Fri, 21 Dec 2018

New package Rsconctdply with initial version 0.1.3
Package: Rsconctdply
Type: Package
Title: Deploys Multiple 'Shiny' Apps using Configuration File
Version: 0.1.3
Author: Sai Chimata
Maintainer: Sai Chimata <schimata@yotabitesllc.com>
Depends: R (>= 3.0.1)
Imports: rjson, rsconnect, dplyr
Description: Provides a tool for mass deployment of shiny apps to 'RStudio Connect' or 'Shiny Server'. Multiple user accounts and servers can be configured for deployment.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-11 16:33:02 UTC; schimata
Repository: CRAN
Date/Publication: 2018-12-22 01:10:04 UTC

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Package tsxtreme updated to version 0.3.2 with previous version 0.3.1 dated 2017-03-23

Title: Bayesian Modelling of Extremal Dependence in Time Series
Description: Characterisation of the extremal dependence structure of time series, avoiding pre-processing and filtering as done typically with peaks-over-threshold methods. It uses the conditional approach of Heffernan and Tawn (2004) <DOI:10.1111/j.1467-9868.2004.02050.x> which is very flexible in terms of extremal and asymptotic dependence structures, and Bayesian methods improve efficiency and allow for deriving measures of uncertainty. For example, the extremal index, related to the size of clusters in time, can be estimated and samples from its posterior distribution obtained.
Author: Thomas Lugrin
Maintainer: Thomas Lugrin <thomas.lugrin@alumni.epfl.ch>

Diff between tsxtreme versions 0.3.1 dated 2017-03-23 and 0.3.2 dated 2018-12-21

 DESCRIPTION           |   10 
 MD5                   |   16 -
 NEWS.md               |    5 
 build/partial.rdb     |binary
 src/etfit.cpp         |  698 +++++++++++++++++++++++++-------------------------
 src/etfit.h           |   12 
 src/etfit_externC.cpp |   36 +-
 src/init.c            |    2 
 src/tsxtreme.h        |    2 
 9 files changed, 402 insertions(+), 379 deletions(-)

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New package xspliner with initial version 0.0.2
Package: xspliner
Title: Assisted Model Building, using Surrogate Black-Box Models to Train Interpretable Spline Based Additive Models
Version: 0.0.2
Authors@R: c( person("Krystian", "Igras", email = "krystian8207@gmail.com", role = c("aut", "cre")), person("Przemyslaw", "Biecek", role = c("aut", "ths")))
Description: Builds generalized linear model with automatic data transformation. The 'xspliner' helps to build simple, interpretable models that inherits informations provided by more complicated ones. The resulting model may be treated as explanation of provided black box, that was supplied prior to the algorithm.
Depends: R (>= 3.0)
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: stats, pdp, dplyr, ggplot2, mgcv, magrittr, purrr, tidyr
Suggests: ALEPlot, factorMerger, testthat, knitr, rmarkdown, ResourceSelection, randomForest, e1071, caret, breakDown, DALEX, xgboost, gridExtra, grid
VignetteBuilder: knitr
URL: https://ModelOriented.github.io/xspliner/
BugReports: https://github.com/ModelOriented/xspliner/issues
NeedsCompilation: no
Packaged: 2018-12-11 23:05:34 UTC; krystian
Author: Krystian Igras [aut, cre], Przemyslaw Biecek [aut, ths]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-21 15:20:03 UTC

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New package LUCIDus with initial version 0.9.0
Package: LUCIDus
Type: Package
Title: Latent Unknown Clustering with Integrated Data
Version: 0.9.0
Author: Cheng Peng, Zhao Yang, David V. Conti
Maintainer: Cheng Peng <chengpen@usc.edu>
Description: An implementation for the 'LUCID' method to jointly estimate latent unknown clusters/subgroups with integrated data. An EM algorithm is used to obtain the latent cluster assignment and model parameter estimates. Feature selection is achieved by applying the regularization method.
Depends: R (>= 3.1.0)
Imports: mvtnorm, nnet, glmnet, glasso, Matrix, lbfgs, stats, methods, networkD3, foreach, doParallel
Suggests: testthat, knitr, rmarkdown
License: GPL-2
URL: https://github.com/USCbiostats/LUCIDus
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-12 07:08:56 UTC; Cheng
Repository: CRAN
Date/Publication: 2018-12-21 15:20:13 UTC

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New package liayson with initial version 1.0.1
Package: liayson
Type: Package
Title: Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes
Version: 1.0.1
Date: 2018-12-10
Author: Noemi Andor
Maintainer: Noemi Andor <liayson.scRNA.R@gmail.com>
Description: Given an RNA-seq derived cell-by-gene matrix and an DNA-seq derived copy number segmentation, LIAYSON predicts the number of clones present in a tumor, their size, the copy number profile of each clone and the clone membership of each single cell.
License: GPL-2
URL: https://github.com/noemiandor/liayson, https://groups.google.com/d/forum/liayson
Depends: R (>= 3.0)
Imports: phangorn, RColorBrewer, ape, parallel, plyr, matlab, biomaRt, distances, arules, e1071, proxy, gplots, methods
Suggests: mclust, fpc, NbClust, modeest, pastecs, vegan
Packaged: 2018-12-12 21:02:19 UTC; noemi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-12-21 15:30:03 UTC
RoxygenNote: 6.1.0

