Sun, 18 Nov 2018

Package RcppMsgPack updated to version 0.2.3 with previous version 0.2.2 dated 2018-05-06

Title: 'MsgPack' C++ Header Files and Interface Functions for R
Description: 'MsgPack' header files are provided for use by R packages, along with the ability to access, create and alter 'MsgPack' objects directly from R. 'MsgPack' is an efficient binary serialization format. It lets you exchange data among multiple languages like 'JSON' but it is faster and smaller. Small integers are encoded into a single byte, and typical short strings require only one extra byte in addition to the strings themselves. This package provides headers from the 'msgpack-c' implementation for C and C++(11) for use by R, particularly 'Rcpp'. The included 'msgpack-c' headers are licensed under the Boost Software License (Version 1.0); the code added by this package as well the R integration are licensed under the GPL (>= 2). See the files 'COPYRIGHTS' and 'AUTHORS' for a full list of copyright holders and contributors to 'msgpack-c'.
Author: Travers Ching and Dirk Eddelbuettel; the authors and contributors of MsgPack
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppMsgPack versions 0.2.2 dated 2018-05-06 and 0.2.3 dated 2018-11-18

 ChangeLog                       |   33 +++
 DESCRIPTION                     |    8 
 MD5                             |   30 +--
 NAMESPACE                       |    1 
 R/functions.r                   |   97 ++++++++++
 README.md                       |    2 
 build/partial.rdb               |binary
 build/vignette.rds              |binary
 inst/NEWS.Rd                    |   10 +
 inst/doc/vignette.html          |  300 +++++++++++++++++++++++++++-----
 man/msgpack_read.Rd             |only
 man/msgpack_write.Rd            |only
 src/RcppExports.cpp             |    6 
 src/anyvector.h                 |    4 
 src/example1.cpp                |    6 
 src/rcppmsgpack_c_functions.cpp |  369 +++++++++++++++++++++-------------------
 tests/tests.r                   |  343 +++++++++++++++++++------------------
 17 files changed, 802 insertions(+), 407 deletions(-)

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New package TSMCP with initial version 1.0
Package: TSMCP
Type: Package
Title: Fast Two Stage Multiple Change Point Detection
Version: 1.0
Author: Yaguang Li [aut, cre], Baisuo Jin [aut]
Maintainer: Yaguang Li <liyg@mail.ustc.edu.cn>
Depends: R (>= 3.3.0), plus, lars
Suggests: MASS
Description: A novel and fast two stage method for simultaneous multiple change point detection and variable selection for piecewise stationary autoregressive (PSAR) processes and linear regression model. It also simultaneously performs variable selection for each autoregressive model and hence the order selection.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-09 06:36:29 UTC; ustcr7
Repository: CRAN
Date/Publication: 2018-11-18 19:00:09 UTC

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Package tiler updated to version 0.2.1 with previous version 0.2.0 dated 2018-06-09

Title: Create Geographic and Non-Geographic Map Tiles
Description: Creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as 'leaflet'. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with 'leaflet' when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires 'Python' and the 'gdal' library for 'Python'. 'Windows' users are recommended to install 'OSGeo4W' (<https://trac.osgeo.org/osgeo4w/>) as an easy way to obtain the required 'gdal' support for 'Python'.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

