Fri, 29 Mar 2019

New package steps with initial version 0.2.0
Package: steps
Type: Package
Title: Spatially- and Temporally-Explicit Population Simulator
Version: 0.2.0
Date: 2019-03-27
Authors@R: c( person("Casey", "Visintin", email = "casey.visintin@unimelb.edu.au", role=c("aut", "cre")), person("Nick", "Golding", email = "nick.golding.research@gmail.com", role = "ctb"), person("Skipton", "Woolley", email = "skip.woolley@csiro.au", role = "ctb"), person("John", "Baumgartner", email = "john.baumgartner@mq.edu.au", role = "ctb") )
Maintainer: Casey Visintin <casey.visintin@unimelb.edu.au>
Description: Software to simulate population dynamics across space and time.
Depends: R (>= 3.2.2)
License: GPL (>= 2)
Imports: Rcpp, magrittr, RColorBrewer, plyr, raster, rgdal, sp, methods, igraph, scales, future, future.apply, rasterVis, viridisLite, memuse
LinkingTo: Rcpp
RoxygenNote: 6.1.1
Suggests: testthat, fields, knitr, rmarkdown, foreach
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2019-03-29 03:26:37 UTC; casey
Author: Casey Visintin [aut, cre], Nick Golding [ctb], Skipton Woolley [ctb], John Baumgartner [ctb]
Repository: CRAN
Date/Publication: 2019-03-29 22:10:03 UTC

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Package conflicted updated to version 1.0.2 with previous version 1.0.1 dated 2018-10-02

Title: An Alternative Conflict Resolution Strategy
Description: R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between conflicted versions 1.0.1 dated 2018-10-02 and 1.0.2 dated 2019-03-29

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Package autoFRK updated to version 1.1.0 with previous version 1.0.0 dated 2018-04-05

Title: Automatic Fixed Rank Kriging
Description: Automatic fixed rank kriging for (irregularly located) spatial data using a class of basis functions with multi-resolution features and ordered in terms of their resolutions. The model parameters are estimated by maximum likelihood (ML) and the number of basis functions is determined by Akaike's information criterion (AIC). For spatial data with either one realization or independent replicates, the ML estimates and AIC are efficiently computed using their closed-form expressions when no missing value occurs. Details regarding the basis function construction, parameter estimation, and AIC calculation can be found in Tzeng and Huang (2018) <doi:10.1080/00401706.2017.1345701>. For data with missing values, the ML estimates are obtained using the expectation- maximization algorithm. Apart from the number of basis functions, there are no other tuning parameters, making the method fully automatic. Users can also include a stationary structure in the spatial covariance, which utilizes 'LatticeKrig' package.
Author: ShengLi Tzeng [aut, cre], Hsin-Cheng Huang [aut], Wen-Ting Wang [ctb], Douglas Nychka [ctb], Colin Gillespie [ctb]
Maintainer: ShengLi Tzeng <slt.cmu@gmail.com>

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Package snipEM updated to version 1.0.1 with previous version 1.0 dated 2014-10-06

Title: Snipping Methods for Robust Estimation and Clustering
Description: Snipping methods optimally removing scattered cells for robust estimation and cluster analysis.
Author: Alessio Farcomeni, Andy Leung
Maintainer: Alessio Farcomeni <alessio.farcomeni@uniroma1.it>

Diff between snipEM versions 1.0 dated 2014-10-06 and 1.0.1 dated 2019-03-29

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Package scBio updated to version 0.1.4 with previous version 0.1.3 dated 2019-03-24

Title: Single Cell Genomics for Enhancing Cell Composition Inference from Bulk Genomics Data
Description: Cellular population mapping (CPM) a deconvolution algorithm in which single-cell genomics is required in only one or a few samples, where in other samples of the same tissue, only bulk genomics is measured and the underlying fine resolution cellular heterogeneity is inferred.
Author: Amit Frishberg [aut, cre], Naama Peshes-Yaloz [aut], Irit Gat-Viks [aut]
Maintainer: Amit Frishberg <amfrishberg@gmail.com>

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Package mma updated to version 8.0-0 with previous version 7.0-0 dated 2018-11-20

Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis. The analysis method is described in Yu et al. (2014) <doi:10.4172/2155-6180.1000189> "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>

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Package g3viz updated to version 1.0.0 with previous version 0.1.4 dated 2019-01-23