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New package hctrial with initial version 0.1.0
Package: hctrial
Type: Package
Title: Using Historical Controls for Designing Phase II Clinical Trials
Version: 0.1.0
Authors@R: person("Dominic", "Edelmann", email = "dominic.edelmann@dkfz-heidelberg.de", role = c("aut", "cre"))
Description: Provides functions for designing phase II clinical trials adjusting for the heterogeneity of the population using known subgroups or historical controls.
Depends: R (>= 3.5.0)
License: GPL-2 | GPL-3
LazyData: TRUE
RoxygenNote: 6.1.1
Imports: clinfun, GenBinomApps, stats
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-12-12 08:06:44 UTC; edelmand
Author: Dominic Edelmann [aut, cre]
Maintainer: Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>
Repository: CRAN
Date/Publication: 2018-12-21 15:20:06 UTC

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New package GenoScan with initial version 0.1
Package: GenoScan
Type: Package
Title: A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence Data Analysis
Version: 0.1
Date: 2018-11-13
Author: Zihuai He
Maintainer: Zihuai He <zihuai@stanford.edu>
Description: Functions for whole-genome sequencing studies, including genome-wide scan, candidate region scan and single window test.
License: GPL-3
Depends: R(>= 2.10.0), SKAT, Matrix, MASS, seqminer, data.table
NeedsCompilation: no
Packaged: 2018-12-11 18:20:45 UTC; zhe
Repository: CRAN
Date/Publication: 2018-12-21 15:20:16 UTC

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New package fam.recrisk with initial version 0.1
Package: fam.recrisk
Type: Package
Title: Familial Recurrence Risk
Version: 0.1
Date: 2018-12-07
Authors@R: c(person("Schaid", "Daniel", role="aut"), person("Jason", "Sinnwell", email="sinnwell.jason@mayo.edu",role=c("aut","cre")))
Description: Given vectors of family sizes and number of affecteds per family, calculates the risk of disease recurrence in an unaffected person, conditional on a family having at least k affected members. Methods also model heterogeneity of disease risk across families by fitting a mixture model, allowing for high and low risk families.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 3.2.0), stats, utils
NeedsCompilation: no
Author: Schaid Daniel [aut], Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Packaged: 2018-12-11 22:48:35 UTC; sinnwell
Repository: CRAN
Date/Publication: 2018-12-21 15:20:10 UTC

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New package Buddle with initial version 1.0
Package: Buddle
Type: Package
Title: A Deep Learning Package for Statistical Classification Analysis
Version: 1.0
Date: 2018-12-11
Author: Jiwoong Kim <ji_woong_kim@hotmail.com>
Maintainer: Jiwoong Kim <jwboys26@gmail.com>
Description: Statistical classification has been popular among various fields and stayed in the limelight of scientists of those fields. Examples of the fields include clinical trials where the statistical classification of patients is indispensable to predict the clinical courses of diseases. Considering the negative impact of diseases on performing daily tasks, correctly classifying patients based on the clinical information is vital in that we need to identify patients of the high-risk group to develop a severe state and arrange medical treatment for them at an opportune moment. Deep learning - a part of artificial intelligence - has gained much attention, and research on it burgeons during past decades. It is a veritable technique which was originally designed for the classification, and hence, the EzDL package can provide sublime solutions to various challenging classification problems encountered in the clinical trials. The EzDL package is based on the back-propagation algorithm which performs a multi-layer feed-forward neural network. This package contains two functions: Buddle_Main() and Buddle_Predict(). Buddle_Main() builds a feed-forward neural network model and trains the model. Buddle_Predict() provokes the trained model which is the output of Buddle_Main(), classifies given data, and make a final prediction for the data.
Encoding: UTF-8
Depends: R (>= 3.2.2)
License: GPL-2
LazyData: TRUE
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2018-12-10 23:34:21 UTC; NEW0830
Repository: CRAN
Date/Publication: 2018-12-21 15:50:03 UTC

