Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved standard evaluation adapter methods for important common 'dplyr' data manipulation tasks. In addition the 'seplyr' package supplies several new "key operations bound together" methods. These include 'group_summarize()' (which combines grouping, arranging and calculation in an atomic unit), 'add_group_summaries()' (which joins grouped summaries into a 'data.frame' in a well documented manner), 'add_group_indices()' (which adds per-group identifiers to a 'data.frame' without depending on row-order), 'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()' (which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between seplyr versions 0.5.7 dated 2018-06-30 and 0.5.8 dated 2018-06-30

 DESCRIPTION      |    6 +++---
 MD5              |   12 ++++++------
 NEWS.md          |    3 +++
 R/gather_se.R    |   26 +++++++++++++++++++-------
 R/spread_se.R    |   28 ++++++++++++++++++----------
 man/gather_se.Rd |   13 ++++++++-----
 man/spread_se.Rd |   18 ++++++++++--------
 7 files changed, 67 insertions(+), 39 deletions(-)

More information about seplyr at CRAN
Permanent link

Package DataVisualizations updated to version 1.1.1 with previous version 1.0.0 dated 2018-05-06

Title: Visualizations of High-Dimensional Data
Description: A collection of various visualizations methods is provided. With regards to classified high-dimensional data several visualizations are presented, e.g. the heat map and silhouette plot. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through the combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). The visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables, the Shepard density plot as well as the Bland-Altman plot are presented here. For a classification of countries, a map of the world or Germany can be visualized. More detailed explanations can be found in the book of Thrun, M.C.:"Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>. Furthermore, for categorical features the ABC analysis improved Pie charts, slope charts and fan plots are usable. Additionally, for measurements across a geographic area an easy to use function for a Choropleth map is presented here. At last, the PDE-optimized violin plot for either classified or non-classified, univariate or multivariate data is available here. The the PDE-optimized violin plot is an alternative for the box-and-whisker plot (boxplot).
Author: Michael Thrun [aut, cre, cph], Felix Pape [aut, rev], Onno Hansen-Goos [ctr, ctb], Alfred Ultsch [dtc, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between DataVisualizations versions 1.0.0 dated 2018-05-06 and 1.1.1 dated 2018-06-30

 DESCRIPTION                                |   23 ++++----
 MD5                                        |   75 ++++++++++++++++++---------
 NAMESPACE                                  |   29 +++++++---
 R/ClassBoxPlot.R                           |only
 R/ClassPDEplot.R                           |only
 R/ClassPDEplotMaxLikeli.R                  |only
 R/ClassViolinPlot.R                        |only
 R/DrawWorldWithCls.R                       |only
 R/Heatmap.R                                |    6 +-
 R/InspectDistances.R                       |   12 ++--
 R/MAplot.R                                 |    2 
 R/PDEscatter.R                             |   80 ++++++++++++++++-------------
 R/PDEviolinPlot.R                          |only
 R/QQplotForStandardization.R               |only
 R/QQplotWithFit.R                          |only
 R/ShepardDensityPlot.R                     |    1 
 R/ShepardScatterPlot.R                     |    2 
 R/SilhouettePlot.R                         |    6 +-
 R/inPSphere2D.R                            |    1 
 R/plotChoroplethMap.R                      |   73 +++++++++++++++++++++++++-
 R/plotWorldmap.R                           |    6 +-
 R/stat_pde_density.R                       |only
 build                                      |only
 inst                                       |only
 man/ChoroplethPostalCodesAndAGS_Germany.Rd |    2 
 man/ClassBoxPlot.Rd                        |only
 man/ClassPDEplot.Rd                        |only
 man/ClassPDEplotMaxLikeli.Rd               |only
 man/ClassViolinPlot.Rd                     |only
 man/DataVisualizations-package.Rd          |   45 +++++-----------
 man/DrawWorldWithCls.Rd                    |only
 man/ITS.Rd                                 |    2 
 man/InspectDistances.Rd                    |    2 
 man/InspectScatterOfData.Rd                |    2 
 man/InspectVariable.Rd                     |    2 
 man/MTY.Rd                                 |    2 
 man/PDEplot.Rd                             |   12 +---
 man/PDEscatter.Rd                          |   16 +++--
 man/PDEviolinPlot.Rd                       |only
 man/PixelMatrixPlot.Rd                     |    4 -
 man/QQplotForStandardization.Rd            |only
 man/QQplotWithFit.Rd                       |only
 man/StatPDEdensity.Rd                      |only
 man/inPSphere2D.Rd                         |    2 
 man/plotWorldmap.Rd                        |   18 ------
 man/stat_pde_density.Rd                    |only
 vignettes                                  |only
 47 files changed, 262 insertions(+), 163 deletions(-)