Diff between tiler versions 0.2.0 dated 2018-06-09 and 0.2.1 dated 2018-11-18

 tiler-0.2.0/tiler/inst/tiler.png       |only
 tiler-0.2.1/tiler/DESCRIPTION          |   23 ++++++---------
 tiler-0.2.1/tiler/LICENSE              |    2 -
 tiler-0.2.1/tiler/MD5                  |   29 +++++++++----------
 tiler-0.2.1/tiler/NEWS.md              |    9 ++++--
 tiler-0.2.1/tiler/R/options.R          |   19 +++++-------
 tiler-0.2.1/tiler/R/tile.R             |    6 +++-
 tiler-0.2.1/tiler/R/zzz.R              |    3 --
 tiler-0.2.1/tiler/README.md            |   42 +++++++++++++++++++++-------
 tiler-0.2.1/tiler/build/vignette.rds   |binary
 tiler-0.2.1/tiler/inst/doc/tiler.R     |   23 +++++++++++++++
 tiler-0.2.1/tiler/inst/doc/tiler.Rmd   |   43 +++++++++++++++++++++++++++-
 tiler-0.2.1/tiler/inst/doc/tiler.html  |   49 ++++++++++++++++++++++++++++-----
 tiler-0.2.1/tiler/man/tile_viewer.Rd   |    3 +-
 tiler-0.2.1/tiler/man/tiler_options.Rd |   18 +++++-------
 tiler-0.2.1/tiler/vignettes/tiler.Rmd  |   43 +++++++++++++++++++++++++++-
 16 files changed, 236 insertions(+), 76 deletions(-)

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New package shinyEffects with initial version 0.1.0
Package: shinyEffects
Type: Package
Title: Customize Your Web Apps with Fancy Effects
Version: 0.1.0
Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com", role = c("aut", "cre")))
Maintainer: David Granjon <dgranjon@ymail.com>
Description: Add fancy CSS effects to your 'shinydashboards' or 'shiny' apps. 100% compatible with 'shinydashboardPlus' and 'bs4Dash'.
License: GPL-2
Imports: htmltools, shiny, shinydashboard
Suggests: shinydashboardPlus, bs4Dash, knitr
URL: https://github.com/DivadNojnarg/shinyEffects, https://divadnojnarg.github.io/shinyEffects/
BugReports: https://github.com/DivadNojnarg/shinyEffects/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-09 14:38:28 UTC; macdavidgranjon
Author: David Granjon [aut, cre]
Repository: CRAN
Date/Publication: 2018-11-18 18:40:03 UTC

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New package rfviz with initial version 1.0.0
Package: rfviz
Type: Package
Title: Interactive Visualization Tool for Random Forests
Version: 1.0.0
Authors@R: person("Chris", "Beckett", email = "chrisbeckett8@gmail.com", role = c("aut", "cre"))
Description: An interactive data visualization and exploration toolkit that implements Breiman and Cutler's original random forest Java based visualization tools in R, for supervised and unsupervised classification and regression within the algorithm random forest.
Depends: R (>= 3.5.0), randomForest, loon, tcltk
License: GPL (>= 2)
URL: https://www.stat.berkeley.edu/~breiman/RandomForests/cc_graphics.htm
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: stats, utils, base
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-11-08 17:28:53 UTC; chris
Author: Chris Beckett [aut, cre]
Maintainer: Chris Beckett <chrisbeckett8@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-18 18:30:03 UTC

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New package RFishBC with initial version 0.1.1
Package: RFishBC
Version: 0.1.1
Date: 2018-11-12
Title: Back-Calculation of Fish Length
Authors@R: person("Derek","Ogle", email="derek@derekogle.com", role=c("aut","cre"), comment=c(ORCID="0000-0002-0370-9299"))
Description: Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software.
URL: http://derekogle.com/RFishBC
BugReports: https://github.com/droglenc/RFishBC/issues
License: GPL-3
LazyData: true
Depends: R (>= 3.2.0)
Imports: graphics, grDevices, clisymbols, crayon, readbitmap, rlang, settings, stringr, tidyr, withr
Suggests: FSA, covr, pkgdown, testthat
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-12 14:06:13 UTC; dogle
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>
Repository: CRAN
Date/Publication: 2018-11-18 18:30:17 UTC

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New package RainfallErosivityFactor with initial version 0.1.0
Package: RainfallErosivityFactor
Type: Package
Title: The Rainfall-Runoff Erosivity Factor
Version: 0.1.0
Author: Edilson Marcelino Silva [aut], Dione Pereira Cardoso [aut, cre], Marx Leandro Naves Silva [ctb], Joel Augusto Muniz [ctb], Daniel Furtado Ferreira [ctb], Junior Cesar Avanzi [ctb]
Maintainer: Dione Pereira Cardoso <cardoso.dione@gmail.com>
Description: Determination of rainfall-runoff erosivity factor.
Depends: R (>= 2.10)
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-11-08 17:11:14 UTC; UX303L
Repository: CRAN
Date/Publication: 2018-11-18 18:30:14 UTC