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New package antaresEditObject with initial version 0.1.5
Package: antaresEditObject
Type: Package
Title: Edit an 'Antares' Simulation
Version: 0.1.5
Authors@R: c( person("Frederic", "Breant", email = "frederic.breant@rte-france.com", role = c("aut", "cre")), person("Victor", "Perrier", email = "victor.perrier@dreamRs.fr", role = c("aut")), person("Baptiste", "Seguinot", email = "baptiste.seguinot@rte-france.com", role = "ctb"), person("Benoit", "Thieurmel", email = "benoit.thieurmel@datastorm.fr", role = "ctb"), person("Titouan", "Robert", email = "titouan.robert@datastorm.fr", role = "ctb"), person("Jalal-Edine", "Zawam", email = "jalal-edine.zawam@rte-france.com", role = "ctb"), person("RTE", role = "cph"))
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
License: GPL (>= 2) | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: antaresRead
Imports: assertthat, grDevices, data.table, whisker
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2018-12-11 12:55:45 UTC; perri
Author: Frederic Breant [aut, cre], Victor Perrier [aut], Baptiste Seguinot [ctb], Benoit Thieurmel [ctb], Titouan Robert [ctb], Jalal-Edine Zawam [ctb], RTE [cph]
Maintainer: Frederic Breant <frederic.breant@rte-france.com>
Repository: CRAN
Date/Publication: 2018-12-21 15:40:03 UTC

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New package AeRobiology with initial version 1.0.0
Package: AeRobiology
Type: Package
Title: A Computational Tool for Aerobiological Data
Version: 1.0.0
Author: Jesus Rojo, Antonio Picornell, Jose Oteros
Maintainer: "Jesus Rojo, Antonio Picornell, Jose Oteros" <aerobiology.package@gmail.com>
Description: Different tools for managing aeriobiological databases, elaborating the main calculations and visualization of results. In a first step, data are checked using tools for quality control and all missing gaps are completed. Then, the main parameters of the pollen season are calculated and represented graphically. Multiple graphical tools are available: pollen calendars, phenological plots, time series, tendencies, interactive plots, abundance plots...
License: GPL-3
Depends: R (>= 2.10)
Imports: devtools, plyr, dplyr, reshape2, writexl, ggvis, lubridate, plotly, ggplot2, imager, tidyr, circular, scales, grDevices, zoo, grid
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-12 14:43:43 UTC; MSI
Repository: CRAN
Date/Publication: 2018-12-21 15:40:07 UTC

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New package webddx with initial version 0.1.0
Package: webddx
Type: Package
Title: Interact with Online Differential Diagnosis-Generating Tools
Version: 0.1.0
Authors@R: c(person("Raoul", "Wadhwa", email = "raoulwadhwa@gmail.com", role = c("aut", "cre")), person("Marvin", "Natowicz", role = "aut"), person("Deborah", "Park", role = "ctb"))
Description: Freely available online differential-diagnosis generating tools are changing clinical medicine and biomedical research. With webddx, useRs can generate differential diagnosis lists given a set of symptoms. The web tools would likely be directly used in clinical practice, but programmatic interaction and data manipulation can sharply increase efficiency and reproducibility of research in clinical informatics. Relevant visualizations can also be created with webddx.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: jsonlite (>= 1.5)
Suggests: covr, testthat
URL: https://github.com/rrrlw/webddx
BugReports: https://github.com/rrrlw/webddx/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-12-11 14:27:08 UTC; WADHWAR
Author: Raoul Wadhwa [aut, cre], Marvin Natowicz [aut], Deborah Park [ctb]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-21 14:20:03 UTC

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Package spatialEco updated to version 1.1-1 with previous version 1.1-0 dated 2018-03-06

Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling and modelling. Functions include models for species population density, download utilities for climate and global deforestation spatial products, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, polygon and point-distance landscape metrics, auto-logistic model, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre], Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>

Diff between spatialEco versions 1.1-0 dated 2018-03-06 and 1.1-1 dated 2018-12-21