Title: Interactively Visualize Genomic Mutation Data using a Lollipop-Diagram
Description: R interface for 'g3-lollipop' JavaScript library. Visualize genomic mutation data using an interactive lollipop diagram in Rstudio or your browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <g3viz.group@gmail.com>

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Package fakemake updated to version 1.4.1 with previous version 1.4.0 dated 2018-11-02

Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in handy if you are developing R packages and can not use a proper build system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between fakemake versions 1.4.0 dated 2018-11-02 and 1.4.1 dated 2019-03-29

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Package EdSurvey updated to version 2.3.2 with previous version 2.2.3 dated 2019-03-18

Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analysis functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: OECD <http://www.oecd.org/>, including PISA, TALIS, PIAAC, and IEA <http://www.iea.nl/>, including TIMSS, TIMSS Advanced, PIRLS, ICCS, ICILS, and CivEd.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Alex Lishinski [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>

Diff between EdSurvey versions 2.2.3 dated 2019-03-18 and 2.3.2 dated 2019-03-29

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New package unine with initial version 0.1.0
Package: unine
Type: Package
Title: Unine Light Stemmer
Version: 0.1.0
Authors@R: c(person("Michaël", "Benesty", role = c("aut", "cre", "cph"), email = "michael@benesty.fr"), person("Jacques Savoy", role = c("cph"), email = "Jacques.Savoy@unine.ch"))
Maintainer: Michaël Benesty <michael@benesty.fr>
Description: Implementation of "light" stemmers for French, German, Italian, Spanish, Portuguese, Finnish, Swedish. They are based on the same work as the "light" stemmers found in 'SolR' <https://lucene.apache.org/solr/> or 'ElasticSearch' <https://www.elastic.co/fr/products/elasticsearch>. A "light" stemmer consists in removing inflections only for noun and adjectives. Indexing verbs for these languages is not of primary importance compared to nouns and adjectives. The stemming procedure for French is described in (Savoy, 1999) <doi:10.1002/(SICI)1097-4571(1999)50:10%3C944::AID-ASI9%3E3.3.CO;2-H>.
URL: https://github.com/pommedeterresautee/unine, https://pommedeterresautee.github.io/unine/, http://members.unine.ch/jacques.savoy/clef/
BugReports: https://github.com/pommedeterresautee/unine/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp (>= 1.0.0), methods
SystemRequirements: C++11
RoxygenNote: 6.1.1
NeedsCompilation: yes
Suggests: testthat, covr, stringi
Packaged: 2019-03-26 21:42:58 UTC; geantvert
Author: Michaël Benesty [aut, cre, cph], Jacques Savoy [cph]
Repository: CRAN
Date/Publication: 2019-03-29 17:50:02 UTC

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New package PRSim with initial version 1.0
Package: PRSim
Type: Package
Title: Stochastic Simulation of Streamflow Time Series using Phase Randomization
Version: 1.0
Date: 2019-03-10
Authors@R: c(person("Manuela", "Brunner", role = c("aut", "cre"), email = "manuela.brunner@wsl.ch", comment = c(ORCID = "0000-0001-8824-877X")), person("Reinhard", "Furrer", role = c("aut"), email = "reinhard.furrer@math.uzh.ch", comment = c(ORCID = "0000-0002-6319-2332")))
Author: Manuela Brunner [aut, cre] (<https://orcid.org/0000-0001-8824-877X>), Reinhard Furrer [aut] (<https://orcid.org/0000-0002-6319-2332>)
Maintainer: Manuela Brunner <manuela.brunner@wsl.ch>
Description: Provides a simulation framework to simulate streamflow time series with similar main characteristics as observed data. These characteristics include the distribution of daily streamflow values and their temporal correlation as expressed by short- and long-range dependence. The approach is based on the randomization of the phases of the Fourier transform. We further use the flexible four-parameter Kappa distribution, which allows for the extrapolation to yet unobserved low and high flows.
URL: https://git.math.uzh.ch/reinhard.furrer/PRSim-devel
BugReports: https://git.math.uzh.ch/reinhard.furrer/PRSim-devel
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: homtest
Suggests: lattice
Imports: stats
NeedsCompilation: no
Packaged: 2019-03-25 07:34:20 UTC; furrer
Repository: CRAN
Date/Publication: 2019-03-29 17:10:03 UTC