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New package NPBayesImputeCat with initial version 0.1
Package: NPBayesImputeCat
Type: Package
Title: Non-Parametric Bayesian Multiple Imputation for Categorical Data
Version: 0.1
Date: 2018-11-09
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Jingchen Hu <jingchen.monika.hu@gmail.com>
Description: These routines create multiple imputations of missing at random categorical data, and create multiply imputed synthesis of categorical data, with or without structural zeros. Imputations and syntheses are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
License: GPL (>= 3)
Depends: methods, Rcpp (>= 0.10.2)
LinkingTo: Rcpp
RcppModules: clcm
NeedsCompilation: yes
Repository: CRAN
Packaged: 2018-11-09 18:15:56 UTC; jingchenmonikahu
Date/Publication: 2018-11-18 19:00:12 UTC

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Package lvnet updated to version 0.3.4 with previous version 0.3.3 dated 2018-04-25

Title: Latent Variable Network Modeling
Description: Estimate, fit and compare Structural Equation Models (SEM) and network models (Gaussian Graphical Models; GGM) using OpenMx. Allows for two possible generalizations to include GGMs in SEM: GGMs can be used between latent variables (latent network modeling; LNM) or between residuals (residual network modeling; RNM). For details, see Epskamp, Rhemtulla and Borsboom (2017) <doi:10.1007/s11336-017-9557-x>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

Diff between lvnet versions 0.3.3 dated 2018-04-25 and 0.3.4 dated 2018-11-18

 lvnet-0.3.3/lvnet/R/BayesLNM.R         |only
 lvnet-0.3.3/lvnet/R/BayesRNM.R         |only
 lvnet-0.3.4/lvnet/DESCRIPTION          |    6 ++--
 lvnet-0.3.4/lvnet/MD5                  |   19 ++++++------
 lvnet-0.3.4/lvnet/NAMESPACE            |    2 +
 lvnet-0.3.4/lvnet/NEWS                 |    6 ++++
 lvnet-0.3.4/lvnet/R/generateRIMmodel.R |    4 --
 lvnet-0.3.4/lvnet/R/lvnet.R            |    4 --
 lvnet-0.3.4/lvnet/R/lvnetLasso.R       |   49 ++++++++++++++++++++++++++++++---
 lvnet-0.3.4/lvnet/R/methods.R          |    2 -
 lvnet-0.3.4/lvnet/README.md            |only
 lvnet-0.3.4/lvnet/man/lvnetLasso.Rd    |   12 +++++---
 12 files changed, 76 insertions(+), 28 deletions(-)

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New package lmviz with initial version 0.1.1
Package: lmviz
Type: Package
Title: A Package to Visualize Linear Models Features and Play with Them
Version: 0.1.1
Author: Francesco Pauli (see file LICENSEMEDIA for credits on sounds and images)
Maintainer: Francesco Pauli <francesco.pauli@deams.units.it>
Description: Contains three shiny applications. Two are meant to explore linear model inference feature through simulation. The third is a game to learn interpreting diagnostic plots.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: shiny, shinyjs, lmtest, mgcv, methods
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-08 21:56:51 UTC; Franz
Repository: CRAN
Date/Publication: 2018-11-18 18:30:10 UTC

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Package IsoSpecR updated to version 1.9.1 with previous version 1.0.3 dated 2017-01-12

Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most probable masses of a chemical compound given the frequencies of the composing isotopes and their masses. It finds the smallest set of isotopologues with a given probability. The probability is assumed to be that of the product of multinomial distributions, each corresponding to one particular element and parametrized by the frequencies of finding these elements in nature. These numbers are supplied by IUPAC - the International Union of Pure and Applied Chemistry.
Author: Mateusz Krzysztof Lacki and Michal Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>