 spatialEco-1.1-0/spatialEco/R/se.news.R                      |only
 spatialEco-1.1-0/spatialEco/R/zzz.R                          |only
 spatialEco-1.1-0/spatialEco/inst/NEWS                        |only
 spatialEco-1.1-0/spatialEco/man/se.news.Rd                   |only
 spatialEco-1.1-1/spatialEco/DESCRIPTION                      |   17 -
 spatialEco-1.1-1/spatialEco/MD5                              |  135 ++++----
 spatialEco-1.1-1/spatialEco/NAMESPACE                        |    9 
 spatialEco-1.1-1/spatialEco/NEWS                             |only
 spatialEco-1.1-1/spatialEco/R/DAYMET_tiles-data.R            |    2 
 spatialEco-1.1-1/spatialEco/R/ants-data.R                    |    3 
 spatialEco-1.1-1/spatialEco/R/breeding.density.R             |   11 
 spatialEco-1.1-1/spatialEco/R/class.comparison.R             |    8 
 spatialEco-1.1-1/spatialEco/R/concordance.R                  |    9 
 spatialEco-1.1-1/spatialEco/R/conf.interval.R                |    3 
 spatialEco-1.1-1/spatialEco/R/correlogram.R                  |    2 
 spatialEco-1.1-1/spatialEco/R/crossCorrelation.R             |  108 +++---
 spatialEco-1.1-1/spatialEco/R/csi.R                          |   16 
 spatialEco-1.1-1/spatialEco/R/curvature.R                    |  101 ++++--
 spatialEco-1.1-1/spatialEco/R/daymet.point.R                 |    6 
 spatialEco-1.1-1/spatialEco/R/daymet.tiles.R                 |    8 
 spatialEco-1.1-1/spatialEco/R/dispersion.R                   |    9 
 spatialEco-1.1-1/spatialEco/R/dissection.R                   |    3 
 spatialEco-1.1-1/spatialEco/R/download.daymet.R              |   21 -
 spatialEco-1.1-1/spatialEco/R/download.hansen.R              |   36 +-
 spatialEco-1.1-1/spatialEco/R/effect.size.R                  |   15 
 spatialEco-1.1-1/spatialEco/R/hli.R                          |   42 +-
 spatialEco-1.1-1/spatialEco/R/hybrid.kmeans.R                |only
 spatialEco-1.1-1/spatialEco/R/kl.divergence.R                |   10 
 spatialEco-1.1-1/spatialEco/R/land.metrics.R                 |   67 ++--
 spatialEco-1.1-1/spatialEco/R/logistic.regression.R          |    2 
 spatialEco-1.1-1/spatialEco/R/morans.plot.R                  |only
 spatialEco-1.1-1/spatialEco/R/optimized.sample.variance.R    |    3 
 spatialEco-1.1-1/spatialEco/R/raster.kendall.R               |  179 ++++++++---
 spatialEco-1.1-1/spatialEco/R/raster.mds.R                   |   12 
 spatialEco-1.1-1/spatialEco/R/raster.modifed.ttest.R         |   90 ++---
 spatialEco-1.1-1/spatialEco/R/sg.smooth.R                    |only
 spatialEco-1.1-1/spatialEco/R/smooth.time.series.R           |only
 spatialEco-1.1-1/spatialEco/R/spherical.sd.R                 |only
 spatialEco-1.1-1/spatialEco/R/subsample.distance.R           |only
 spatialEco-1.1-1/spatialEco/R/swvi.R                         |only
 spatialEco-1.1-1/spatialEco/R/tpi.R                          |    6 
 spatialEco-1.1-1/spatialEco/inst/CITATION                    |    4 
 spatialEco-1.1-1/spatialEco/man/DAYMET_tiles.Rd              |    2 
 spatialEco-1.1-1/spatialEco/man/ants.Rd                      |    3 
 spatialEco-1.1-1/spatialEco/man/breeding.density.Rd          |   14 
 spatialEco-1.1-1/spatialEco/man/class.comparison.Rd          |   13 
 spatialEco-1.1-1/spatialEco/man/concordance.Rd               |    8 
 spatialEco-1.1-1/spatialEco/man/conf.interval.Rd             |    3 
 spatialEco-1.1-1/spatialEco/man/correlogram.Rd               |    2 
 spatialEco-1.1-1/spatialEco/man/crossCorrelation.Rd          |   41 +-
 spatialEco-1.1-1/spatialEco/man/csi.Rd                       |   15 
 spatialEco-1.1-1/spatialEco/man/curvature.Rd                 |   60 ++-
 spatialEco-1.1-1/spatialEco/man/daymet.point.Rd              |   10 
 spatialEco-1.1-1/spatialEco/man/daymet.tiles.Rd              |    9 
 spatialEco-1.1-1/spatialEco/man/dispersion.Rd                |    9 
 spatialEco-1.1-1/spatialEco/man/download.daymet.Rd           |   28 +
 spatialEco-1.1-1/spatialEco/man/download.hansen.Rd           |   48 ++
 spatialEco-1.1-1/spatialEco/man/effect.size.Rd               |   15 
 spatialEco-1.1-1/spatialEco/man/hli.Rd                       |   13 
 spatialEco-1.1-1/spatialEco/man/hybrid.kmeans.Rd             |only
 spatialEco-1.1-1/spatialEco/man/kl.divergence.Rd             |   10 
 spatialEco-1.1-1/spatialEco/man/land.metrics.Rd              |   62 ++-
 spatialEco-1.1-1/spatialEco/man/logistic.regression.Rd       |    2 
 spatialEco-1.1-1/spatialEco/man/morans.plot.Rd               |only
 spatialEco-1.1-1/spatialEco/man/optimal.k.Rd                 |    3 
 spatialEco-1.1-1/spatialEco/man/optimized.sample.variance.Rd |    3 
 spatialEco-1.1-1/spatialEco/man/poly.regression.Rd           |    4 
 spatialEco-1.1-1/spatialEco/man/pseudo.absence.Rd            |    4 
 spatialEco-1.1-1/spatialEco/man/raster.deviation.Rd          |    3 
 spatialEco-1.1-1/spatialEco/man/raster.kendall.Rd            |   51 ++-
 spatialEco-1.1-1/spatialEco/man/raster.mds.Rd                |   12 
 spatialEco-1.1-1/spatialEco/man/raster.modifed.ttest.Rd      |   27 -
 spatialEco-1.1-1/spatialEco/man/rasterCorrelation.Rd         |    3 
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 spatialEco-1.1-1/spatialEco/man/swvi.Rd                      |only
 78 files changed, 937 insertions(+), 477 deletions(-)

