Wed, 03 Jan 2018

Package memo updated to version 1.0.1 with previous version 1.0 dated 2016-08-25

Title: In-Memory Caching for Repeated Computations
Description: A simple in-memory, LRU cache that can be wrapped around any function to memoize it. The cache can be keyed on a hash of the input data (using 'digest') or on pointer equivalence.
Author: Peter Meilstrup <peter.meilstrup@gmail.com>
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>

Diff between memo versions 1.0 dated 2016-08-25 and 1.0.1 dated 2018-01-03

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Package CsChange updated to version 0.1.2 with previous version 0.1.1 dated 2017-12-18

Title: Testing for Change in C-Statistic
Description: Calculate the confidence interval and p value for change in C-statistic. The adjusted C-statistic is calculated by using formula as "Somers' Dxy rank correlation"/2+0.5. The confidence interval was calculated by using the bootstrap method. The p value was calculated by using the Z testing method. Please refer to the article of Peter Ganz et al. (2016) <doi:10.1001/jama.2016.5951>.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

Diff between CsChange versions 0.1.1 dated 2017-12-18 and 0.1.2 dated 2018-01-03

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Package TukeyRegion updated to version 0.1.1 with previous version 0.1.0 dated 2017-12-07

Title: Tukey Region and Median
Description: Tukey regions are polytopes in the Euclidean space, viz. upper-level sets of the Tukey depth function on given data. The bordering hyperplanes of a Tukey region are computed as well as its vertices, facets, centroid, and volume. In addition, the Tukey median set, which is the non-empty Tukey region having highest depth level, and its barycenter (= Tukey median) are calculated. Tukey regions are visualized in dimension two and three. For details see Liu, Mosler, and Mozharovskyi (2017) <arXiv:1412.5122>.
Author: Pavlo Mozharovskyi [aut, cre], C.B. Barber [aut, cph], The Geometry Center University of Minnesota [cph]
Maintainer: Pavlo Mozharovskyi <pavlo.mozharovskyi@ensai.fr>

Diff between TukeyRegion versions 0.1.0 dated 2017-12-07 and 0.1.1 dated 2018-01-03

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Package stargazer updated to version 5.2.1 with previous version 5.2 dated 2015-07-14

Title: Well-Formatted Regression and Summary Statistics Tables
Description: Produces LaTeX code, HTML/CSS code and ASCII text for well-formatted tables that hold regression analysis results from several models side-by-side, as well as summary statistics.
Author: Marek Hlavac <mhlavac@alumni.princeton.edu>
Maintainer: Marek Hlavac <mhlavac@alumni.princeton.edu>

Diff between stargazer versions 5.2 dated 2015-07-14 and 5.2.1 dated 2018-01-03

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Package rdrobust updated to version 0.99 with previous version 0.98 dated 2017-06-09

Title: Robust Data-Driven Statistical Inference in Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>

Diff between rdrobust versions 0.98 dated 2017-06-09 and 0.99 dated 2018-01-03

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Package geostatsp updated to version 1.6.0 with previous version 1.5.4 dated 2017-07-19

Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>

Diff between geostatsp versions 1.5.4 dated 2017-07-19 and 1.6.0 dated 2018-01-03

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Package RFc (with last version 0.1-2) was removed from CRAN

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

2016-06-22 0.1-2
2016-04-20 0.1-1

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Package RobustGaSP updated to version 0.5.4 with previous version 0.5.3 dated 2017-01-27

Title: Robust Gaussian Stochastic Process Emulation
Description: Robust parameter estimation and prediction of Gaussian stochastic process emulators. Important functions : rgasp(), predict.rgasp().
Author: Mengyang Gu [aut, cre], Jesus Palomo [aut], James Berger [aut]
Maintainer: Mengyang Gu <mgu6@jhu.edu>

Diff between RobustGaSP versions 0.5.3 dated 2017-01-27 and 0.5.4 dated 2018-01-03

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Package MESS updated to version 0.5.0 with previous version 0.4-15 dated 2017-04-09

Title: Miscellaneous Esoteric Statistical Scripts
Description: A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book.
Author: Claus Thorn Ekstrøm [aut, cre]
Maintainer: Claus Thorn Ekstrøm <claus@rprimer.dk>

Diff between MESS versions 0.4-15 dated 2017-04-09 and 0.5.0 dated 2018-01-03

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Package LSDinterface updated to version 0.3.3 with previous version 0.3.1 dated 2017-11-27

Title: Reading LSD Results (.res) Files
Description: Interfaces R with LSD. Reads object-oriented data in results files (.res) produced by LSD and creates appropriate multi-dimensional arrays in R. Supports multiple core parallelization of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente (documentation and downloads available at <http://labsimdev.org>).
Author: Marcelo C. Pereira
Maintainer: Marcelo C. Pereira <marcelocpereira@uol.com.br>

Diff between LSDinterface versions 0.3.1 dated 2017-11-27 and 0.3.3 dated 2018-01-03

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Package ggformula updated to version 0.6.1 with previous version 0.6 dated 2017-08-26

Title: Formula Interface to the Grammar of Graphics
Description: Provides a formula interface to 'ggplot2' graphics.
Author: Daniel Kaplan [aut], Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@calvin.edu>

Diff between ggformula versions 0.6 dated 2017-08-26 and 0.6.1 dated 2018-01-03

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Package discgolf updated to version 0.2.0 with previous version 0.1.0 dated 2016-04-21

Title: Discourse API Client
Description: Client for the Discourse API. Discourse is a open source discussion forum platform (<https://www.discourse.org/>). It comes with 'RESTful' API access to an installation. This client requires that you are authorized to access a Discourse installation, either yours or another.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between discgolf versions 0.1.0 dated 2016-04-21 and 0.2.0 dated 2018-01-03