Diff between IsoSpecR versions 1.0.3 dated 2017-01-12 and 1.9.1 dated 2018-11-18

 IsoSpecR-1.0.3/IsoSpecR/src/lang.h             |only
 IsoSpecR-1.9.1/IsoSpecR/DESCRIPTION            |   11 
 IsoSpecR-1.9.1/IsoSpecR/LICENCE                |    2 
 IsoSpecR-1.9.1/IsoSpecR/MD5                    |   70 +
 IsoSpecR-1.9.1/IsoSpecR/NAMESPACE              |    2 
 IsoSpecR-1.9.1/IsoSpecR/R/IsoSpecR.R           |   21 
 IsoSpecR-1.9.1/IsoSpecR/R/RcppExports.R        |    4 
 IsoSpecR-1.9.1/IsoSpecR/R/data_description.R   |    2 
 IsoSpecR-1.9.1/IsoSpecR/inst                   |only
 IsoSpecR-1.9.1/IsoSpecR/man/IsoSpecify.Rd      |   12 
 IsoSpecR-1.9.1/IsoSpecR/src/IsoSpecR_init.c    |only
 IsoSpecR-1.9.1/IsoSpecR/src/RcppExports.cpp    |    2 
 IsoSpecR-1.9.1/IsoSpecR/src/Rinterface.cpp     |  223 +++--
 IsoSpecR-1.9.1/IsoSpecR/src/allocator.cpp      |    9 
 IsoSpecR-1.9.1/IsoSpecR/src/allocator.h        |   20 
 IsoSpecR-1.9.1/IsoSpecR/src/conf.h             |   12 
 IsoSpecR-1.9.1/IsoSpecR/src/cwrapper.cpp       |  425 ++++-------
 IsoSpecR-1.9.1/IsoSpecR/src/cwrapper.h         |  173 ++--
 IsoSpecR-1.9.1/IsoSpecR/src/dirtyAllocator.cpp |    7 
 IsoSpecR-1.9.1/IsoSpecR/src/dirtyAllocator.h   |   12 
 IsoSpecR-1.9.1/IsoSpecR/src/element_tables.cpp |   24 
 IsoSpecR-1.9.1/IsoSpecR/src/element_tables.h   |   31 
 IsoSpecR-1.9.1/IsoSpecR/src/isoMath.cpp        |  298 -------
 IsoSpecR-1.9.1/IsoSpecR/src/isoMath.h          |   32 
 IsoSpecR-1.9.1/IsoSpecR/src/isoSpec++.cpp      |  955 ++++++++++++-------------
 IsoSpecR-1.9.1/IsoSpecR/src/isoSpec++.h        |  618 +++++++++++-----
 IsoSpecR-1.9.1/IsoSpecR/src/marginalTrek++.cpp |  478 ++++++------
 IsoSpecR-1.9.1/IsoSpecR/src/marginalTrek++.h   |  273 ++++++-
 IsoSpecR-1.9.1/IsoSpecR/src/misc.cpp           |   11 
 IsoSpecR-1.9.1/IsoSpecR/src/misc.h             |   56 +
 IsoSpecR-1.9.1/IsoSpecR/src/mman.cpp           |only
 IsoSpecR-1.9.1/IsoSpecR/src/mman.h             |only
 IsoSpecR-1.9.1/IsoSpecR/src/operators.cpp      |   30 
 IsoSpecR-1.9.1/IsoSpecR/src/operators.h        |   70 +
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 IsoSpecR-1.9.1/IsoSpecR/src/tabulator.cpp      |only
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 IsoSpecR-1.9.1/IsoSpecR/tests                  |only
 40 files changed, 2099 insertions(+), 1799 deletions(-)

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New package cusum with initial version 0.1.0
Package: cusum
Title: CUSUM Charts for Monitoring of Hospital Performance
Version: 0.1.0
Authors@R: c( person("Lena", "Hubig", email = "cs@lenahubig.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9454-1232")))
Description: Provides functions for constructing and evaluating CUSUM charts and RA-CUSUM charts with focus on false signal probability.
Depends: R (>= 3.5.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stats, graphics, checkmate
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-08 14:10:46 UTC; lena
Author: Lena Hubig [aut, cre] (<https://orcid.org/0000-0002-9454-1232>)
Maintainer: Lena Hubig <cs@lenahubig.de>
Repository: CRAN
Date/Publication: 2018-11-18 18:20:02 UTC