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Package ps updated to version 1.3.0 with previous version 1.2.1 dated 2018-11-06

Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut], Dave Daeschler [aut], Giampaolo Rodola' [aut], Gábor Csárdi [aut, cre], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between ps versions 1.2.1 dated 2018-11-06 and 1.3.0 dated 2018-12-21

 DESCRIPTION                  |    8 +-
 MD5                          |   29 ++++----
 NAMESPACE                    |    1 
 NEWS.md                      |    5 +
 R/linux.R                    |   26 +++++++
 R/package.R                  |    2 
 R/system.R                   |   35 ++++++++++
 build/ps.pdf                 |binary
 man/ps_cpu_count.Rd          |only
 src/api-linux.c              |   12 +++
 src/api-macos.c              |   20 ++++++
 src/api-windows.c            |  141 +++++++++++++++++++++++++++++++++++++++++++
 src/dummy.c                  |    2 
 src/init.c                   |   10 +--
 src/ps.h                     |    2 
 tests/testthat/test-system.R |    8 ++
 16 files changed, 279 insertions(+), 22 deletions(-)

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Package prophet updated to version 0.4 with previous version 0.3.0.1 dated 2018-06-15

Title: Automatic Forecasting Procedure
Description: Implements a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data. Prophet is robust to missing data and shifts in the trend, and typically handles outliers well.
Author: Sean Taylor [cre, aut], Ben Letham [aut]
Maintainer: Sean Taylor <sjt@fb.com>

Diff between prophet versions 0.3.0.1 dated 2018-06-15 and 0.4 dated 2018-12-21

 DESCRIPTION                        |   14 +-
 MD5                                |   32 ++++--
 NAMESPACE                          |    2 
 R/data.R                           |only
 R/diagnostics.R                    |    1 
 R/make_holidays.R                  |only
 R/plot.R                           |    4 
 R/prophet.R                        |  181 +++++++++++++++++++++++++++++--------
 data                               |only
 inst/doc/quick_start.html          |   34 +++---
 man/add_country_holidays.Rd        |only
 man/construct_holiday_dataframe.Rd |only
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 man/get_holiday_names.Rd           |only
 man/make_holiday_features.Rd       |    5 -
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 man/plot_forecast_component.Rd     |    3 
 man/validate_inputs.Rd             |    3 
 src/install.libs.R                 |   16 ++-
 tests/testthat/test_diagnostics.R  |    3 
 tests/testthat/test_prophet.R      |   53 +++++++++-
 21 files changed, 261 insertions(+), 90 deletions(-)

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New package HyRiM with initial version 1.0.0
Package: HyRiM
Type: Package
Title: Multicriteria Risk Management using Zero-Sum Games with Vector-Valued Payoffs that are Probability Distributions
Version: 1.0.0
Date: 2018-12-11
Imports: compare, orthopolynom
Author: Stefan Rass, Sandra Koenig
Maintainer: Austrian Institute of Technology <hyrim@ait.ac.at>
Description: Construction and analysis of multivalued zero-sum matrix games over the abstract space of probability distributions, which describe the losses in each scenario of defense vs. attack action. The distributions can be compiled directly from expert opinions or other empirical data (insofar available). The package implements the methods put forth in the EU project HyRiM (Hybrid Risk Management for Utility Networks), FP7 EU Project Number 608090.
License: GPL-3
NeedsCompilation: no
Packaged: 2018-12-11 07:51:34 UTC; stefan
Encoding: UTF-8
Suggests: knitr, rmarkdown
Repository: CRAN
Date/Publication: 2018-12-21 14:20:07 UTC

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Package hdrcde updated to version 3.3 with previous version 3.2 dated 2018-01-29

Title: Highest Density Regions and Conditional Density Estimation
Description: Computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate,and multimodal regression.
Author: Rob Hyndman [aut, cre, cph], Jochen Einbeck [ctb], Matthew Wand [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

Diff between hdrcde versions 3.2 dated 2018-01-29 and 3.3 dated 2018-12-21

 DESCRIPTION           |    9 ++---
 MD5                   |   27 +++++++--------
 NEWS.md               |   89 ++++++++++++++++++++++++++------------------------
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 man/plot.cde.Rd       |    5 +-
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 15 files changed, 175 insertions(+), 141 deletions(-)

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Package googleAnalyticsR updated to version 0.6.0 with previous version 0.5.0 dated 2018-02-16