More information about DataVisualizations at CRAN
Permanent link

Package BANEScarparkinglite updated to version 0.1.2 with previous version 0.1.1 dated 2018-01-23

Title: Working with Car Parking Data for Bath and North East Somerset
Description: Contains functions for importing and working with the BANES car parking records and other related datasets. For the full version of the package, including all datasets, see the repo at <https://github.com/owenjonesuob/BANEScarparking>. The original dataset of parking records can be found at <https://data.bathhacked.org/Government-and-Society/BANES-Historic-Car-Park-Occupancy/x29s-cczc>.
Author: Owen Jones [aut, cre], Ryan Kenning [aut, ctb]
Maintainer: Owen Jones <olj23@bath.ac.uk>

Diff between BANEScarparkinglite versions 0.1.1 dated 2018-01-23 and 0.1.2 dated 2018-06-30

 BANEScarparkinglite-0.1.1/BANEScarparkinglite/man/get_daily_weather.Rd                |only
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/DESCRIPTION                             |    6 
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/MD5                                     |   13 
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/NAMESPACE                               |    1 
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/NEWS.md                                 |   11 
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/R/web_scraping.R                        |  252 +++++-----
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/README.md                               |   22 
 BANEScarparkinglite-0.1.2/BANEScarparkinglite/inst/tests/testthat/test-web_scraping.R |   19 
 8 files changed, 171 insertions(+), 153 deletions(-)

More information about BANEScarparkinglite at CRAN
Permanent link

Package seplyr updated to version 0.5.7 with previous version 0.5.6 dated 2018-06-23

Title: Improved Standard Evaluation Interfaces for Common Data Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved standard evaluation adapter methods for important common 'dplyr' data manipulation tasks. In addition the 'seplyr' package supplies several new "key operations bound together" methods. These include 'group_summarize()' (which combines grouping, arranging and calculation in an atomic unit), 'add_group_summaries()' (which joins grouped summaries into a 'data.frame' in a well documented manner), 'add_group_indices()' (which adds per-group identifiers to a 'data.frame' without depending on row-order), 'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()' (which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between seplyr versions 0.5.6 dated 2018-06-23 and 0.5.7 dated 2018-06-30

 DESCRIPTION                     |    8 ++++----
 MD5                             |   26 +++++++++++++++-----------
 NAMESPACE                       |    2 ++
 NEWS.md                         |    6 ++++++
 R/complete_se.R                 |    2 +-
 R/gather_se.R                   |only
 R/in_group_indices.R            |    5 +----
 R/mutate_se.R                   |    4 +---
 R/spread_se.R                   |only
 inst/doc/MutatePartitioner.html |    4 ++--
 inst/doc/named_map_builder.html |    4 ++--
 inst/doc/rename_se.html         |    4 ++--
 inst/doc/seplyr.html            |    4 ++--
 inst/doc/using_seplyr.html      |    4 ++--
 man/gather_se.Rd                |only
 man/spread_se.Rd                |only
 16 files changed, 40 insertions(+), 33 deletions(-)

More information about seplyr at CRAN
Permanent link

New package expands with initial version 2.1.2
Package: expands
Type: Package
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Version: 2.1.2
Date: 2018-06-29
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (<http://www.ncbi.nlm.nih.gov/pubmed/24177718>). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 2.1 include: (i) new parameter ploidy in runExPANdS.R allows specification of non-diploid background ploidies (e.g. for near-triploid cell lines); (ii) parallel computing option is available. Further documentation and FAQ available at <http://dna-discovery.stanford.edu/software/expands>.
License: GPL-2
URL: http://dna-discovery.stanford.edu/software/expands, https://github.com/noemiandor/expands, https://groups.google.com/d/forum/expands
Depends: R (>= 2.10)
Imports: flexclust, plyr, RColorBrewer, gplots, NbClust, moments (>= 0.13), rJava (>= 0.5-0), flexmix (>= 2.3), matlab (>= 0.8.9), ape (>= 3.2), commonsMath (>= 1.1), parallel
Suggests: phylobase (>= 0.6.8)
SystemRequirements: Java (>= 5.0)
Packaged: 2018-06-30 00:40:39 UTC; noemi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-06-30 15:08:14 UTC
RoxygenNote: 6.0.1