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New package pct with initial version 0.1.1
Package: pct
Type: Package
Title: Propensity to Cycle Tool
Version: 0.1.1
Authors@R: c( person("Robin", "Lovelace", email = "rob00x@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5679-6536")), person("Layik", "Hama", email = "layik.hama@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0003-1912-4890")) )
Description: Functions and example data to teach and increase the reproducibility of the methods and code underlying the Propensity to Cycle Tool (PCT), a research project and web application hosted at <https://www.pct.bike/>. For an academic paper on the methods, see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Depends: R (>= 3.5.0)
License: GPL-3
URL: http://www.pct.bike/, https://itsleeds.github.io/pct/
BugReports: https://github.com/ITSLeeds/pct/issues
Encoding: UTF-8
LazyData: true
Imports: boot, stplanr (>= 0.2.8), readr, sf
Suggests: testthat, knitr, curl, covr, pbapply, ggplot2, remotes, rmarkdown, leaflet
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Language: en-GB
NeedsCompilation: no
Packaged: 2019-03-25 17:09:03 UTC; robin
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Repository: CRAN
Date/Publication: 2019-03-29 17:30:03 UTC

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New package intensity.analysis with initial version 0.1.6
Package: intensity.analysis
Type: Package
Title: Intensity of Change for Comparing Categorical Maps from Sequential Intervals
Version: 0.1.6
Author: Robert Gilmore Pontius Jr. <rpontius@clarku.edu>, Sam Khallaghi <SKhallaghi@clarku.edu>
Maintainer: Sam Khallaghi <SKhallaghi@clarku.edu>
Description: Calculate metrics of change intensity for category, transition and interval levels in categorical maps from sequential intervals. For more information please consult: Aldwaik,Safaa Zakaria and Robert Gilmore Pontius Jr. (2012). "Intensity analysis to unify measurements of size and stationarity of land changes by interval, category, and transition". Landscape and Urban Planning. 106, 103-114. <doi:10.1016/j.landurbplan.2012.02.010>.
License: GPL (>= 2)
Depends: R (>= 3.3.0), rgdal
Imports: diffeR, raster, ggplot2, reshape2, graphics, grDevices, stats, utils
Encoding: UTF-8
NeedsCompilation: no
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2019-03-25 18:50:58 UTC; samkh
Repository: CRAN
Date/Publication: 2019-03-29 17:40:02 UTC

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Package distrEx updated to version 2.8.0 with previous version 2.7.0 dated 2018-07-22

Title: Extensions of Package 'distr'
Description: Extends package 'distr' by functionals, distances, and conditional distributions.
Author: Matthias Kohl [cre, cph], Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

Diff between distrEx versions 2.7.0 dated 2018-07-22 and 2.8.0 dated 2019-03-29

 DESCRIPTION                              |   22 
 MD5                                      |   58 +-
 NAMESPACE                                |    9 
 R/AllClass.R                             |    5 
 R/AsymTotalVarDist.R                     |  113 +++-
 R/CvMDist.R                              |   23 
 R/DiagnUtils.R                           |only
 R/DiscreteMVDistribution.R               |    8 
 R/Expectation.R                          |  818 +++++++++++++++++++++----------
 R/GammaWeibullExpectation.R              |only
 R/HellingerDist.R                        |   59 +-
 R/Internalfunctions.R                    |   19 
 R/OAsymTotalVarDist.R                    |   84 ++-
 R/TotalVarDist.R                         |   39 +
 R/distrExIntegrate.R                     |  174 +++++-
 R/liesInSupport.R                        |    6 
 R/sysdata.rda                            |binary
 inst/NEWS                                |   81 +++
 man/0distrEx-package.Rd                  |   22 
 man/AsymTotalVarDist.Rd                  |   23 
 man/CvMDist.Rd                           |   17 
 man/DiscreteMVDistribution-class.Rd      |    5 
 man/E.Rd                                 |  165 ++++--
 man/HellingerDist.Rd                     |   24 
 man/OAsymTotalVarDist.Rd                 |   24 
 man/TotalVarDist.Rd                      |   26 
 man/distrExIntegrate.Rd                  |   62 ++
 man/internals.Rd                         |   76 ++
 man/liesInSupport.Rd                     |    8 
 tests/Examples/distrEx-Ex_i386.Rout.save |  134 +----
 tests/Examples/distrEx-Ex_x64.Rout.save  |  134 +----
 31 files changed, 1516 insertions(+), 722 deletions(-)