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Package ltsk updated to version 1.0.5 with previous version 1.0.4 dated 2015-09-11

Title: Local Time Space Kriging
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang <dliang@umces.edu>

Diff between ltsk versions 1.0.4 dated 2015-09-11 and 1.0.5 dated 2018-01-03

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Package sofa updated to version 0.3.0 with previous version 0.2.0 dated 2016-10-12

Title: Connector to 'CouchDB'
Description: Provides an interface to the 'NoSQL' database 'CouchDB' (<http://couchdb.apache.org>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' databases such as 'Cloudant' (<https://docs.cloudant.com>). Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between sofa versions 0.2.0 dated 2016-10-12 and 0.3.0 dated 2018-01-03

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Package rsq updated to version 1.0.1 with previous version 1.0 dated 2017-03-28

Title: R-Squared and Related Measures
Description: Calculate generalized R-squared, partial R-squared, and partial correlation coefficients for generalized linear models (including quasi models with well defined variance functions).
Author: Dabao Zhang
Maintainer: Dabao Zhang <zhangdb@stat.purdue.edu>

Diff between rsq versions 1.0 dated 2017-03-28 and 1.0.1 dated 2018-01-03

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Permanent link

Package macleish updated to version 0.3.2 with previous version 0.3.1 dated 2017-09-28

Title: Retrieve Data from MacLeish Field Station
Description: Download data from the Ada and Archibald MacLeish Field Station in Whately, MA. The Ada and Archibald MacLeish Field Station is a 260-acre patchwork of forest and farmland located in West Whately, MA that provides opportunities for faculty and students to pursue environmental research, outdoor education, and low-impact recreation (see <http://www.smith.edu/ceeds/macleish.php> for more information). This package contains weather data over several years, and spatial data on various man-made and natural structures.
Author: Benjamin S. Baumer [aut, cre], Rose Goueth [aut], Wencong Li [aut], Weijia Zhang [aut], Nicholas Horton [aut]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>

Diff between macleish versions 0.3.1 dated 2017-09-28 and 0.3.2 dated 2018-01-03

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Permanent link

Package frequencyConnectedness updated to version 0.2.0 with previous version 0.1.6 dated 2017-06-09

Title: Spectral Decomposition of Connectedness Measures
Description: Accompanies a paper (Barunik, Krehlik (2017) <doi:10.2139/ssrn.2627599>) dedicated to spectral decomposition of connectedness measures and their interpretation. We implement all the developed estimators as well as the historical counterparts. For more information, see the help or GitHub page (<https://github.com/tomaskrehlik/frequencyConnectedness>) for relevant information.
Author: Tomas Krehlik [aut, cre]
Maintainer: Tomas Krehlik <tomas.krehlik@gmail.com>

Diff between frequencyConnectedness versions 0.1.6 dated 2017-06-09 and 0.2.0 dated 2018-01-03

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More information about frequencyConnectedness at CRAN
Permanent link

Package unitedR updated to version 0.3 with previous version 0.2 dated 2015-12-04

Title: Assessment and Evaluation of Formations in United
Description: United is a software tool which can be downloaded at the following website <http://www.schroepl.net/pbm/software/united/>. In general, it is a virtual manager game for football teams. This package contains helpful functions for determining an optimal formation for a virtual match in United. E.g. knowing that the opponent has a strong defensive it is advisable to beat him in the midfield. Furthermore, this package contains functions for computing the optimal usage of hardness in a game.
Author: David Schindler [aut, cre]
Maintainer: David Schindler <dv.schindler@gmail.com>

Diff between unitedR versions 0.2 dated 2015-12-04 and 0.3 dated 2018-01-03

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More information about unitedR at CRAN
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Package rbacon updated to version 2.3.1.2 with previous version 2.3.1.1 dated 2017-12-15

Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre], J. Andres Christen [aut], Judith Esquivel Vazquez [ctb], Ted Belding [cph], James Theiler [cph], Brian Gough [cph], Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

Diff between rbacon versions 2.3.1.1 dated 2017-12-15 and 2.3.1.2 dated 2018-01-03

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More information about rbacon at CRAN
Permanent link

New package ConvergenceClubs with initial version 1.0.0
Package: ConvergenceClubs
Title: Finding Convergence Clubs
Description: Functions for clustering regions that form convergence clubs, according to the definition of Phillips and Sul (2009) <doi:10.1002/jae.1080>.
Version: 1.0.0
Authors@R: c( person("Roberto", "Sichera",, "roberto.sichera@unipa.it", c("aut", "cre", "cph")), person("Pietro", "Pizzuto",, "pietro.pizzuto02@unipa.it", "aut") )
URL: https://github.com/rhobis/ConvergenceClubs
BugReports: https://github.com/rhobis/ConvergenceClubs/issues
Depends: R (>= 3.0.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: lmtest (>= 0.9-35), sandwich (>= 2.3-4)
NeedsCompilation: no
Packaged: 2018-01-03 16:04:46 UTC; roberto
Author: Roberto Sichera [aut, cre, cph], Pietro Pizzuto [aut]
Maintainer: Roberto Sichera <roberto.sichera@unipa.it>
Repository: CRAN
Date/Publication: 2018-01-03 19:04:55 UTC