More information about expands at CRAN
Permanent link

Package penalized updated to version 0.9-50.1 with previous version 0.9-50 dated 2017-02-01

Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi, Matthew Lueder
Maintainer: ORPHANED

Diff between penalized versions 0.9-50 dated 2017-02-01 and 0.9-50.1 dated 2018-06-30

 DESCRIPTION             |   15 
 MD5                     |   16 
 R/checkinput.R          |    9 
 build/vignette.rds      |binary
 data/nki70.RData        |binary
 inst/doc/penalized.R    |    6 
 inst/doc/penalized.Rnw  | 1101 ++++++++++++++++++++++++------------------------
 inst/doc/penalized.pdf  |binary
 vignettes/penalized.Rnw |    2 
 9 files changed, 574 insertions(+), 575 deletions(-)

More information about penalized at CRAN
Permanent link

Package sealr updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-06

Title: Sealing the R Objects Test and Assert Conditions
Description: Record the state of R object. Outputs include object class and attributes. This helps reduce errors in test results by manual description. The goal is to improve the efficiency of data analysis and package development.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>

Diff between sealr versions 0.1.0 dated 2018-04-06 and 0.1.1 dated 2018-06-30

 sealr-0.1.0/sealr/inst/Dockerfile                    |only
 sealr-0.1.0/sealr/inst/docker-compose.yml            |only
 sealr-0.1.1/sealr/DESCRIPTION                        |    8 -
 sealr-0.1.1/sealr/MD5                                |   21 +-
 sealr-0.1.1/sealr/NEWS.md                            |    5 
 sealr-0.1.1/sealr/R/design.R                         |   17 +-
 sealr-0.1.1/sealr/R/transcribe.R                     |  142 ++++++++++---------
 sealr-0.1.1/sealr/README.md                          |   32 +++-
 sealr-0.1.1/sealr/build/vignette.rds                 |binary
 sealr-0.1.1/sealr/inst/doc/sealr1.html               |   10 -
 sealr-0.1.1/sealr/man/figures/sealr_introduction.png |only
 sealr-0.1.1/sealr/tests/testthat/test-seal.R         |    1 
 sealr-0.1.1/sealr/tests/testthat/test-transcribe.R   |    2 
 13 files changed, 139 insertions(+), 99 deletions(-)

More information about sealr at CRAN
Permanent link

Package interplot updated to version 0.2.1 with previous version 0.1.5 dated 2016-11-20

Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Author: Frederick Solt [aut], Yue Hu [aut, cre], Brenton Kenkel [ctb]
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>

Diff between interplot versions 0.1.5 dated 2016-11-20 and 0.2.1 dated 2018-06-30