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New package IndexConstruction with initial version 0.1-1
Package: IndexConstruction
Type: Package
Title: Index Construction for Time Series Data
Version: 0.1-1
Date: 2019-03-25
Author: Simon Trimborn <simon.trimborn@nus.edu.sg>
Maintainer: Simon Trimborn <simon.trimborn@nus.edu.sg>
LazyLoad: yes
LazyData: true
Depends: R (>= 2.10)
Imports: KernSmooth, fGarch, lubridate, xts, RcppBDT, zoo
Description: Derivation of indexes for benchmarking purposes. The methodology of the CRyptocurrency IndeX (CRIX) family with flexible number of constituents is implemented. Also functions for market capitalization and volume weighted indexes with fixed number of constituents are available. The methodology behind the functions provided gets introduced in Trimborn and Haerdle (2018) <doi:10.1016/j.jempfin.2018.08.004>.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2019-03-25 02:08:44 UTC; matsim
Repository: CRAN
Date/Publication: 2019-03-29 16:50:03 UTC

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New package IMWatson with initial version 0.5.0
Package: IMWatson
Type: Package
Title: Chat with Watson's Assistant API
Version: 0.5.0
Author: Ignacio Martinez
Maintainer: Ignacio Martinez <ignacio@protonmail.com>
Description: Chat with a chatbot created with the 'IBM Watson Assistant' <https://www.ibm.com/cloud/watson-assistant/>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: httr, jsonlite, R6, assertive, magrittr, shiny, V8, shinyjs, glue, shinydashboard
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-03-24 19:50:48 UTC; rstudio
Repository: CRAN
Date/Publication: 2019-03-29 16:40:03 UTC

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Package georob updated to version 0.3-8 with previous version 0.3-7 dated 2018-08-27

Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust and Gaussian (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift Kriging predictions, along with utility functions for variogram modelling in ad hoc geostatistical analyses, model building, model evaluation by cross-validation, (conditional) simulation of Gaussian processes, unbiased back-transformation of Kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut], Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>

Diff between georob versions 0.3-7 dated 2018-08-27 and 0.3-8 dated 2019-03-29

 ChangeLog                            |   11 +++++++
 DESCRIPTION                          |   10 +++---
 MD5                                  |   30 ++++++++++----------
 NAMESPACE                            |    2 -
 NEWS                                 |    4 ++
 R/georob.predict.R                   |    2 -
 R/georob.private.functions.R         |   52 ++++++++++++++++++++++++++++++-----
 R/georob.simulation.R                |   14 +++++++--
 build/vignette.rds                   |binary
 inst/doc/georob_vignette.Rnw         |   22 ++++++++------
 inst/doc/georob_vignette.pdf         |binary
 man/georob.Rd                        |    6 ++--
 man/georobSimulation.Rd              |    6 ++--
 vignettes/georob_vignette.Rnw        |   22 ++++++++------
 vignettes/r_coalash_objects.RData    |binary
 vignettes/r_meuse_zinc_objects.RData |binary
 16 files changed, 123 insertions(+), 58 deletions(-)

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Package gdmp updated to version 0.2.0 with previous version 0.1.0 dated 2016-09-29

Title: Genomic Data Management
Description: Manage and analyze high-dimensional SNP data from chips with multiple densities.
Author: Gamal Abdel-Azim [aut, cre]
Maintainer: Gamal Abdel-Azim <gamal.azim@gmail.com>

Diff between gdmp versions 0.1.0 dated 2016-09-29 and 0.2.0 dated 2019-03-29

 DESCRIPTION         |   10 +++++-----
 MD5                 |   14 +++++++-------
 R/dataEdit.R        |    9 +++++----
 man/read.findhap.Rd |    6 +++---
 src/cGetHCS.c       |    2 +-
 src/cIdentical.c    |    2 +-
 src/gt.c            |    2 +-
 src/readGenotypes.c |    4 ++--
 8 files changed, 25 insertions(+), 24 deletions(-)