Title: Google Analytics API into R
Description: Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, and Multi-Channel Funnel API.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>), Artem Klevtsov [ctb], Johann deBoer [ctb], David Watkins [ctb], Olivia Brode-Roger [ctb], Jas Sohi [ctb], Zoran Selinger [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

Diff between googleAnalyticsR versions 0.5.0 dated 2018-02-16 and 0.6.0 dated 2018-12-21

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More information about googleAnalyticsR at CRAN
Permanent link

Package crmPack updated to version 0.2.9 with previous version 0.2.7 dated 2018-03-13

Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose escalation designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. The focus is on Bayesian inference, making it very easy to setup a new design with its own JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove [aut], Wai Yin Yeung [aut], Giuseppe Palermo [aut, cre], Thomas Jaki [aut]
Maintainer: Giuseppe Palermo <giuseppe.palermo@roche.com>

Diff between crmPack versions 0.2.7 dated 2018-03-13 and 0.2.9 dated 2018-12-21

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More information about crmPack at CRAN
Permanent link

Package copula updated to version 0.999-19 with previous version 0.999-18 dated 2017-09-01

Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] (<https://orcid.org/0000-0001-8009-4665>), Ivan Kojadinovic [aut] (<https://orcid.org/0000-0002-2903-1543>), Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>), Johanna G. Nešlehová [ctb] (evTestK(), <https://orcid.org/0000-0001-9634-4796>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

Diff between copula versions 0.999-18 dated 2017-09-01 and 0.999-19 dated 2018-12-21

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Package tm updated to version 0.7-6 with previous version 0.7-5 dated 2018-07-29

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] (<https://orcid.org/0000-0001-7656-8338>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>

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New package subtee with initial version 0.3-3
Package: subtee
Type: Package
Title: Subgroup Treatment Effect Estimation in Clinical Trials
Version: 0.3-3
Date: 2018-12-11
Author: Nicolas Ballarini [aut, cre], Bjoern Bornkamp [aut], Marius Thomas [aut, cre], Baldur Magnusson [ctb]
Maintainer: Nicolas Ballarini <nicolas.ballarini@meduniwien.ac.at>
Description: Naive and adjusted treatment effect estimation for subgroups. Model averaging and bagging are proposed to address the problem of selection bias in treatment effect estimates for subgroups. The package can be used for all commonly encountered type of outcomes in clinical trials (continuous, binary, survival, count). Additional functions are provided to build the subgroup variables to be used and to plot the results using forest plots.
Imports: MASS, ggplot2, survival, matrixStats
Suggests: knitr, parallel
VignetteBuilder: knitr
Depends: R (>= 2.10)
License: GPL-2
NeedsCompilation: no
Packaged: 2018-12-11 13:39:51 UTC; nico
Repository: CRAN
Date/Publication: 2018-12-21 13:50:03 UTC

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Package Rdimtools updated to version 0.4.2 with previous version 0.4.1 dated 2018-11-15

Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques. Intrinsic dimension estimation methods for exploratory analysis are also provided. For more details on dimensionality techniques, see the paper by Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in statistical approach, or Engel, Huttenberger, and Hamann (2012) <doi:10.4230/OASIcs.VLUDS.2011.135> for a broader multi-disciplinary overview.
Author: Changhee Suh [aut], Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>

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New package RcmdrPlugin.TeachStat with initial version 1.0.10
Package: RcmdrPlugin.TeachStat
Type: Package
Title: RCommander Plugin for Teaching Statistical Methods
Version: 1.0.10
Authors@R: c( person("Toms R.", "Cotos Yaez", email="cotos@uvigo.es",role = "aut",comment = c(ORCID = "0000-0002-7732-6565")), person("Manuel A.", "Mosquera Rodrguez", email = "mamrguez@uvigo.es", role = c("aut","cre"),comment = c(ORCID = "0000-0002-4769-6119")), person("Ana", "Prez Gonzlez", email = "anapg@uvigo.es", role = "aut",comment = c(ORCID = "0000-0003-4706-7125")), person("Benigno", "Reguengo Lareo", role = "aut"))
Description: RCommander plugin for teaching statistical methods. It adds a new menu for making easier the teaching of the main concepts about the main statistical methods.
License: GPL (>= 2)
Imports: Rcmdr (>= 2.3-0), Hmisc, tcltk2, randtests, tseries
Suggests: tkrplot
LazyData: TRUE
Encoding: latin1
NeedsCompilation: no
Packaged: 2018-12-11 17:01:43 UTC; alfredo
Author: Toms R. Cotos Yaez [aut] (<https://orcid.org/0000-0002-7732-6565>), Manuel A. Mosquera Rodrguez [aut, cre] (<https://orcid.org/0000-0002-4769-6119>), Ana Prez Gonzlez [aut] (<https://orcid.org/0000-0003-4706-7125>), Benigno Reguengo Lareo [aut]
Maintainer: Manuel A. Mosquera Rodrguez <mamrguez@uvigo.es>
Repository: CRAN
Date/Publication: 2018-12-21 14:00:17 UTC