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New package bpbounds with initial version 0.1.0
Package: bpbounds
Title: Nonparametric Bounds for the Average Causal Effect Due to Balke and Pearl and Extensions
Version: 0.1.0
Authors@R: c(person("Tom", "Palmer", email = "tom.palmer@lancaster.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4655-4511")), person("Roland", "Ramsahai", role = c("aut")), person("Vanessa", "Didelez", role = c("aut"), comment = c(ORCID = "0000-0001-8587-7706")), person("Nuala", "Sheehan", role = c("aut")))
Description: Implementation of the nonparametric bounds for the average causal effect under an instrumental variable model by Balke and Pearl (Bounds on Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-1176). The package can calculate bounds for a binary outcome, a binary treatment/phenotype, and an instrument with either 2 or 3 categories. The package implements bounds for situations where these 3 variables are measured in the same dataset (trivariate data) or where the outcome and instrument are measured in one study and the treatment/phenotype and instrument are measured in another study (bivariate data).
Depends: R (>= 3.5.0)
Imports: methods
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: dplyr, testthat, knitr, rmarkdown, tidyr
VignetteBuilder: knitr
RoxygenNote: 6.1.0
URL: https://github.com/remlapmot/bpbounds
BugReports: https://github.com/remlapmot/bpbounds/issues
NeedsCompilation: no
Packaged: 2018-11-09 17:42:31 UTC; remlapmot
Author: Tom Palmer [aut, cre] (<https://orcid.org/0000-0003-4655-4511>), Roland Ramsahai [aut], Vanessa Didelez [aut] (<https://orcid.org/0000-0001-8587-7706>), Nuala Sheehan [aut]
Maintainer: Tom Palmer <tom.palmer@lancaster.ac.uk>
Repository: CRAN
Date/Publication: 2018-11-18 19:00:06 UTC

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Package BART updated to version 2.0 with previous version 1.9 dated 2018-08-18

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 1.9 dated 2018-08-18 and 2.0 dated 2018-11-18

 BART-1.9/BART/R/class.ind.R                      |only
 BART-1.9/BART/inst/cxx-ex/cmbart.cpp             |only
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 BART-1.9/BART/src/cmbart.cpp                     |only
 BART-2.0/BART/DESCRIPTION                        |   10 
 BART-2.0/BART/MD5                                |  134 ++++-----
 BART-2.0/BART/NAMESPACE                          |    6 
 BART-2.0/BART/NEWS                               |   16 +
 BART-2.0/BART/R/abart.R                          |    8 
 BART-2.0/BART/R/crisk.bart.R                     |   16 -
 BART-2.0/BART/R/crisk2.bart.R                    |   16 -
 BART-2.0/BART/R/gbart.R                          |   33 +-
 BART-2.0/BART/R/lbart.R                          |    8 
 BART-2.0/BART/R/mbart.R                          |  336 ++++++++++++-----------
 BART-2.0/BART/R/mc.abart.R                       |    8 
 BART-2.0/BART/R/mc.gbart.R                       |   13 
 BART-2.0/BART/R/mc.lbart.R                       |    8 
 BART-2.0/BART/R/mc.mbart.R                       |  152 +++++-----
 BART-2.0/BART/R/mc.pbart.R                       |    8 
 BART-2.0/BART/R/mc.wbart.R                       |    8 
 BART-2.0/BART/R/pbart.R                          |    8 
 BART-2.0/BART/R/predict.mbart.R                  |   61 ++--
 BART-2.0/BART/R/wbart.R                          |    6 
 BART-2.0/BART/build/vignette.rds                 |binary
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 BART-2.0/BART/man/lbart.Rd                       |   14 
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New package argonR with initial version 0.1.0
Package: argonR
Type: Package
Title: R Interface to Argon HTML Design
Version: 0.1.0
Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com", role = c("aut", "cre")), person(family = "Creative Tim", role = c("ctb", "cph"), comment = "Argon theme for Bootstrap 4"), person("Winston", "Chang", role = c("ctb", "cph"), comment = "Unexported functions from htmltools"))
Maintainer: David Granjon <dgranjon@ymail.com>
Description: R wrapper around the argon HTML library. More at <https://demos.creative-tim.com/argon-design-system/>.
URL: https://github.com/RinteRface/argonR
BugReports: https://github.com/RinteRface/argonR/issues
Imports: htmltools, utils
Suggests: magrittr, knitr, rmarkdown
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-09 14:44:34 UTC; macdavidgranjon
Author: David Granjon [aut, cre], Creative Tim [ctb, cph] (Argon theme for Bootstrap 4), Winston Chang [ctb, cph] (Unexported functions from htmltools)
Repository: CRAN
Date/Publication: 2018-11-18 18:40:06 UTC