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New package BNPmix with initial version 0.1.1
Package: BNPmix
Type: Package
Title: Algorithms for Pitman-Yor Process Mixtures
Version: 0.1.1
Date: 2019-03-14
Author: Riccardo Corradin
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Description: Contains different algorithms to both univariate and multivariate Pitman-Yor process mixture models, and Griffiths-Milne Dependent Dirichlet process mixture models. Pitman-Yor process mixture models are flexible Bayesian nonparametric models to deal with density estimation. Estimation could be done via importance conditional sampler, or via slice sampler, as done by Walker (2007) <doi:10.1080/03610910601096262>, or using a marginal sampler, as in Escobar and West (1995) <doi:10.2307/2291069> and extensions. The package contains also the procedures to estimate via importance conditional sampler a GM-Dependent Dirichlet process mixture model.
License: LGPL-3 | file LICENSE
NeedsCompilation: yes
Imports: methods, ggplot2
Depends: R (>= 3.3.0)
LinkingTo: RcppArmadillo, Rcpp(>= 0.12.13)
RoxygenNote: 6.1.1
Encoding: UTF-8
Packaged: 2019-03-24 15:06:11 UTC; Riccardo
Repository: CRAN
Date/Publication: 2019-03-29 16:30:03 UTC

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New package tapkee with initial version 1.0
Package: tapkee
Type: Package
Title: Wrapper for 'tapkee' Dimension Reduction Library
Version: 1.0
Date: 2019-03-22
Author: Alexey Shipunov
Maintainer: Alexey Shipunov <dactylorhiza@gmail.com>
Description: Wrapper for using 'tapkee' command line utility, it allows to run it from inside R and catch the results for further analysis and plotting. 'Tapkee' is a program for fast dimension reduction (see <http://tapkee.lisitsyn.me/> for more details).
SystemRequirements: 'tapkee' (http://tapkee.lisitsyn.me/)
Suggests: scatterplot3d, rgl
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2019-03-22 18:39:12 UTC; alexey
Repository: CRAN
Date/Publication: 2019-03-29 15:30:03 UTC

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New package sapfluxnetr with initial version 0.0.6
Package: sapfluxnetr
Title: Working with 'Sapfluxnet' Project Data
Version: 0.0.6
Authors@R: c( person("Victor", "Granda", email = "victorgrandagarcia@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0469-1991")), person("Rafael", "Poyatos", email = "r.poyatos@creaf.uab.cat", role = "aut", comment = c(ORCID = "0000-0003-0521-2523")), person("Victor", "Flo", email = "v.flo@creaf.uab.cat", role = "aut", comment = c(ORCID = "0000-0003-1908-4577")), person("Jacob", "Nelson", email = "", role = 'ctb', comment = c(ORCID = "0000-0002-4663-2420")), person("Sapfluxnet Core Team", email = "sapfluxnet@creaf.uab.cat", role = 'cph') )
Description: Access, modify, aggregate and plot data from the 'Sapfluxnet' project (<http:sapfluxnet.creaf.cat>), the first global database of sap flow measurements.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, furrr, ggplot2, glue, lubridate, magrittr, methods, purrr, rlang, stats, stringr, tibble, tibbletime, tidyr, utils
RoxygenNote: 6.1.1
Collate: 'data.R' 'getters.R' 'helpers.R' 'imports.R' 'metrics.R' 'sfn_data_classes.R' 'sfn_data_generics.R' 'sfn_data_methods.R' 'sfn_dplyr.R' 'visualizations.R'
Suggests: future, knitr, remotes, rmarkdown, testthat, tidyverse, xtable
VignetteBuilder: knitr
URL: https://github.com/sapfluxnet/sapfluxnetr
BugReports: https://github.com/sapfluxnet/sapfluxnetr/issues
NeedsCompilation: no
Packaged: 2019-03-13 19:08:25 UTC; malditobarbudo
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>), Rafael Poyatos [aut] (<https://orcid.org/0000-0003-0521-2523>), Victor Flo [aut] (<https://orcid.org/0000-0003-1908-4577>), Jacob Nelson [ctb] (<https://orcid.org/0000-0002-4663-2420>), Sapfluxnet Core Team [cph]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Repository: CRAN
Date/Publication: 2019-03-29 15:10:03 UTC

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New package Rxnat with initial version 1.0.4
Package: Rxnat
Type: Package
Version: 1.0.4
Title: Queries and Extracts Images from Extensible Neuroimaging Archive Toolkit Public/Private Datasets
Description: Allows communication with Extensible Neuroimaging Archive Toolkit <https://www.xnat.org>. 'Rxnat' is using the 'XNAT' REST API to perform data queries and download images.
Authors@R: person("Adi", "Gherman", ,"adig@jhu.edu", c("aut", "cre"))
Maintainer: Adi Gherman <adig@jhu.edu>
Imports: RCurl, httr, utils
Suggests: testthat, knitr, rmarkdown, covr
License: GPL-2
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
BugReports: https://github.com/adigherman/Rxnat/issues
NeedsCompilation: no
Packaged: 2019-03-22 20:02:24 UTC; adi
Author: Adi Gherman [aut, cre]
Repository: CRAN
Date/Publication: 2019-03-29 15:30:06 UTC