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New package mirtjml with initial version 1.2
Package: mirtjml
Type: Package
Title: Joint Maximum Likelihood Estimation for High-Dimensional Item Factor Analysis
Version: 1.2
Date: 2018-12-11
Authors@R: c( person("Siliang", "Zhang", email = "zhangsiliang123@gmail.com", role = c("aut", "cre")), person("Yunxiao", "Chen", role = "aut"), person("Xiaoou", "Li", role = "aut") )
Author: Siliang Zhang [aut, cre], Yunxiao Chen [aut], Xiaoou Li [aut]
Maintainer: Siliang Zhang <zhangsiliang123@gmail.com>
Description: Provides constrained joint maximum likelihood estimation algorithms for item factor analysis (IFA) based on multidimensional item response theory models. So far, we provide functions for exploratory and confirmatory IFA based on the multidimensional two parameter logistic (M2PL) model for binary response data. Comparing with traditional estimation methods for IFA, the methods implemented in this package scale better to data with large numbers of respondents, items, and latent factors. The computation is facilitated by multiprocessing 'OpenMP' API. For more information, please refer to: 1. Chen, Y., Li, X., & Zhang, S. (2018). Joint Maximum Likelihood Estimation for High-Dimensional Exploratory Item Factor Analysis. Psychometrika, 1-23. <doi:10.1007/s11336-018-9646-5>; 2. Chen, Y., Li, X., & Zhang, S. (2017). Structured Latent Factor Analysis for Large-scale Data: Identifiability, Estimability, and Their Implications. arXiv preprint <arXiv:1712.08966>.
License: GPL-3
URL: https://github.com/slzhang-fd/mirtjml
BugReports: https://github.com/slzhang-fd/mirtjml/issues
LazyData: true
Depends: R (>= 3.1)
Imports: Rcpp (>= 0.12.17), stats, GPArotation
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.1.0
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2018-12-11 13:28:39 UTC; siliangzhang
Repository: CRAN
Date/Publication: 2018-12-21 13:50:06 UTC

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Package lobstr updated to version 1.0.1 with previous version 1.0.0 dated 2018-11-04

Title: Visualize R Data Structures with Trees
Description: A set of tools for inspecting and understanding R data structures inspired by str(). Includes ast() for visualizing abstract syntax trees, ref() for showing shared references, cst() for showing call stack trees, and obj_size() for computing object sizes.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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New package kernhaz with initial version 0.1.0
Package: kernhaz
Type: Package
Title: Kernel Estimation of Hazard Function in Survival Analysis
Version: 0.1.0
Authors@R: c( person(given = "Iveta", family = "Selingerova", email = "selingerova@math.muni.cz", role = c("aut", "cre")), person(given = "Marie", family = "Langrova", role = "ctb"))
Description: Producing kernel estimates of the unconditional and conditional hazard function for right-censored data including methods of bandwidth selection.
Depends: R(>= 3.2.0)
Imports: rgl, foreach, doParallel, GA
Suggests: survival
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-11 12:50:22 UTC; selingerova
Author: Iveta Selingerova [aut, cre], Marie Langrova [ctb]
Maintainer: Iveta Selingerova <selingerova@math.muni.cz>
Repository: CRAN
Date/Publication: 2018-12-21 13:40:03 UTC

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New package FastLZeroSpikeInference with initial version 2018.12.10
Package: FastLZeroSpikeInference
Maintainer: Sean Jewell <swjewell@uw.edu>
Author: Sean Jewell, Toby Dylan Hocking
Version: 2018.12.10
License: GPL-3
Title: Fast Nonconvex Deconvolution of Calcium Imaging Data
Description: Estimate spike times from calcium imaging data using an L0 penalty.
Depends: R (>= 2.10)
Suggests: testthat
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2018-12-11 17:14:12 UTC; jewellsean
Repository: CRAN
Date/Publication: 2018-12-21 13:50:12 UTC

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Package effsize updated to version 0.7.4 with previous version 0.7.1 dated 2017-03-21

Title: Efficient Effect Size Computation
Description: A collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.
Author: Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano <marco.torchiano@polito.it>

Diff between effsize versions 0.7.1 dated 2017-03-21 and 0.7.4 dated 2018-12-21

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Package topicmodels updated to version 0.2-8 with previous version 0.2-7 dated 2017-11-03

Title: Topic Models
Description: Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
Author: Bettina Grün [aut, cre] (<https://orcid.org/0000-0001-7265-4773>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Bettina Grün <Bettina.Gruen@jku.at>

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Package slam updated to version 0.1-44 with previous version 0.1-43 dated 2018-04-23

Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), David Meyer [aut], Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between slam versions 0.1-43 dated 2018-04-23 and 0.1-44 dated 2018-12-21