More information about argonR at CRAN
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Package TraMineR updated to version 2.0-10 with previous version 2.0-9 dated 2018-08-20

Title: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph], Nicolas Müller [aut], Reto Bürgin [aut], Pierre-Alexandre Fonta [aut], Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>

Diff between TraMineR versions 2.0-9 dated 2018-08-20 and 2.0-10 dated 2018-11-18

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Package sigmajs updated to version 0.1.2 with previous version 0.1.1 dated 2018-08-31

Title: Interface to 'Sigma.js' Graph Visualization Library
Description: Interface to 'sigma.js' graph visualization library including animations, plugins and shiny proxies.
Author: John Coene [aut, cre] (<https://orcid.org/0000-0002-6637-4107>)
Maintainer: John Coene <jcoenep@gmail.com>

Diff between sigmajs versions 0.1.1 dated 2018-08-31 and 0.1.2 dated 2018-11-18

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Package icd updated to version 3.3 with previous version 3.2.1 dated 2018-08-18

Title: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
Description: Calculate comorbidities, Charlson and van Walraven scores, perform fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9 and ICD-10 codes. This package enables a work flow from raw lists of ICD codes in hospital databases to comorbidities. ICD-9 and ICD-10 comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Common ambiguities and code formats are handled.
Author: Jack O. Wasey [aut, cre, cph] (<https://orcid.org/0000-0003-3738-4637>), William Murphy [ctb] (Van Walraven scores), Anobel Odisho [ctb] (Hierarchical Condition Codes), Vitaly Druker [ctb] (AHRQ CCS), Ed Lee [ctb] (explain codes in table format)
Maintainer: Jack O. Wasey <jack@jackwasey.com>