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New package rapidxmlr with initial version 0.1.0
Package: rapidxmlr
Type: Package
Title: 'Rapidxml' C++ Header Files
Date: 2019-03-13
Version: 0.1.0
Authors@R: c( person("David", "Cooley", ,"david.cooley.au@gmail.com", role = c("aut", "cre")), person("Marcin", "Kalicinski", , role = "ctb", comment = "Author of c++ rapidxml library") )
Description: Provides XML parsing capability through the 'Rapidxml' 'C++' header-only library.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-03-14 07:39:26 UTC; dave
Author: David Cooley [aut, cre], Marcin Kalicinski [ctb] (Author of c++ rapidxml library)
Maintainer: David Cooley <david.cooley.au@gmail.com>
Repository: CRAN
Date/Publication: 2019-03-29 15:10:09 UTC

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New package EWOC2 with initial version 1.0
Package: EWOC2
Type: Package
Title: Escalation with Overdose Control using 2 Drug Combinations
Version: 1.0
Date: 2019-03-15
Author: Quanlin Li and Mourad Tighiouart
Maintainer: Quanlin Li <choplum@gmail.com>
Description: Implements escalation with overdose control (EWOC) trial designs using two drug combinations described by Tighiouart, Li and Rogatko (2017) <doi:10.1002/sim.6961>. It calculates the recommended dose for next cohorts and perform simulations to obtain operating characteristics.
License: GPL (>= 2)
Depends: rjags
Imports: MASS
NeedsCompilation: no
Packaged: 2019-03-20 02:25:01 UTC; liq
Repository: CRAN
Date/Publication: 2019-03-29 15:20:03 UTC

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Package DZEXPM updated to version 2.0 with previous version 1.0 dated 2017-06-24

Title: Estimation and Prediction of Skewed Spatial Processes
Description: MCMC method to estimate and predict skewed spatial processes. A real data set is included. Reference: Wang, Yang and Majumdar (2018) <doi.org/10.1007/s00180-017-0741-3>.
Author: Jiangyan Wang, Miao Yang and Anandamayee Majumdar
Maintainer: "Jiangyan Wang" <wangjiangyan2007@126.com>

Diff between DZEXPM versions 1.0 dated 2017-06-24 and 2.0 dated 2019-03-29

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New package dotdot with initial version 0.1.0
Package: dotdot
Type: Package
Title: Enhanced Assignment Operator to Overwrite or Grow Objects
Version: 0.1.0
Author: Antoine Fabri
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Description: Use '..' on the right hand side of the ':=' operator as a shorthand for the left hand side, so that 'var := f(..) + ..' is equivalent to 'var <- f(var) + var'. This permits the user to be explicit about growing an object or overwriting it using its previous value, avoids repeating a variable name, and saves keystrokes, time, visual space and cognitive load.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, htmltools
NeedsCompilation: no
Packaged: 2019-03-23 22:56:57 UTC; Antoine
Repository: CRAN
Date/Publication: 2019-03-29 15:50:02 UTC

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New package clusternor with initial version 0.0-3
Package: clusternor
Version: 0.0-3
Date: 2019-03-28
Title: A Parallel Clustering Non-Uniform Memory Access ('NUMA') Optimized Package
Authors@R: c(person("Disa", "Mhembere", role = c("aut", "cre"), email = "disa@cs.jhu.edu"), person("Neurodata (https://neurodata.io)", role="cph"))
Description: The clustering 'NUMA' Optimized Routines package or 'clusternor' is a highly optimized package for performing clustering in parallel with accelerations specifically targeting multi-core Non-Uniform Memory Access ('NUMA') hardware architectures. Disa Mhembere, Da Zheng, Carey E. Priebe, Joshua T. Vogelstein, Randal Burns (2019) <arXiv:1902.09527>.
LinkingTo: Rcpp
Depends: R (>= 3.0), Rcpp (>= 0.12.8)
License: Apache License 2.0
URL: https://github.com/neurodata/knorR
SystemRequirements: GNU make C++11, pthreads
BugReports: https://github.com/flashxio/knor/issues
RoxygenNote: 6.1.1
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Suggests: testthat
Packaged: 2019-03-29 05:47:47 UTC; disa
Author: Disa Mhembere [aut, cre], Neurodata (https://neurodata.io) [cph]
Maintainer: Disa Mhembere <disa@cs.jhu.edu>
Repository: CRAN
Date/Publication: 2019-03-29 15:40:03 UTC