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Package gcKrig updated to version 1.1.3 with previous version 1.1.2 dated 2018-07-31

Title: Analysis of Geostatistical Count Data using Gaussian Copulas
Description: Provides a variety of functions to analyze and model geostatistical count data with Gaussian copulas, including 1) data simulation and visualization; 2) correlation structure assessment (here also known as the Normal To Anything); 3) calculate multivariate normal rectangle probabilities; 4) likelihood inference and parallel prediction at predictive locations.
Author: Zifei Han
Maintainer: Zifei Han <hanzifei1@gmail.com>

Diff between gcKrig versions 1.1.2 dated 2018-07-31 and 1.1.3 dated 2018-12-21

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New package SGL with initial version 1.2
Package: SGL
Type: Package
Title: Fit a GLM (or Cox Model) with a Combination of Lasso and Group Lasso Regularization
Version: 1.2
Date: 2018-12-20
Author: Noah Simon, Jerome Friedman, Trevor Hastie, and Rob Tibshirani
Maintainer: Noah Simon <nrsimon@uw.edu>
Description: Fit a regularized generalized linear model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. Fits linear, logistic and Cox models.
License: GPL
LazyLoad: yes
Packaged: 2018-12-21 00:28:03 UTC; noahsimon
Repository: CRAN
Date/Publication: 2018-12-21 09:20:09 UTC
NeedsCompilation: yes

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Package readr updated to version 1.3.1 with previous version 1.3.0 dated 2018-12-11

Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Romain Francois [aut], R Core Team [ctb] (Date time code adapted from R), RStudio [cph, fnd], Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jim Hester <james.hester@rstudio.com>

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Package RDieHarder updated to version 0.2.0 with previous version 0.1.4 dated 2018-03-15

Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to the 'DieHarder' suite of random number generators and tests that was developed by Robert G. Brown and David Bauer, extending earlier work by George Marsaglia and others. The 'DieHarder' library is included, but if a version is already installed it will be used instead.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package callr updated to version 3.1.1 with previous version 3.1.0 dated 2018-12-10

Title: Call R from R
Description: It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>), Winston Chang [aut], RStudio [cph, fnd], Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between callr versions 3.1.0 dated 2018-12-10 and 3.1.1 dated 2018-12-21

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 21 files changed, 136 insertions(+), 73 deletions(-)

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Package bookdown updated to version 0.9 with previous version 0.8 dated 2018-12-03

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Christophe Dervieux [ctb], Clifton Franklund [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Ellis Valentiner [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Noam Ross [ctb], Peter Hickey [ctb], Sahir Bhatnagar [ctb], Steve Simpson [ctb], Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>), Vincent Fulco [ctb], Yixuan Qiu [ctb], Zhuoer Dong [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between bookdown versions 0.8 dated 2018-12-03 and 0.9 dated 2018-12-21

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 6 files changed, 34 insertions(+), 10 deletions(-)

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Package benford.analysis updated to version 0.1.5 with previous version 0.1.4.1 dated 2017-03-22

Title: Benford Analysis for Data Validation and Forensic Analytics
Description: Provides tools that make it easier to validate data using Benford's Law.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>

Diff between benford.analysis versions 0.1.4.1 dated 2017-03-22 and 0.1.5 dated 2018-12-21

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 8 files changed, 103 insertions(+), 32 deletions(-)

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Package mixOmics (with last version 6.3.2) was removed from CRAN

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

2018-06-01 6.3.2
2017-11-26 6.3.1
2017-10-13 6.3.0
2017-08-17 6.2.0
2017-05-11 6.1.3
2017-02-27 6.1.2
2016-10-19 6.1.1
2016-09-04 6.1.0
2016-06-14 6.0.0
2015-11-19 5.2.0
2015-08-29 5.1.2
2015-07-30 5.1.1
2015-04-28 5.0-4
2014-09-01 5.0-3
2014-08-10 5.0-2
2013-11-10 5.0-1
2013-09-03 4.1-5
2013-03-06 4.1-4
2013-02-20 4.1-3

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Package bayesm updated to version 3.1-1 with previous version 3.1-0.1 dated 2017-07-21

Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda, Rossi 2009) For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>

Diff between bayesm versions 3.1-0.1 dated 2017-07-21 and 3.1-1 dated 2018-12-21

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 13 files changed, 341 insertions(+), 328 deletions(-)

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Package bigalgebra updated to version 0.8.4.1 with previous version 0.8.4 dated 2014-04-16

Title: BLAS routines for native R matrices and big.matrix objects.
Description: This package provides arithmetic functions for R matrix and big.matrix objects.
Author: Michael J. Kane, Bryan Lewis, and John W. Emerson
Maintainer: ORPHANED

Diff between bigalgebra versions 0.8.4 dated 2014-04-16 and 0.8.4.1 dated 2018-12-21

 DESCRIPTION      |   11 +++++++----
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 3 files changed, 10 insertions(+), 7 deletions(-)

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