 interplot-0.1.5/interplot/inst/CITATION                    |only
 interplot-0.2.1/interplot/DESCRIPTION                      |   13 
 interplot-0.2.1/interplot/MD5                              |   46 -
 interplot-0.2.1/interplot/NAMESPACE                        |    7 
 interplot-0.2.1/interplot/NEWS.md                          |   19 
 interplot-0.2.1/interplot/R/Interplot.R                    |   26 
 interplot-0.2.1/interplot/R/Interplot_default.R            |  269 ++++++-
 interplot-0.2.1/interplot/R/Interplot_mi.R                 |  306 ++++++--
 interplot-0.2.1/interplot/R/Interplot_mlm.R                |  196 ++++-
 interplot-0.2.1/interplot/R/Interplot_mlmmi.R              |  180 ++++
 interplot-0.2.1/interplot/R/Interplot_plot.R               |  101 +-
 interplot-0.2.1/interplot/README.md                        |    5 
 interplot-0.2.1/interplot/build/vignette.rds               |binary
 interplot-0.2.1/interplot/inst/doc/interplot-vignette.R    |   28 
 interplot-0.2.1/interplot/inst/doc/interplot-vignette.Rmd  |   93 ++
 interplot-0.2.1/interplot/inst/doc/interplot-vignette.html |  490 ++++++++++---
 interplot-0.2.1/interplot/man/interplot.Rd                 |   28 
 interplot-0.2.1/interplot/man/interplot.default.Rd         |   25 
 interplot-0.2.1/interplot/man/interplot.lmerMod.Rd         |   12 
 interplot-0.2.1/interplot/man/interplot.lmmi.Rd            |   25 
 interplot-0.2.1/interplot/man/interplot.mlmmi.Rd           |   12 
 interplot-0.2.1/interplot/man/interplot.plot.Rd            |   22 
 interplot-0.2.1/interplot/vignettes/interplot-vignette.Rmd |   93 ++
 interplot-0.2.1/interplot/vignettes/pew1_w.csv             |only
 interplot-0.2.1/interplot/vignettes/vignette.bib           |   83 ++
 25 files changed, 1718 insertions(+), 361 deletions(-)

More information about interplot at CRAN
Permanent link

Package glmpathcr updated to version 1.0.7 with previous version 1.0.6 dated 2018-06-05

Title: Fit a Penalized Continuation Ratio Model for Predicting an Ordinal Response
Description: Provides a function for fitting a penalized constrained continuation ratio model using the glmpath algorithm and methods for extracting coefficient estimates, predicted class, class probabilities, and plots.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer <archer.43@osu.edu>

Diff between glmpathcr versions 1.0.6 dated 2018-06-05 and 1.0.7 dated 2018-06-30

 DESCRIPTION            |    8 ++++----
 MD5                    |   16 ++++++++--------
 R/glmpathcr.R          |    9 +++++++--
 R/plot.glmpathcr.R     |   16 ++++++++--------
 R/predict.glmpathcr.R  |    8 +++++++-
 build/partial.rdb      |binary
 inst/NEWS.Rd           |    9 ++++++++-
 inst/doc/glmpathcr.pdf |binary
 man/glmpathcr.Rd       |    4 +++-
 9 files changed, 45 insertions(+), 25 deletions(-)

More information about glmpathcr at CRAN
Permanent link

Package survival updated to version 2.42-4 with previous version 2.42-3.1 dated 2018-04-24

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

Diff between survival versions 2.42-3.1 dated 2018-04-24 and 2.42-4 dated 2018-06-30