More information about ConvergenceClubs at CRAN
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New package woeR with initial version 0.1.3
Package: woeR
Title: Weight of Evidence Based Segmentation of a Variable
Version: 0.1.3
Author: Kashish Soien
Maintainer: Kashish Soien <kashish.soien19@gmail.com>
Description: Segment a numeric variable based on a dichotomous dependent variable by using the weight of evidence (WOE) approach (Ref: Siddiqi, N. (2006) <doi:10.1002/9781119201731.biblio>). The underlying algorithm adopts a recursive approach to create segments that are diverse in respect of their WOE values and meet the demands of user-defined parameters. The algorithm also aims to maintain a monotonic trend in WOE values of consecutive segments. As such, it can be particularly helpful in improving robustness of linear and logistic regression models.
Imports: dplyr
Suggests: smbinning
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
BugReports: https://github.com/kraken19/woeR/issues
NeedsCompilation: no
Packaged: 2018-01-03 16:41:17 UTC; kashish
Repository: CRAN
Date/Publication: 2018-01-03 18:05:01 UTC

More information about woeR at CRAN
Permanent link

Package wbstats updated to version 0.2 with previous version 0.1.1 dated 2016-12-08

Title: Programmatic Access to Data and Statistics from the World Bank API
Description: Tools for searching and downloading data and statistics from the World Bank Data API (<http://data.worldbank.org/developers/api-overview>) and the World Bank Data Catalog API (<http://data.worldbank.org/developers/data-catalog-api>).
Author: Jesse Piburn [aut, cre], UT-Battelle, LLC [cph]
Maintainer: Jesse Piburn <piburnjo@ornl.gov>

Diff between wbstats versions 0.1.1 dated 2016-12-08 and 0.2 dated 2018-01-03

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New package TSstudio with initial version 0.1.0
Package: TSstudio
Type: Package
Title: Tools for Time Series Analysis and Forecasting
Version: 0.1.0
Author: Rami Krispin
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Description: Provides a set of interactive visualization tools for time series analysis supporting ts, mts, zoo and xts objects. That includes visualization functions for forecasting model performance (forecasted vs. actual), time series interactive plots (single and multiple series) and seasonality plots.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: reshape2 (>= 1.4.2), lubridate (>= 1.6.0), plotly (>= 4.7.1), magrittr (>= 1.5), xts (>= 0.10-1), zoo (>= 1.8-0), forecast (>= 8.2)
Suggests: knitr, rmarkdown, devtools
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-01-03 17:27:14 UTC; krispra
Repository: CRAN
Date/Publication: 2018-01-03 18:37:08 UTC

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New package reinforcelearn with initial version 0.1.0
Package: reinforcelearn
Type: Package
Title: Reinforcement Learning
Version: 0.1.0
Authors@R: person("Markus", "Dumke", email = {"markusdumke@gmail.com"}, role = c("aut", "cre"))
Description: Implements reinforcement learning environments and algorithms as described in Sutton & Barto (1998, ISBN:0262193981). The Q-Learning algorithm can be used with different types of function approximation (tabular and neural network), eligibility traces (Singh & Sutton (1996) <doi:10.1007/BF00114726>) and experience replay (Mnih et al. (2013) <arXiv:1312.5602>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.0)
RoxygenNote: 6.0.1
BugReports: https://github.com/markusdumke/reinforcelearn/issues
URL: http://markusdumke.github.io/reinforcelearn
SystemRequirements: (Python and gym only required if gym environments are used)
Imports: checkmate (>= 1.8.4), R6 (>= 2.2.2), nnet (>= 7.3-12), purrr (>= 0.2.4)
Suggests: reticulate, keras, knitr, rmarkdown, testthat, covr, lintr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-01-03 16:33:57 UTC; Markus
Author: Markus Dumke [aut, cre]
Maintainer: Markus Dumke <markusdumke@gmail.com>
Repository: CRAN
Date/Publication: 2018-01-03 18:30:47 UTC

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New package PKNCA with initial version 0.8.4
Package: PKNCA
Type: Package
Title: Perform Pharmacokinetic Non-Compartmental Analysis
Version: 0.8.4
Date: 2018-01-02
Authors@R: c( person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre")), person("Clare", "Buckeridge", email="clare.buckeridge@pfizer.com", role="aut"), person("Sridhar", "Duvvuri", role="ctb"))
Imports: dplyr (>= 0.5.0), digest, plyr, nlme, parallel, lattice, rlang, stats, tidyr, utils
Suggests: cowplot, ggplot2, knitr, rmarkdown, testthat
Description: Compute standard Non-Compartmental Analysis (NCA) parameters and summarize them. In addition to this core work, it also provides standardized plotting routines, basic assessments for biocomparison or drug interaction, and model-based estimation routines for calculating doses to reach specific values of AUC or Cmax.
License: AGPL-3
URL: https://github.com/billdenney/pknca
BugReports: https://github.com/billdenney/pknca/issues
NeedsCompilation: no
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Packaged: 2018-01-02 15:42:53 UTC; William Denney
Author: Bill Denney [aut, cre], Clare Buckeridge [aut], Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
X-CRAN-Comment: Orphaned on 2017-12-16 as there was no response to requests for needed corrections. Unarchived on 2018-01-03.
Repository: CRAN
Date/Publication: 2018-01-03 18:10:16 UTC

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Package pangaear updated to version 0.6.0 with previous version 0.3.0 dated 2017-03-08

Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database (<https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre], Kara Woo [aut], Andrew MacDonald [aut], Naupaka Zimmerman [aut], Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between pangaear versions 0.3.0 dated 2017-03-08 and 0.6.0 dated 2018-01-03