Diff between icd versions 3.2.1 dated 2018-08-18 and 3.3 dated 2018-11-18

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 icd-3.3/icd/NAMESPACE                                                                 |    2 
 icd-3.3/icd/NEWS.md                                                                   |   10 
 icd-3.3/icd/R/RcppExports.R                                                           |   62 
 icd-3.3/icd/R/attr.R                                                                  |    7 
 icd-3.3/icd/R/categorize.R                                                            |    2 
 icd-3.3/icd/R/class.R                                                                 |   53 
 icd-3.3/icd/R/comorbid.R                                                              |    4 
 icd-3.3/icd/R/convert.R                                                               |   25 
 icd-3.3/icd/R/datadocs.R                                                              |    8 
 icd-3.3/icd/R/factor_nosort.R                                                         |    1 
 icd-3.3/icd/R/filter.R                                                                |    5 
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 icd-3.3/icd/R/valid.R                                                                 |    2 
 icd-3.3/icd/R/zzz.R                                                                   |   12 
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 icd-3.3/icd/src/appendMinor.cpp                                                       |   15 
 icd-3.3/icd/src/attr.h                                                                |    2 
 icd-3.3/icd/src/categorize.cpp                                                        |    4 
 icd-3.3/icd/src/comorbidIcd10.cpp                                                     |    6 
 icd-3.3/icd/src/comorbidMatMul.cpp                                                    |    7 
 icd-3.3/icd/src/convert.h                                                             |    3 
 icd-3.3/icd/src/cutil.h                                                               |   26 
 icd-3.3/icd/src/fastIntToString.h                                                     |    2 
 icd-3.3/icd/src/guess.cpp                                                             |   96 -
 icd-3.3/icd/src/icd_types.h                                                           |    4 
 icd-3.3/icd/src/is.h                                                                  |    1 
 icd-3.3/icd/src/local.h                                                               |    4 
 icd-3.3/icd/src/longToWide.cpp                                                        |   15 
 icd-3.3/icd/src/manip.cpp                                                             |    4 
 icd-3.3/icd/src/manip.h                                                               |    2 
 icd-3.3/icd/src/ranges.h                                                              |   18 
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 icd-3.3/icd/src/registration.c                                                        |    8 
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 icd-3.3/icd/src/util.cpp                                                              |  272 ---
 icd-3.3/icd/src/util.h                                                                |   12 
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New package sctransform with initial version 0.1.0
Package: sctransform
Type: Package
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Version: 0.1.0
Authors@R: person(given = 'Christoph', family = 'Hafemeister', email = 'chafemeister@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-6365-8254'))
Description: A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction/denoising.
URL: https://github.com/ChristophH/sctransform
BugReports: https://github.com/ChristophH/sctransform/issues
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: MASS, Matrix, parallel, methods
Suggests: matrixStats, testthat
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-16 10:54:11 UTC; chafemeister
Author: Christoph Hafemeister [aut, cre] (<https://orcid.org/0000-0001-6365-8254>)
Maintainer: Christoph Hafemeister <chafemeister@nygenome.org>
Repository: CRAN
Date/Publication: 2018-11-18 16:30:03 UTC

More information about sctransform at CRAN
Permanent link

Package scPDSI updated to version 0.1.3 with previous version 0.1.2 dated 2018-10-31

Title: Calculation of the Conventional and Self-Calibrating Palmer Drought Severity Index
Description: Calculating the monthly conventional and self-calibrating Palmer Drought Severity Index (PDSI and scPDSI) using the precipitation and potential evapotranspiration data. The function to calculate PDSI is based on the C++ source codes developed by Nathan Wells, Steve Goddard and Michael J. Hayes, University of Nebraska-Lincoln. Reference: Palmer W. (1965). Meteorological drought. U.s.department of Commerce Weather Bureau Research Paper, <https://www.ncdc.noaa.gov/temp-and-precip/drought/docs/palmer.pdf>; Wells N., Goddard S., Hayes M. J. (2004). A Self-Calibrating Palmer Drought Severity Index. Journal of Climate, 17(12):2335-2351, <DOI:10.1175/1520-0442(2004)017%3C2335:ASPDSI%3E2.0.CO;2>.
Author: Ruida Zhong [aut, cre], Xiaohong Chen [aut, ctb], Zhaoli Wang [aut, ctb], Chengguang Lai [aut, ctb], Steve Goddard [ctb], Nathan Wells [ctb], Mike Hayes [ctb]
Maintainer: Ruida Zhong <zrd2017@163.com>

Diff between scPDSI versions 0.1.2 dated 2018-10-31 and 0.1.3 dated 2018-11-18

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Permanent link

Package pems.utils updated to version 0.2.26.4 with previous version 0.2.17.8 dated 2016-03-02

Title: Portable Emissions (and Other Mobile) Measurement System Utilities
Description: Utility functions for the handling, analysis and visualisation of data from portable emissions measurement systems ('PEMS') and other similar mobile activity monitoring devices. The package includes a dedicated 'pems' data class that manages many of the quality control, unit handling and data archiving issues that can hinder efforts to standardise 'PEMS' research.
Author: Karl Ropkins [aut, cre], Adrian Felipe Ortega Calle [ctb]
Maintainer: Karl Ropkins <karl.ropkins@gmail.com>

Diff between pems.utils versions 0.2.17.8 dated 2016-03-02 and 0.2.26.4 dated 2018-11-18

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Package cleanNLP updated to version 2.3.0 with previous version 2.0.3 dated 2018-01-22