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Package XGR updated to version 1.1.5 with previous version 1.1.4 dated 2018-08-14

Title: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between XGR versions 1.1.4 dated 2018-08-14 and 1.1.5 dated 2019-03-29

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 338 files changed, 2905 insertions(+), 1752 deletions(-)

More information about XGR at CRAN
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New package funcy with initial version 1.0.1
Package: funcy
Type: Package
Title: Functional Clustering Algorithms
Version: 1.0.1
Date: 2019-03-04
Authors@R: c( person(given="Christina", family="Yassouridis", email="chris.yassou@gmail.com", role=c("aut", "cre")), person(given="Dominik", family="Ernst", role="ctb"), person(given="Madison", family="Giacofci", role="ctb"), person(given="Sophie", family="Lambert-Lacroix", role="ctb"), person(given="Guillemette", family="Marot", role="ctb"), person(given="Franck", family="Picard", role="ctb"), person(given="Nicoleta", family="Serban", role="ctb"), person(given="Huijing", family="Jiang", role="ctb"), person(given="Gareth", family="James", role="ctb"), person(given="Catherine", family="Sugar", role="ctb"), person(given="Hans-Georg", family="Mueller", role="ctb"), person(given="Jie", family="Peng", role="ctb"), person(given="Chiou", family="Jeng-Min", role="ctb"), person(given="Pai-Ling", family="Li", role="ctb") )
Description: Unified framework to cluster functional data according to one of seven models. All models are based on the projection of the curves onto a basis. The main function funcit() calls wrapper functions for the existing algorithms, so that input parameters are the same. A list is returned with each entry representing the same or extended output for the corresponding method. Method specific as well as general visualization tools are available.
License: GPL-2
Depends: flexclust, splines
Imports: MASS, Matrix, fda, methods, wavethresh, kernlab, parallel, car, fields, calibrate, cluster, sm, plyr
Suggests: scatterplot3d, funHDDC, testthat
LazyLoad: yes
Encoding: UTF-8
NeedsCompilation: yes
RoxygenNote: 6.1.1
Author: Christina Yassouridis [aut, cre], Dominik Ernst [ctb], Madison Giacofci [ctb], Sophie Lambert-Lacroix [ctb], Guillemette Marot [ctb], Franck Picard [ctb], Nicoleta Serban [ctb], Huijing Jiang [ctb], Gareth James [ctb], Catherine Sugar [ctb], Hans-Georg Mueller [ctb], Jie Peng [ctb], Chiou Jeng-Min [ctb], Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <chris.yassou@gmail.com>
Repository: CRAN
Packaged: 2019-03-29 12:38:49 UTC; chris
Date/Publication: 2019-03-29 14:50:03 UTC

More information about funcy at CRAN
Permanent link

New package AMR with initial version 0.6.1
Package: AMR
Version: 0.6.1
Date: 2019-03-28
Title: Antimicrobial Resistance Analysis
Authors@R: c( person( given = c("Matthijs", "S."), family = "Berends", email = "m.s.berends@umcg.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800")), person( given = c("Christian", "F."), family = "Luz", email = "c.f.luz@umcg.nl", role = "aut", comment = c(ORCID = "0000-0001-5809-5995")), person( given = c("Erwin", "E.", "A."), family = "Hassing", email = "e.hassing@certe.nl", role = "ctb"), person( given = "Corinna", family = "Glasner", email = "c.glasner@umcg.nl", role = c("aut", "ths"), comment = c(ORCID = "0000-0003-1241-1328")), person( given = c("Alex", "W."), family = "Friedrich", email = "alex.friedrich@umcg.nl", role = c("aut", "ths"), comment = c(ORCID = "0000-0003-4881-038X")), person( given = c("Bhanu", "N.", "M."), family = "Sinha", email = "b.sinha@umcg.nl", role = c("aut", "ths"), comment = c(ORCID = "0000-0003-1634-0010")))
Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
Depends: R (>= 3.1.0)
Imports: backports, crayon (>= 1.3.0), data.table (>= 1.9.0), dplyr (>= 0.7.0), ggplot2, hms, knitr (>= 1.0.0), microbenchmark, rlang (>= 0.3.1), tidyr (>= 0.7.0)
Suggests: covr (>= 3.0.1), curl, readxl, rmarkdown, rstudioapi, rvest (>= 0.3.2), testthat (>= 1.0.2), xml2 (>= 1.0.0)
VignetteBuilder: knitr
URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
BugReports: https://gitlab.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-03-28 21:26:56 UTC; uscloud
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut] (<https://orcid.org/0000-0001-5809-5995>), Erwin E. A. Hassing [ctb], Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Alex W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Repository: CRAN
Date/Publication: 2019-03-29 12:00:03 UTC