 DESCRIPTION                |    6 -
 MD5                        |  154 +++++++++++++++++++++++---------------------
 NAMESPACE                  |   43 ++++++++++--
 R/Surv.R                   |  156 +++++++++++++++++++++++++++++++++++++--------
 R/print.coxph.penal.S      |    8 +-
 R/survfitCI.R              |   42 +++++++-----
 R/tmerge.R                 |    7 +-
 R/xtras.R                  |    3 
 data/bladder.rda           |binary
 data/cancer.rda            |binary
 data/cgd.rda               |binary
 data/colon.rda             |binary
 data/flchain.rda           |binary
 data/genfan.rda            |binary
 data/heart.rda             |binary
 data/kidney.rda            |binary
 data/leukemia.rda          |binary
 data/logan.rda             |binary
 data/lung.rda              |binary
 data/mgus.rda              |binary
 data/mgus2.rda             |binary
 data/myeloid.rda           |binary
 data/nwtco.rda             |binary
 data/ovarian.rda           |binary
 data/pbc.rda               |binary
 data/rats.rda              |binary
 data/retinopathy.rda       |binary
 data/rhDNase.rda           |binary
 data/solder.rda            |binary
 data/stanford2.rda         |binary
 data/survexp.rda           |binary
 data/transplant.rda        |binary
 data/uspop2.rda            |binary
 data/veteran.rda           |binary
 inst/NEWS.Rd               |   33 ++++++++-
 inst/doc/adjcurve.pdf      |binary
 inst/doc/compete.R         |    1 
 inst/doc/compete.Rnw       |   18 +++--
 inst/doc/compete.pdf       |binary
 inst/doc/multi.pdf         |binary
 inst/doc/population.pdf    |binary
 inst/doc/splines.pdf       |binary
 inst/doc/tests.pdf         |binary
 inst/doc/tiedtimes.pdf     |binary
 inst/doc/timedep.R         |    4 -
 inst/doc/timedep.Rnw       |   10 --
 inst/doc/timedep.pdf       |binary
 inst/doc/validate.pdf      |binary
 man/cgd.Rd                 |    2 
 man/levels.Surv.Rd         |only
 man/mgus.Rd                |    6 -
 man/mgus2.Rd               |    4 -
 man/ratetable.Rd           |   34 ++++++---
 man/solder.Rd              |    4 -
 man/survexp.Rd             |    2 
 man/survexp.us.Rd          |   38 +++-------
 man/tmerge.Rd              |    6 +
 man/xtfrm.Surv.Rd          |only
 noweb/Readme               |    9 ++
 noweb/concordance2.Rnw     |only
 noweb/exact.nw             |   49 +++++++-------
 noweb/survfitCI.Rnw        |   82 +++++++++++++++--------
 noweb/tmerge.Rnw           |    7 +-
 src/coxexact.c             |   50 +++++++-------
 tests/fr_cancer.Rout.save  |   21 +++---
 tests/fr_kidney.Rout.save  |   33 ++++++---
 tests/fr_ovarian.Rout.save |    9 +-
 tests/fr_rat1.Rout.save    |   15 ++--
 tests/fr_rat2.Rout.save    |   21 +++---
 tests/fr_resid.Rout.save   |   12 ++-
 tests/mstate.R             |    1 
 tests/mstate.Rout.save     |    8 +-
 tests/surv.R               |   16 ++++
 tests/surv.Rout.save       |   31 +++++++-
 tests/tmerge2.R            |   26 +++++++
 tests/tmerge2.Rout.save    |   38 +++++++++-
 tests/tmerge3.R            |only
 tests/tmerge3.Rout.save    |only
 tests/yates0.Rout.save     |only
 vignettes/compete.Rnw      |   18 +++--
 vignettes/timedep.Rnw      |   10 --
 81 files changed, 695 insertions(+), 342 deletions(-)

More information about survival at CRAN
Permanent link

Package shallot updated to version 0.4.4 with previous version 0.4.3 dated 2017-10-02

Title: Random Partition Distribution Indexed by Pairwise Information
Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>. The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior and posterior simulation. Posterior simulation is based on a user-supplied likelihood. Supporting functions for partition estimation and plotting are also provided.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between shallot versions 0.4.3 dated 2017-10-02 and 0.4.4 dated 2018-06-30

 shallot-0.4.3/shallot/inst/java/scala-2.10               |only
 shallot-0.4.3/shallot/man/plot.partition.Rd              |only
 shallot-0.4.3/shallot/man/sample.partitions.posterior.Rd |only
 shallot-0.4.3/shallot/man/sampling.model.Rd              |only
 shallot-0.4.4/shallot/DESCRIPTION                        |   10 
 shallot-0.4.4/shallot/MD5                                |   26 
 shallot-0.4.4/shallot/NAMESPACE                          |    6 
 shallot-0.4.4/shallot/NEWS                               |    3 
 shallot-0.4.4/shallot/R/onLoad.R                         |   16 
 shallot-0.4.4/shallot/R/shallot.R                        |  431 ++-------------
 shallot-0.4.4/shallot/inst/COPYRIGHT                     |    2 
 shallot-0.4.4/shallot/inst/java/scala-2.11/shallot.jar   |binary
 shallot-0.4.4/shallot/inst/java/scala-2.12/shallot.jar   |binary
 shallot-0.4.4/shallot/java/shallot-sources.jar           |binary
 shallot-0.4.4/shallot/man/sample.partitions.Rd           |    1 
 shallot-0.4.4/shallot/man/shallot-package.Rd             |   12 
 16 files changed, 109 insertions(+), 398 deletions(-)

More information about shallot at CRAN
Permanent link

Package RRF updated to version 1.8 with previous version 1.7 dated 2017-01-26

Title: Regularized Random Forest
Description: Feature Selection with Regularized Random Forest. This package is based on the 'randomForest' package by Andy Liaw. The key difference is the RRF() function that builds a regularized random forest.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener, Regularized random forest for classification by Houtao Deng. Regularized random forest for regression by Xin Guan.
Maintainer: Houtao Deng <softwaredeng@gmail.com>