Title: A Tidy Data Model for Natural Language Processing
Description: Provides a set of fast tools for converting a textual corpus into a set of normalized tables. Users may make use of the 'udpipe' back end with no external dependencies, a Python back end with 'spaCy' <https://spacy.io> or the Java back end 'CoreNLP' <http://stanfordnlp.github.io/CoreNLP/>. Exposed annotation tasks include tokenization, part of speech tagging, named entity recognition, entity linking, sentiment analysis, dependency parsing, coreference resolution, and word embeddings. Summary statistics regarding token unigram, part of speech tag, and dependency type frequencies are also included to assist with analyses.
Author: Taylor B. Arnold [aut, cre]
Maintainer: Taylor B. Arnold <taylor.arnold@acm.org>

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Package SpaDES.core updated to version 0.2.3 with previous version 0.2.2 dated 2018-08-13

Title: Core Utilities for Developing and Running Spatially Explicit Discrete Event Simulation Models
Description: Provide the core discrete event simulation (DES) framework for implementing spatially explicit simulation models. The core DES components facilitate modularity, and easily enable the user to include additional functionality by running user-built simulation modules.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>), Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>), Yong Luo [ctb], Steve Cumming [ctb], Ceres Barros [ctb], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>

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Package pinbasic updated to version 1.2.2 with previous version 1.2.1 dated 2018-08-19

Title: Fast and Stable Estimation of the Probability of Informed Trading (PIN)
Description: Utilities for fast and stable estimation of the probability of informed trading (PIN) in the model introduced by Easley et al. (2002) <DOI:10.1111/1540-6261.00493> are implemented. Since the basic model developed by Easley et al. (1996) <DOI:10.1111/j.1540-6261.1996.tb04074.x> is nested in the former due to equating the intensity of uninformed buys and sells, functions can also be applied to this simpler model structure, if needed. State-of-the-art factorization of the model likelihood function as well as most recent algorithms for generating initial values for optimization routines are implemented. In total, two likelihood factorizations and three methodologies for starting values are included. Furthermore, functions for simulating datasets of daily aggregated buys and sells, calculating confidence intervals for the probability of informed trading and posterior probabilities of trading days' conditions are available.
Author: Andreas Recktenwald [aut, cre]
Maintainer: Andreas Recktenwald <arecktenwald85@gmail.com>

Diff between pinbasic versions 1.2.1 dated 2018-08-19 and 1.2.2 dated 2018-11-18

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Package pdR updated to version 1.6 with previous version 1.5 dated 2017-02-01

Title: Threshold Model and Unit Root Tests in Cross-section and Time Series Data
Description: Threshold model, panel version of Hylleberg et al. (1990) <DOI:10.1016/0304-4076(90)90080-D> seasonal unit root tests, and panel unit root test of Chang (2002) <DOI:10.1016/S0304-4076(02)00095-7>.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

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Package PDFEstimator (with last version 0.1-1) was removed from CRAN

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

2018-11-17 0.1-1

Permanent link
Package SII updated to version 1.0.3.1 with previous version 1.0.3 dated 2013-12-10

Title: Calculate ANSI S3.5-1997 Speech Intelligibility Index
Description: This package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), a standard method for computing the intelligibility of speech from acoustical measurements of speech, noise, and hearing thresholds. This package includes data frames corresponding to Tables 1 - 4 in the ANSI standard as well as a function utilizing these tables and user-provided hearing threshold and noise level measurements to compute the SII score. The methods implemented here extend the standard computations to allow calculation of SII when the measured frequencies do not match those required by the standard by applying interpolation to obtain values for the required frequencies -- Development of this package was funded by the Center for Bioscience Education and Technology (CBET) of the Rochester Institute of Technology (RIT).
Author: Gregory R. Warnes
Maintainer: Gregory R. Warnes <greg@warnes.net>

Diff between SII versions 1.0.3 dated 2013-12-10 and 1.0.3.1 dated 2018-11-18

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Package rcompanion updated to version 2.0.3 with previous version 2.0.0 dated 2018-08-14

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of Extension Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

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