Tue, 02 Jan 2018

Package tibbletime updated to version 0.1.0 with previous version 0.0.2 dated 2017-10-06

Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension that allows for the creation of time aware tibbles. Some immediate advantages of this include: the ability to perform time-based subsetting on tibbles, quickly summarising and aggregating results by time periods, and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre], Matt Dancho [aut]
Maintainer: Davis Vaughan <dvaughan@business-science.io>

Diff between tibbletime versions 0.0.2 dated 2017-10-06 and 0.1.0 dated 2018-01-02

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Package provenance updated to version 1.9 with previous version 1.8 dated 2017-11-22

Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between provenance versions 1.8 dated 2017-11-22 and 1.9 dated 2018-01-02

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Package naivebayes updated to version 0.9.2 with previous version 0.9.1 dated 2017-01-15

Title: High Performance Implementation of the Naive Bayes Algorithm
Description: High performance implementation of the Naive Bayes algorithm.
Author: Michal Majka
Maintainer: Michal Majka <michalmajka@hotmail.com>

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Package httping updated to version 0.2.0 with previous version 0.1.0 dated 2016-01-03

Title: 'Ping' 'URLs' to Time 'Requests'
Description: A suite of functions to ping 'URLs' and to time 'HTTP' 'requests'. Designed to work with 'httr'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package miRNAss updated to version 1.4 with previous version 1.3 dated 2017-11-02

Title: Genome-Wide Discovery of Pre-miRNAs with few Labeled Examples
Description: Machine learning method specifically designed for pre-miRNA prediction. It takes advantage of unlabeled sequences to improve the prediction rates even when there are just a few positive examples, when the negative examples are unreliable or are not good representatives of its class. Furthermore, the method can automatically search for negative examples if the user is unable to provide them. MiRNAss can find a good boundary to divide the pre-miRNAs from other groups of sequences; it automatically optimizes the threshold that defines the classes boundaries, and thus, it is robust to high class imbalance. Each step of the method is scalable and can handle large volumes of data.
Author: Cristian Yones
Maintainer: Cristian Yones <cyones@sinc.unl.edu.ar>

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Package biomartr updated to version 0.7.0 with previous version 0.5.2 dated 2017-09-20

Title: Genomic Data Retrieval
Description: Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
Author: Hajk-Georg Drost [aut, cre] (http://orcid.org/0000-0002-1567-306X)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>

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Package Rdimtools updated to version 0.2.0 with previous version 0.1.3 dated 2017-11-24

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

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Package qualvar updated to version 0.2.0 with previous version 0.1.0 dated 2015-08-19

Title: Implements Indices of Qualitative Variation Proposed by Wilcox (1973)
Description: Implements indices of qualitative variation proposed by Wilcox (1973).
Author: Joel Gombin [aut, cre]
Maintainer: Joel Gombin <joel.gombin@gmail.com>

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Package qlcData updated to version 0.2.0 with previous version 0.1.0 dated 2015-10-21

Title: Processing Data for Quantitative Language Comparison (QLC)
Description: This is a collection of functions to read, recode, and transcode data for QLC.
Author: Michael Cysouw
Maintainer: Michael Cysouw <cysouw@mac.com>

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Package huxtable updated to version 2.0.0 with previous version 1.2.0 dated 2017-12-17

Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar functionality to 'xtable', but does more, with a simpler interface. Includes a 'huxreg' function for quick creation of regression tables. Allows export to Microsoft Word or PowerPoint using the 'officer' package.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package burnr updated to version 0.2.2 with previous version 0.2.1 dated 2017-09-22

Title: Fire-History Analysis in R
Description: Basic tools to analyze forest fire history data (e.g. FHX) in R.
Author: Steven Malevich [aut, cre], Christopher Guiterman [ctb], Ellis Margolis [ctb]
Maintainer: Steven Malevich <malevich@email.arizona.edu>

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Package tidycensus updated to version 0.4 with previous version 0.3.1 dated 2017-10-26

Title: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many geographies.
Author: Kyle Walker [aut, cre], Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>

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Package mlrMBO updated to version 1.1.1 with previous version 1.1.0 dated 2017-05-12

Title: A Toolbox for Model-Based Optimization of Expensive Black-Box Functions
Description: Flexible and comprehensive R toolbox for model-based optimization ('MBO'), also known as Bayesian optimization. It is designed for both single- and multi-objective optimization with mixed continuous, categorical and conditional parameters. The machine learning toolbox 'mlr' provide dozens of regression learners to model the performance of the target algorithm with respect to the parameter settings. It provides many different infill criteria to guide the search process. Additional features include multi-point batch proposal, parallel execution as well as visualization and sophisticated logging mechanisms, which is especially useful for teaching and understanding of algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that single components can be easily replaced or adapted by the user for specific use cases.
Author: Bernd Bischl [aut], Jakob Bossek [aut], Jakob Richter [aut, cre], Daniel Horn [aut], Michel Lang [aut], Janek Thomas [aut]
Maintainer: Jakob Richter <code@jakob-r.de>

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Package HydeNet updated to version 0.10.7 with previous version 0.10.6 dated 2017-12-01