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New package mobForest with initial version 1.3.0
Package: mobForest
Type: Package
Title: Model Based Random Forest Analysis
Version: 1.3.0
Date: 2018-01-03
Author: Nikhil Garge [aut], Barry Eggleston [aut], Georgiy Bobashev [aut], Benjamin Carper [cre], Kasey Jones [ctb, cre], Torsten Hothorn [ctb], Kurt Hornik [ctb], Carolin Strobl [ctb], Achim Zeileis [ctb]
Maintainer: Kasey Jones <krjones@rti.org>
Description: Functions to implements random forest method for model based recursive partitioning. The mob() function, developed by Zeileis et al. (2008), within 'party' package, is modified to construct model-based decision trees based on random forests methodology. The main input function mobforest.analysis() takes all input parameters to construct trees, compute out-of-bag errors, predictions, and overall accuracy of forest. The algorithm performs parallel computation using cluster functions within 'parallel' package.
License: GPL (>= 2)
Depends: parallel (>= 3.4.1), party (>= 1.2-4), sandwich (>= 2.4.0), strucchange (>= 1.5-1), zoo (>= 1.8-0)
Imports: methods, modeltools, stats, graphics
Suggests: testthat (>= 1.0.2), mlbench (>= 2.1), lattice
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-01-03 17:43:56 UTC; krjones
Repository: CRAN
Date/Publication: 2018-01-03 18:45:25

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New package GD with initial version 1.0
Package: GD
Type: Package
Title: Geographical Detectors
Date: 2017-12-22
Version: 1.0
Authors@R: person("Yongze Song", email = "yongze.song@postgrad.curtin.edu.au", role = c("aut", "cre"))
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>
Description: Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the discretization of continuous data and four primary functions of geographical detectors.
Imports: BAMMtools, ggplot2, stats, utils
Depends: R (>= 3.4.0)
License: GPL-2
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-01-03 15:50:19 UTC; zack
Author: Yongze Song [aut, cre]
Repository: CRAN
Date/Publication: 2018-01-03 18:17:25 UTC

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New package ether with initial version 0.1.4
Package: ether
Type: Package
Title: Interaction with the 'Ethereum' Blockchain
Version: 0.1.4
Authors@R: person("Andrew", "Collier", email = "andrew@exegetic.biz", role = c("aut", "cre"))
Description: Interacts with the open-source, public 'Ethereum' <https://www.ethereum.org/> blockchain. It provides a distributed computing platform via smart contracts. This package provides functions which interrogate blocks and transactions in the 'Ethereum' blockchain.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: dplyr, httr, jsonlite, Rmpfr
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-01-03 16:38:51 UTC; colliera
Author: Andrew Collier [aut, cre]
Maintainer: Andrew Collier <andrew@exegetic.biz>
Repository: CRAN
Date/Publication: 2018-01-03 18:33:28 UTC

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New package Ball with initial version 1.0.0
Package: Ball
Type: Package
Title: Statistical Inference and Sure Independence Screening via Ball Statistics
Version: 1.0.0
Date: 2017-12-18
Author: XueQin Wang, WenLiang Pan, HePing Zhang, Hongtu Zhu, Yuan Tian, WeiNan Xiao, ChengFeng Liu, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence, ball covariance, and ball correlation, are developed to analyze complex data. The ball divergence and ball covariance based distribution-free tests are implemented to examine equality of multivariate distributions and independence between random vectors of arbitrary dimensions. Furthermore, a generic non-parametric SIS procedure based on ball correlation and all of its variants are implemented to tackle the challenge in the context of ultra high dimensional data.
License: GPL-3
Packaged: 2018-01-03 15:57:52 UTC; Mamba
RoxygenNote: 6.0.1
Depends: R (>= 2.10), gam, survival
Imports: utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Encoding: UTF-8
LazyData: true
URL: https://github.com/Mamba413/Ball
BugReports: https://github.com/Mamba413/Ball/issues
Repository: CRAN
Date/Publication: 2018-01-03 18:25:13 UTC

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Package tigris updated to version 0.6.1 with previous version 0.5.3 dated 2017-05-26

Title: Load Census TIGER/Line Shapefiles into R
Description: Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre], Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>

Diff between tigris versions 0.5.3 dated 2017-05-26 and 0.6.1 dated 2018-01-03

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Package Rsampletrees updated to version 1.0.2 with previous version 1.0.1 dated 2017-08-29

Title: MCMC Sampling of Gene Genealogies Conditional on Genetic Data
Description: Sample ancestral trees conditional on phased or unphased SNP genotype data. The actual tree sampling is done using a C++ program that is launched within R. The package also contains functions for specifying the tree-sampling settings (pre-processing) and for storing and manipulating the sampled trees (post-processing). More information about 'sampletrees' can be found at <http://stat.sfu.ca/statgen/research/sampletrees.html>.
Author: Kelly Burkett, Brad McNeney, Jinko Graham, Jean-Francois Lefebvre
Maintainer: Kelly Burkett <Rsampletrees@gmail.com>

Diff between Rsampletrees versions 1.0.1 dated 2017-08-29 and 1.0.2 dated 2018-01-03

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Package metaplot updated to version 0.3.1 with previous version 0.2.7 dated 2017-12-01

Title: Data-Driven Diagnostic Plots
Description: Designs plots in terms of core structure. See 'example(metaplot)'. Primary arguments are (unquoted) column names; order and type (numeric or not) dictate the resulting plot. Specify any y variables, x variable, any groups variable, and any conditioning variables to metaplot() to generate density plots, boxplots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot() to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide' are honored, producing fully annotated plots with minimal effort. Attribute 'guide' is typically units, but may be encoded() to provide interpretations of categorical values (see '?encode'). Utility unpack() transforms scalar column attributes to row values and pack() does the reverse, supporting tool-neutral storage of metadata along with primary data. The package supports customizable aesthetics such as such as reference lines, unity lines, smooths, log transformation, and linear fits. Compact syntax and integrated metadata promote workflow scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