Diff between RRF versions 1.7 dated 2017-01-26 and 1.8 dated 2018-06-30

 DESCRIPTION    |    8 ++++----
 MD5            |    7 ++++---
 NAMESPACE      |    2 +-
 src/RRF_init.c |only
 src/regTree.c  |    2 +-
 5 files changed, 10 insertions(+), 9 deletions(-)

More information about RRF at CRAN
Permanent link

Package Unicode updated to version 11.0.0-1 with previous version 10.0.0-1 dated 2017-09-19

Title: Unicode Data and Utilities
Description: Data from Unicode 11.0.0 and related utilities.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between Unicode versions 10.0.0-1 dated 2017-09-19 and 11.0.0-1 dated 2018-06-30

 DESCRIPTION   |   13 +++++++------
 MD5           |    4 ++--
 R/sysdata.rda |binary
 3 files changed, 9 insertions(+), 8 deletions(-)

More information about Unicode at CRAN
Permanent link

Package OECD updated to version 0.2.3.999 with previous version 0.2.2 dated 2016-01-17

Title: Search and Extract Data from the OECD
Description: Search and extract data from the OECD.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>

Diff between OECD versions 0.2.2 dated 2016-01-17 and 0.2.3.999 dated 2018-06-30

 OECD-0.2.2/OECD/inst/doc/oecd_vignette_main.R    |only
 OECD-0.2.2/OECD/inst/doc/oecd_vignette_main.Rmd  |only
 OECD-0.2.2/OECD/inst/doc/oecd_vignette_main.pdf  |only
 OECD-0.2.2/OECD/vignettes/oecd_vignette_main.Rmd |only
 OECD-0.2.3.999/OECD/DESCRIPTION                  |   14 
 OECD-0.2.3.999/OECD/MD5                          |   30 -
 OECD-0.2.3.999/OECD/NAMESPACE                    |   16 
 OECD-0.2.3.999/OECD/R/main.R                     |  432 +++++++++++------------
 OECD-0.2.3.999/OECD/build/vignette.rds           |binary
 OECD-0.2.3.999/OECD/inst/doc/OECD.R              |only
 OECD-0.2.3.999/OECD/inst/doc/OECD.Rmd            |only
 OECD-0.2.3.999/OECD/inst/doc/OECD.html           |only
 OECD-0.2.3.999/OECD/man/browse_metadata.Rd       |   47 +-
 OECD-0.2.3.999/OECD/man/get_data_structure.Rd    |   45 +-
 OECD-0.2.3.999/OECD/man/get_dataset.Rd           |  107 ++---
 OECD-0.2.3.999/OECD/man/get_datasets.Rd          |   57 +--
 OECD-0.2.3.999/OECD/man/search_dataset.Rd        |   67 +--
 OECD-0.2.3.999/OECD/tests/testthat.R             |    8 
 OECD-0.2.3.999/OECD/tests/testthat/tests.R       |   36 +
 OECD-0.2.3.999/OECD/vignettes/OECD.Rmd           |only
 20 files changed, 428 insertions(+), 431 deletions(-)

More information about OECD at CRAN
Permanent link

Package ISOcodes updated to version 2018.06.29 with previous version 2017.09.27 dated 2017-09-27

Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes. Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.
Author: Christian Buchta [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between ISOcodes versions 2017.09.27 dated 2017-09-27 and 2018.06.29 dated 2018-06-30

 DESCRIPTION                    |   11 ++++++-----
 MD5                            |   20 ++++++++++----------
 data/ISO_15924.rda             |binary
 data/ISO_4217.rda              |binary
 data/ISO_639_2.rda             |binary
 data/ISO_639_3.rda             |binary
 data/ISO_639_3_Retirements.rda |binary
 data/UN_M.49_Countries.rda     |binary
 data/UN_M.49_Regions.rda       |binary
 man/ISO_3166.Rd                |    2 +-
 man/ISO_4217.Rd                |    2 +-
 11 files changed, 18 insertions(+), 17 deletions(-)

More information about ISOcodes at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.