Title: Hybrid Bayesian Networks Using R and JAGS
Description: Facilities for easy implementation of hybrid Bayesian networks using R. Bayesian networks are directed acyclic graphs representing joint probability distributions, where each node represents a random variable and each edge represents conditionality. The full joint distribution is therefore factorized as a product of conditional densities, where each node is assumed to be independent of its non-descendents given information on its parent nodes. Since exact, closed-form algorithms are computationally burdensome for inference within hybrid networks that contain a combination of continuous and discrete nodes, particle-based approximation techniques like Markov Chain Monte Carlo are popular. We provide a user-friendly interface to constructing these networks and running inference using the 'rjags' package. Econometric analyses (maximum expected utility under competing policies, value of information) involving decision and utility nodes are also supported.
Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>

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Package eulerr updated to version 3.1.0 with previous version 3.0.0 dated 2017-11-15

Title: Area-Proportional Euler and Venn Diagrams with Circles or Ellipses
Description: Generate area-proportional Euler diagrams using numerical optimization. An Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented. Diagrams may be fit with ellipses and circles via a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre], A. Jonathan R. Godfrey [ctb], Tim Kelley [ctb] (Original Nelder-Mead code), David H. Eberly [ctb] (Geometric algorithms)
Maintainer: Johan Larsson <johanlarsson@outlook.com>

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 eulerr-3.1.0/eulerr/src/solver.h                          |    8 
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 eulerr-3.1.0/eulerr/src/utils.cpp                         |   36 
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 eulerr-3.1.0/eulerr/vignettes/introduction.Rnw            |   16 
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 43 files changed, 3929 insertions(+), 2205 deletions(-)

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Package elasticsearchr updated to version 0.2.1 with previous version 0.2.0 dated 2016-12-19

Title: A Lightweight Interface for Interacting with Elasticsearch from R
Description: A lightweight R interface to 'Elasticsearch' - a NoSQL search-engine and column store database (see <https://www.elastic.co/products/elasticsearch> for more information). This package implements a simple Domain-Specific Language (DSL) for indexing, deleting, querying, sorting and aggregating data using 'Elasticsearch'.
Author: Alex Ioannides
Maintainer: Alex Ioannides <alex.ioannides@yahoo.co.uk>

Diff between elasticsearchr versions 0.2.0 dated 2016-12-19 and 0.2.1 dated 2018-01-02

 DESCRIPTION                                     |   10 +--
 MD5                                             |   70 ++++++++++++------------
 NEWS.md                                         |   12 ++--
 R/api.R                                         |   23 ++++---
 R/utils.R                                       |   26 ++++++--
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 build/vignette.rds                              |binary
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 man/aggs.Rd                                     |    1 
 man/check_http_code_throw_error.Rd              |    1 
 man/cleaned_field_names.Rd                      |    1 
 man/create_bulk_upload_file.Rd                  |    4 -
 man/create_metadata.Rd                          |    1 
 man/elastic.Rd                                  |    1 
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 man/elastic_version.Rd                          |    1 
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 man/from_size_search.Rd                         |    1 
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 man/grapes-index-grapes.Rd                      |    1 
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 man/plus-.elastic_api.Rd                        |    1 
 man/print.elastic_api.Rd                        |    1 
 man/query.Rd                                    |    1 
 man/scroll_search.Rd                            |    1 
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 man/valid_json.Rd                               |    1 
 man/valid_url.Rd                                |    1 
 tests/testthat/helper-elasticsearch_test_data.R |   14 +++-
 tests/testthat/test-api.R                       |   33 ++++++++---
 tests/testthat/test-utils.R                     |    2 
 36 files changed, 143 insertions(+), 118 deletions(-)

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Package APML0 updated to version 0.6 with previous version 0.5 dated 2017-10-03

Title: Augmented and Penalized Minimization Method L0
Description: Fit linear, logistic and Cox models regularized with L0, lasso (L1), elastic-net (L1 and L2), or net (L1 and Laplacian) penalty, and their adaptive forms, such as adaptive lasso / elastic-net and net adjusting for signs of linked coefficients. It solves L0 penalty problem by simultaneously selecting regularization parameters and the number of non-zero coefficients. This augmented and penalized minimization method provides an approximation solution to the L0 penalty problem, but runs as fast as L1 regularization problem. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients. It could deal with very high dimensional data and has superior selection performance.
Author: Xiang Li, Shanghong Xie, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li <xli256@its.jnj.com>

Diff between APML0 versions 0.5 dated 2017-10-03 and 0.6 dated 2018-01-02

 DESCRIPTION          |    6 +++---
 MD5                  |    6 +++---
 R/net_logit.R        |    2 +-
 man/APML0-package.Rd |    4 ++--
 4 files changed, 9 insertions(+), 9 deletions(-)

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Package zoon (with last version 0.6) was removed from CRAN

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

2017-01-12 0.6
2016-06-13 0.5
2016-03-11 0.4.23
2015-12-10 0.4.21

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Package rgpui (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:

2014-12-13 0.1-2
2014-03-14 0.1-1

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Package rgp (with last version 0.4-1) was removed from CRAN

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

2014-08-08 0.4-1
2014-03-12 0.4-0
2013-06-25 0.3-4
2011-10-20 0.2-4
2010-12-07 0.2-3
2010-10-15 0.2-2
2010-08-25 0.2-1
2010-05-22 0.1-0

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Package lmeVarComp (with last version 1.0) was removed from CRAN

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

2014-08-27 1.0

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Package mistat (with last version 1.0-4) was removed from CRAN

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

2016-08-03 1.0-4
2015-06-12 1.0-3
2014-01-20 1.0-2
2013-09-26 1.0
2013-08-27 0.999

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