Diff between metaplot versions 0.2.7 dated 2017-12-01 and 0.3.1 dated 2018-01-03

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Package crochet updated to version 2.0.0 with previous version 1.0.0 dated 2017-05-06

Title: Implementation Helper for [ and [<- Of Custom Matrix-Like Types
Description: Functions to help implement the extraction / subsetting / indexing function [ and replacement function [<- of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).
Author: Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>

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Package RcmdrMisc updated to version 1.0-7 with previous version 1.0-6 dated 2017-08-28

Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre], Robert Muenchen [ctb], Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

Diff between RcmdrMisc versions 1.0-6 dated 2017-08-28 and 1.0-7 dated 2018-01-03

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Package bsamGP updated to version 1.1.2 with previous version 1.1.1 dated 2017-11-26

Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference using a spectral analysis of Gaussian process priors. Gaussian processes are represented with a Fourier series based on cosine basis functions. Currently the package includes parametric linear models, partial linear additive models with/without shape restrictions, generalized linear additive models with/without shape restrictions, and density estimation model. To maximize computational efficiency, the actual Markov chain Monte Carlo sampling for each model is done using codes written in FORTRAN 90. This software has been developed using funding supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut, cre], Taeryon Choi [aut], Beomjo Park [aut, cre], Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjo@korea.ac.kr>

Diff between bsamGP versions 1.1.1 dated 2017-11-26 and 1.1.2 dated 2018-01-03

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Package xwf updated to version 0.2-0 with previous version 0.1-1 dated 2017-10-03

Title: Extrema-Weighted Feature Extraction
Description: Extrema-weighted feature extraction for varying length functional data. Functional data analysis method that performs dimensionality reduction based on predefined features and allows for quantile weighting. Method implemented as presented in Van den Boom et al. (2017) <arXiv:1709.10467>.
Author: Willem van den Boom [aut, cre]
Maintainer: Willem van den Boom <willem@wvdboom.nl>

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Package wordcloud2 updated to version 0.2.1 with previous version 0.2.0 dated 2016-07-25

Title: Create Word Cloud by 'htmlwidget'
Description: A fast visualization tool for creating wordcloud by using 'wordcloud2.js'. 'wordcloud2.js' is a JavaScript library to create wordle presentation on 2D canvas or HTML <https://timdream.org/wordcloud2.js/>.
Author: Dawei Lang[aut, cre], Guan-tin Chien[aut, author for 'wordcloud2.js']
Maintainer: Dawei Lang <chiffonlang@icloud.com>

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Package rprojroot updated to version 1.3-2 with previous version 1.3-1 dated 2017-12-18

Title: Finding Files in Project Subdirectories
Description: Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package RcmdrPlugin.NMBU updated to version 1.8.8 with previous version 1.8.7 dated 2016-10-12

Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

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Package odr updated to version 0.7.3 with previous version 0.3.2 dated 2017-09-17

Title: Optimal Design and Statistical Power of Multilevel Randomized Trials
Description: Calculate the optimal sample allocation that minimizes the variance of treatment effect in multilevel randomized trials under fixed budget and cost structure, perform power analyses with and without accommodating costs and budget. The references for proposed methods are: (1) Shen, Z., & Kelcey, B. (2018, April). Optimal design of cluster randomized trials under condition- and unit-specific cost structures. Roundtable discussion to be presented at American Educational Research Association (AERA) annual conference; (2) Shen, Z., & Kelcey, B. (under review). Optimal sample allocation under unequal costs in cluster-randomized trials. Journal of Educational and Behavioral Statistics; (3) Shen, Z.(in progress). Using optimal sample allocation to improve design efficiency for multilevel randomized trials. (Unpublished doctoral dissertation). University of Cincinnati, Cincinnati, OH.
Author: Zuchao Shen [aut, cre]
Maintainer: Zuchao Shen <shenzo@mail.uc.edu>

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Package MetaLandSim updated to version 1.0.1 with previous version 1.0 dated 2017-12-21

Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
Author: Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita, Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>

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Package Hmisc updated to version 4.1-1 with previous version 4.1-0 dated 2017-12-19

Title: Harrell Miscellaneous
Description: Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>

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New package DeLorean with initial version 1.3.0
Package: DeLorean
Title: Estimates Pseudotimes for Single Cell Expression Data
Author: John Reid <john.reid@mrc-bsu.cam.ac.uk>
Maintainer: John Reid <john.reid@mrc-bsu.cam.ac.uk>
Version: 1.3.0
Description: Implements the DeLorean model (Reid & Wernisch (2016) <doi:10.1093/bioinformatics/btw372>) to estimate pseudotimes for single cell expression data. The DeLorean model uses a Gaussian process latent variable model to model uncertainty in the capture time of cross-sectional data.
Depends: R (>= 3.0.2), Rcpp (>= 0.12.0)
Imports: rstan (>= 2.15.1), dplyr (>= 0.4.3), reshape2 (>= 1.4), stringr (>= 0.6.2), ggplot2 (>= 1.0.0), MASS (>= 7.3), broom, coda, parallel, functional, kernlab, fastICA, seriation, memoise
Suggests: knitr (>= 1.8), knitcitations, rmarkdown, formatR, extrafont, testthat, svglite, VGAM
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-01-03 13:32:50 UTC; john
Repository: CRAN
Date/Publication: 2018-01-03 15:13:32 UTC

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Package Biolinv updated to version 0.1-2 with previous version 0.1-1 dated 2017-02-03