More information about AMR at CRAN
Permanent link

Package UCSCXenaTools updated to version 1.1.0 with previous version 1.0.1 dated 2019-03-07

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded. This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package hdi updated to version 0.1-7 with previous version 0.1-6 dated 2016-03-21

Title: High-Dimensional Inference
Description: Implementation of multiple approaches to perform inference in high-dimensional models.
Author: Lukas Meier [aut, cre], Ruben Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann [aut]
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>

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Package lori updated to version 2.1.3 with previous version 2.1.2 dated 2019-03-07

Title: Imputation of Count Data using Side Information
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted. LORI returns estimates of covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>

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Package insight updated to version 0.2.0 with previous version 0.1.2 dated 2019-03-05

Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package easyPubMed updated to version 2.13 with previous version 2.12 dated 2019-03-06

Title: Search and Retrieve Scientific Publication Records from PubMed
Description: Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>

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Package gridSVG updated to version 1.7-1 with previous version 1.7-0 dated 2019-02-12

Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG format. Additional functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut], Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>

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Package tatoo updated to version 1.1.1 with previous version 1.1.0 dated 2018-02-12

Title: Combine and Export Data Frames
Description: Functions to combine data.frames in ways that require additional effort in base R, and to add metadata (id, title, ...) that can be used for printing and xlsx export. The 'Tatoo_report' class is provided as a convenient helper to write several such tables to a workbook, one table per worksheet. Tatoo is built on top of 'openxlsx', but intimate knowledge of that package is not required to use tatoo.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>

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Package rlang updated to version 0.3.3 with previous version 0.3.2 dated 2019-03-21

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package rJava updated to version 0.9-11 with previous version 0.9-10 dated 2018-05-29

Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>

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 inst/javadoc/RectangularArrayBuilder_Test.html                    |    4 
 inst/javadoc/RectangularArrayExamples.html                        |    4 
 inst/javadoc/RectangularArraySummary.html                         |    4 
 inst/javadoc/TestException.html                                   |    4 
 inst/javadoc/allclasses-frame.html                                |    4 
 inst/javadoc/allclasses-noframe.html                              |    4 
 inst/javadoc/constant-values.html                                 |    4 
 inst/javadoc/deprecated-list.html                                 |    4 
 inst/javadoc/help-doc.html                                        |    4 
 inst/javadoc/index-all.html                                       |    4 
 inst/javadoc/index.html                                           |    2 
 inst/javadoc/overview-tree.html                                   |    4 
 inst/javadoc/package-frame.html                                   |    4 
 inst/javadoc/package-summary.html                                 |    4 
 inst/javadoc/package-tree.html                                    |    4 
 inst/javadoc/serialized-form.html                                 |    4 
 inst/jri/JRIEngine.jar                                            |binary
 inst/jri/REngine.jar                                              |binary
 jri/Makevars.win                                                  |    1 
 jri/configure                                                     |   31 ++
 jri/configure.ac                                                  |   39 ++-
 jri/configure.win                                                 |    8 
 jri/src/Rinit.c                                                   |    1 
 jri/src/jri.c                                                     |    4 
 jri/src/jri.h                                                     |   14 -
 jri/src/win32/findjava.c                                          |   24 +-
 man/javaImport.Rd                                                 |    2 
 src/init.c                                                        |   96 ++++++--
 src/jri_glue.c                                                    |    2 
 src/jvm-w32/findjava.c                                            |   37 ++-
 src/rJava.c                                                       |    7 
 src/rJava.h                                                       |    2 
 60 files changed, 468 insertions(+), 216 deletions(-)

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