Title: Modelling and Forecasting Biological Invasions
Description: Analysing and forecasting biological invasions time series with a stochastic, non-mechanistic approach that gives proper weight to the anthropic component, accounts for habitat suitability and provides measures of precision for its estimates.
Author: Luca Butikofer [aut, cre], Beatrix Jones [aut]
Maintainer: Luca Butikofer <lucabutikofer@gmail.com>

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Package utf8 updated to version 1.1.3 with previous version 1.1.2 dated 2017-12-14

Title: Unicode Text Processing
Description: Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.
Author: Patrick O. Perry [aut, cph, cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

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Package trend updated to version 1.1.0 with previous version 1.0.1 dated 2017-11-12

Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

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Package spData updated to version 0.2.6.9 with previous version 0.2.6.8 dated 2017-12-17

Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class sf (defined by the package 'sf'), Spatial (sp), and nb (spdep). Unlike other spatial data packages such as 'rnaturalearth' and 'maps', it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some of the datasets are designed to illustrate specific analysis techniques. cycle_hire and cycle_hire_osm, for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (0000-0003-2392-6140), Jakub Nowosad [aut, cre] (0000-0002-1057-3721), Robin Lovelace [aut] (0000-0001-5679-6536)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package seplyr updated to version 0.5.1 with previous version 0.5.0 dated 2017-11-25

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

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Package PUlasso updated to version 2.1 with previous version 1.2 dated 2017-12-13

Title: High-Dimensional Variable Selection with Presence-Only Data
Description: Efficient algorithm for solving PU (Positive and Unlabelled) problem in low or high dimensional setting with lasso or group lasso penalty. The algorithm uses Maximization-Minorization and (block) coordinate descent. Sparse calculation and parallel computing via 'OpenMP' are supported for the computational speed-up. See Hyebin Song, Garvesh Raskutti (2017) <arXiv:1711.08129>.
Author: Hyebin Song [aut, cre], Garvesh Raskutti [aut]
Maintainer: Hyebin Song <hsong56@wisc.edu>

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Package oaxaca updated to version 0.1.4 with previous version 0.1.3 dated 2016-01-25

Title: Blinder-Oaxaca Decomposition
Description: An implementation of the Blinder-Oaxaca decomposition for linear regression models.
Author: Marek Hlavac <mhlavac@alumni.princeton.edu>
Maintainer: Marek Hlavac <mhlavac@alumni.princeton.edu>

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Package mixlm updated to version 1.2.3 with previous version 1.2.2 dated 2017-11-12

Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm() and glm(). A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [ctb], R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

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Package mcca updated to version 0.2.0 with previous version 0.1.0 dated 2017-11-20

Title: Multi-Category Classification Accuracy
Description: It contains six common multi-category classification accuracy evaluation measures: Hypervolume Under Manifold (HUM), described in Li and Fine (2008) <doi:10.1093/biostatistics/kxm050>. Correct Classification Percentage (CCP), Integrated Discrimination Improvement (IDI), Net Reclassification Improvement (NRI), R-Squared Value (RSQ), described in Li, Jiang and Fine (2013) <doi:10.1093/biostatistics/kxs047>. Polytomous Discrimination Index (PDI), described in Van Calster et al. (2012) <doi:10.1007/s10654-012-9733-3>. Li et al. (2018) <doi:10.1177/0962280217692830>.
Author: Ming Gao, Jialiang Li
Maintainer: Ming Gao <gaoming96@sjtu.edu.cn>

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Package kyotil updated to version 2017.12-27 with previous version 2017.10-31 dated 2017-11-03

Title: Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre], Krisztian Sebestyen [aut], Jason Becker [ctb], Bendix Carstensen [ctb], Daryl Morris [ctb], Josh Pasek [ctb], Dennis Chao [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>

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Package inctools updated to version 1.0.11 with previous version 1.0.10 dated 2017-04-13

Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) <doi:10.1097/EDE.0b013e3182576c07>.
Author: Alex Welte [aut], Eduard Grebe [cre, aut], Avery McIntosh [aut], Petra Bäumler [aut], Reshma Kassanjee [ctb], Hilmarie Brand [ctb], Cari Van Schalkwyk [ctb], Yuruo Li [ctb], Simon Daniel [ctb], Stefano Ongarello [aut], Yusuke Asai [ctb], Jeffrey Eaton [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>

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Package forecastHybrid updated to version 2.0.10 with previous version 1.1.9 dated 2017-08-23

Title: Convenient Functions for Ensemble Time Series Forecasts
Description: Convenient functions for ensemble forecasts in R combining approaches from the 'forecast' package. Forecasts generated from auto.arima(), ets(), thetam(), nnetar(), stlm(), and tbats() can be combined with equal weights, weights based on in-sample errors, or CV weights. Cross validation for time series data and user-supplied models and forecasting functions is also supported to evaluate model accuracy.
Author: David Shaub [aut, cre], Peter Ellis [aut]
Maintainer: David Shaub <davidshaub@gmx.com>

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Package ExtremeBounds updated to version 0.1.6 with previous version 0.1.5.2 dated 2016-08-26

Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac <mhlavac@alumni.princeton.edu>
Maintainer: Marek Hlavac <mhlavac@alumni.princeton.edu>

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Package encode updated to version 0.3.3 with previous version 0.3.2 dated 2017-11-30

Title: Represent Ordered Lists and Pairs as Strings
Description: Interconverts between ordered lists and compact string notation. Useful for capturing code lists, and pair-wise codes and decodes, for text storage. Analogous to factor levels and labels. Generics encode() and decode() perform interconversion, while codes() and decodes() extract components of an encoding. The function encoded() checks whether something is interpretable as an encoding.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package dlsem updated to version 2.1 with previous version 2.0 dated 2017-12-05

Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are an extension of linear structural causal models (Pearl, 2000, Chapter 5) <ISBN:978-0-521-89560-6>, where each factor of the joint probability distribution is a distributed-lag linear regression with constrained lag shapes (Judge et al., 1985, Chapters 9-10) <ISBN: 978-0-471-89530-5>. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>

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Package dbplyr updated to version 1.2.0 with previous version 1.1.0 dated 2017-06-27

Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
Author: Hadley Wickham [aut, cre], Edgar Ruiz [aut], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package csv updated to version 0.5.1 with previous version 0.5 dated 2017-07-10

Title: Read and Write CSV Files with Selected Conventions
Description: Reads and writes CSV with selected conventions. Uses the same generic function for reading and writing to promote consistent formats.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package biogas updated to version 1.9.0 with previous version 1.8.1 dated 2017-08-12

Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas quantity and composition can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@eng.au.dk>

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Package BIGL updated to version 1.1.1 with previous version 1.1.0 dated 2017-09-25

Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>

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New package attempt with initial version 0.1.0
Package: attempt
Title: Easy Condition Handling
Version: 0.1.0
Authors@R: person("Colin", "Fay", email = "contact@colinfay.me", role = c("aut", "cre"))
Description: A friendlier condition handler, inspired by 'purrr' mappers and based on 'rlang'. 'attempt' extends and facilitates condition handling by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Imports: rlang
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-01-03 09:08:20 UTC; colin
Author: Colin Fay [aut, cre]
Maintainer: Colin Fay <contact@colinfay.me>
Repository: CRAN
Date/Publication: 2018-01-03 13:37:16 UTC

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Package SemiCompRisks updated to version 2.8 with previous version 2.7 dated 2017-06-28

Title: Hierarchical Models for Parametric and Semi-Parametric Analyses of Semi-Competing Risks Data
Description: Hierarchical multistate models are considered to perform the analysis of independent/clustered semi-competing risks data. The package allows to choose the specification for model components from a range of options giving users substantial flexibility, including: accelerated failure time or proportional hazards regression models; parametric or non-parametric specifications for baseline survival functions and cluster-specific random effects distribution; a Markov or semi-Markov specification for terminal event following non-terminal event. While estimation is mainly performed within the Bayesian paradigm, the package also provides the maximum likelihood estimation approach for several para- metric models. The package also includes functions for univariate survival analysis as complementary analysis tools.
Author: Kyu Ha Lee, Catherine Lee, Danilo Alvares, and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>

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Package RtutoR updated to version 1.1 with previous version 1.0 dated 2017-12-18

Title: Shiny Apps for Plotting and Exploratory Analysis
Description: Contains Shiny apps for Plotting and Exploratory Analysis. The plotting app provides an automated interface for generating plots using the 'ggplot2' package. Current version of this app supports 10 different plot types along with options to manipulate specific aesthetics and controls related to each plot type. Exploratory Analysis app helps generates an Exploratory analysis report (in PowerPoint format) comprising of Univariate and Bivariate plots & related summary tables.
Author: Anup Nair [aut, cre]
Maintainer: Anup Nair <nairanup50695@gmail.com>

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Package ropenaq updated to version 0.2.5 with previous version 0.2.4 dated 2017-11-20

Title: Accesses Air Quality Data from the Open Data Platform OpenAQ
Description: Allows access to air quality data from the API of the OpenAQ platform <https://docs.openaq.org/>, with the different services the API offers (getting measurements for a given query, getting latest measurements, getting lists of available countries/cities/locations).
Author: Maëlle Salmon [aut, cre], Andrew MacDonald [ctb] (Andrew MacDonald reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24), Andy Teucher [ctb] (Andy Teucher reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24), Mikayla Murphy [ctb]
Maintainer: Maëlle Salmon <maelle.salmon@yahoo.se>

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New package mekko with initial version 0.1.0
Package: mekko
Type: Package
Title: Variable Width Bar Charts: Bar Mekko
Version: 0.1.0
Authors@R: c( person("Eric", "Rynerson", email = "eric.rynerson@gmail.com", role = c("cre", "aut")), person("Julius", "Vainora", role = "ctb"))
Maintainer: Eric Rynerson <eric.rynerson@gmail.com>
Description: Create variable width bar charts i.e. "bar mekko" charts to include important quantitative context. Closely related to mosaic, spine (or spinogram), matrix, submarine, olympic, Mondrian or product plots and tree maps.
Imports: ggplot2 (>= 2.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-01-02 20:25:04 UTC; Eric
Author: Eric Rynerson [cre, aut], Julius Vainora [ctb]
Repository: CRAN
Date/Publication: 2018-01-03 12:20:48 UTC

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Package PoisBinOrd updated to version 1.3 with previous version 1.2 dated 2016-05-13

Title: Data Generation with Poisson, Binary and Ordinal Components
Description: Generation of multiple count, binary and ordinal variables simultaneously given the marginal characteristics and association structure. Throughout the package, the word 'Poisson' is used to imply count data under the assumption of Poisson distribution.
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan <ginan@metu.edu.tr>

Diff between PoisBinOrd versions 1.2 dated 2016-05-13 and 1.3 dated 2018-01-03

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Package PoisBinNonNor updated to version 1.2 with previous version 1.1 dated 2016-05-13

Title: Data Generation with Poisson, Binary and Continuous Components
Description: Generation of multiple count, binary and continuous variables simultaneously given the marginal characteristics and association structure. Throughout the package, the word 'Poisson' is used to imply count data under the assumption of Poisson distribution.
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan <ginan@metu.edu.tr>

Diff between PoisBinNonNor versions 1.1 dated 2016-05-13 and 1.2 dated 2018-01-03

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Package mongolite updated to version 1.5 with previous version 1.4 dated 2017-12-22

Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance 'MongoDB' client based on 'libmongoc' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication. The online user manual provides an overview of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre], MongoDB, Inc [cph] (Bundled mongo-c-driver, see AUTHORS file)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between mongolite versions 1.4 dated 2017-12-22 and 1.5 dated 2018-01-03

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Package CMplot updated to version 3.3.1 with previous version 3.3.0 dated 2017-12-14

Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>

Diff between CMplot versions 3.3.0 dated 2017-12-14 and 3.3.1 dated 2018-01-03

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Package BinNonNor updated to version 1.4 with previous version 1.3 dated 2016-05-13

Title: Data Generation with Binary and Continuous Non-Normal Components
Description: Generation of multiple binary and continuous non-normal variables simultaneously given the marginal characteristics and association structure based on the methodology proposed by Demirtas et al. (2012).
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan <ginan@metu.edu.tr>

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Package tidytree updated to version 0.1.6 with previous version 0.1.5 dated 2017-12-14

Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph] (0000-0002-6485-8781), Bradley Jones [ctb], Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package searchConsoleR updated to version 0.3.0 with previous version 0.2.1 dated 2016-06-24

Title: Google Search Console R Client
Description: Provides an interface with the Google Search Console, formally called Google Webmaster Tools.
Author: Mark Edmondson [aut, cre], Jennifer Bryan [ctb], Parzakonis Manos [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>

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Package kst updated to version 0.3-0 with previous version 0.2-2 dated 2017-12-13

Title: Knowledge Space Theory
Description: Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical framework, which proposes mathematical formalisms to operationalize knowledge structures in a particular domain. The 'kst' package provides basic functionalities to generate, handle, and manipulate knowledge structures and knowledge spaces.
Author: Christina Stahl [aut], David Meyer [aut], Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>

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Package DPpackage updated to version 1.1-7.3 with previous version 1.1-7.2 dated 2017-12-19

Title: Bayesian Nonparametric Modeling in R
Description: Functions to perform inference via simulation from the posterior distributions for Bayesian nonparametric and semiparametric models. Although the name of the package was motivated by the Dirichlet Process prior, the package considers and will consider other priors on functional spaces. So far, DPpackage includes models considering Dirichlet Processes, Dependent Dirichlet Processes, Dependent Poisson- Dirichlet Processes, Hierarchical Dirichlet Processes, Polya Trees, Linear Dependent Tailfree Processes, Mixtures of Triangular distributions, Random Bernstein polynomials priors and Dependent Bernstein Polynomials. The package also includes models considering Penalized B-Splines. Includes semiparametric models for marginal and conditional density estimation, ROC curve analysis, interval censored data, binary regression models, generalized linear mixed models, IRT type models, and generalized additive models. Also contains functions to compute Pseudo-Bayes factors for model comparison, and to elicitate the precision parameter of the Dirichlet Process. To maximize computational efficiency, the actual sampling for each model is done in compiled FORTRAN. The functions return objects which can be subsequently analyzed with functions provided in the 'coda' package.
Author: Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Maintainer: ORPHANED

Diff between DPpackage versions 1.1-7.2 dated 2017-12-19 and 1.1-7.3 dated 2018-01-03

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Package chngpt updated to version 2017.12-26 with previous version 2017.12-3 dated 2017-12-03

Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong
Maintainer: Youyi Fong <youyifong@gmail.com>

Diff between chngpt versions 2017.12-3 dated 2017-12-03 and 2017.12-26 dated 2018-01-03

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Package CATkit updated to version 3.2.3 with previous version 3.0.0.2 dated 2017-02-17

Title: Chronomics Analysis Toolkit (CAT): Periodicity Analysis
Description: Calculates auto- and cross-correlation functions and plots an actogram and a smoothing function from a time series to identify and visualize periodic components. Tests presence of anticipated rhythm and estimates rhythm parameters; fits model consisting of multiple rhythmic components to data; performs least squares spectral analysis and other cosinor-based analyses, including population-mean cosinor (pmc).
Author: Cathy Lee Gierke, Ruth Helget, Germaine Cornelissen-Guillaume
Maintainer: Cathy Lee Gierke <leegi001@umn.edu>

Diff between CATkit versions 3.0.0.2 dated 2017-02-17 and 3.2.3 dated 2018-01-03

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Package hBayesDM updated to version 0.5.0 with previous version 0.4.0 dated 2017-05-23

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

Diff between hBayesDM versions 0.4.0 dated 2017-05-23 and 0.5.0 dated 2018-01-03

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 110 files changed, 3374 insertions(+), 2327 deletions(-)

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Package CINNA updated to version 1.1.3 with previous version 1.1.2 dated 2017-10-23

Title: Deciphering Central Informative Nodes in Network Analysis
Description: Functions for computing, comparing and demonstrating top informative centrality measures within a network.
Author: Minoo Ashtiani, Mohieddin Jafari
Maintainer: Minoo Ashtiani <m_ashtiani@pasteur.ac.ir>

Diff between CINNA versions 1.1.2 dated 2017-10-23 and 1.1.3 dated 2018-01-03

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Package compound.Cox updated to version 3.7 with previous version 3.6 dated 2017-11-18

Title: Estimation, Gene Selection, and Survival Prediction Based on the Compound Covariate Method Under the Cox Model
Description: Estimation, gene selection, and survival prediction based on the compound covariate method under the Cox model with high-dimensional gene expressions. Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>, statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627> and Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>. Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between compound.Cox versions 3.6 dated 2017-11-18 and 3.7 dated 2018-01-03

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 6 files changed, 22 insertions(+), 29 deletions(-)

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