Tue, 05 Mar 2019

Package taxotools updated to version 0.0.11 with previous version 0.0.9 dated 2019-02-26

Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>

Diff between taxotools versions 0.0.9 dated 2019-02-26 and 0.0.11 dated 2019-03-05

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Package sparseHessianFD updated to version 0.3.3.4 with previous version 0.3.3.3 dated 2018-03-27

Title: Numerical Estimation of Sparse Hessians
Description: Estimates Hessian of a scalar-valued function, and returns it in a sparse Matrix format. The sparsity pattern must be known in advance. The algorithm is especially efficient for hierarchical models with a large number of heterogeneous units. See Braun, M. (2017) <doi:10.18637/jss.v082.i10>.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>

Diff between sparseHessianFD versions 0.3.3.3 dated 2018-03-27 and 0.3.3.4 dated 2019-03-05

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New package seqmon with initial version 2.3
Package: seqmon
Type: Package
Title: Group Sequential Design Class for Clinical Trials
Version: 2.3
Date: 2019-3-5
Author: David A Schoenfeld and Hui Zheng
Maintainer: Hui Zheng <hzheng1@mgh.harvard.edu>
Description: S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
License: MIT + file LICENSE
Depends: methods
Suggests:
NeedsCompilation: no
Packaged: 2019-03-05 18:55:26 UTC; hz029
Repository: CRAN
Date/Publication: 2019-03-05 23:10:06 UTC

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Package lifecontingencies updated to version 1.3.6 with previous version 1.3.5 dated 2018-09-18

Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrements tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [aut, cre] (<https://orcid.org/0000-0002-0315-8888>), Christophe Dutang [ctb] (<https://orcid.org/0000-0001-6732-1501>), Reinhold Kainhofer [ctb] (<https://orcid.org/0000-0002-7895-1311>), Kevin J Owens [ctb], Ernesto Schirmacher [ctb], Gian Paolo Clemente [ctb] (<https://orcid.org/0000-0001-6795-4595>), Ivan Williams [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>

Diff between lifecontingencies versions 1.3.5 dated 2018-09-18 and 1.3.6 dated 2019-03-05

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Package HGNChelper updated to version 0.7.1 with previous version 0.5.2 dated 2018-07-06

Title: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols
Description: Contains functions for identifying and correcting HGNC human gene symbols and MGI mouse gene symbols which have been converted to date format by Excel, withdrawn, or aliased. Also contains functions for reversibly converting between HGNC symbols and valid R names.
Author: Levi Waldron and Markus Riester
Maintainer: Levi Waldron <lwaldron.research@gmail.com>

Diff between HGNChelper versions 0.5.2 dated 2018-07-06 and 0.7.1 dated 2019-03-05

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Package weightr updated to version 2.0.1 with previous version 2.0.0 dated 2019-02-28

Title: Estimating Weight-Function Models for Publication Bias
Description: Estimates the Vevea and Hedges (1995) weight-function model. By specifying arguments, users can also estimate the modified model described in Vevea and Woods (2005), which may be more practical with small datasets. Users can also specify moderators to estimate a linear model. The package functionality allows users to easily extract the results of these analyses as R objects for other uses. In addition, the package includes a function to launch both models as a Shiny application. Although the Shiny application is also available online, this function allows users to launch it locally if they choose.
Author: Kathleen M. Coburn [aut, cre], Jack L. Vevea [aut]
Maintainer: Kathleen M. Coburn <kcoburn@ucmerced.edu>

Diff between weightr versions 2.0.0 dated 2019-02-28 and 2.0.1 dated 2019-03-05

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Package tidyRSS updated to version 1.2.8 with previous version 1.2.7 dated 2018-11-03

Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis, 'tidyRSS' parses RSS, Atom XML, JSON and geoRSS feeds and returns a tidy data frame.
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>

Diff between tidyRSS versions 1.2.7 dated 2018-11-03 and 1.2.8 dated 2019-03-05

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New package probhat with initial version 0.1.1
Package: probhat
Title: Generalized Kernel Smoothing
Version: 0.1.1
Date: 2019-02-28
License: GPL (>= 2)
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Author: Abby Spurdle
URL: https://sites.google.com/site/asrpws
Description: Computes nonparametric probability distributions (probability density functions, cumulative distribution functions and quantile functions) using kernel smoothing. Supports univariate, multivariate and conditional distributions, and weighted data (possibly useful mixed with fuzzy clustering or frequency data). Also, supports empirical continuous cumulative distribution functions and their inverses, and random number generation.
Depends: graphics, stats
Imports: barsurf
Suggests: intoo, bivariate, mvtnorm, fclust, moments, scatterplot3d
NeedsCompilation: no
Packaged: 2019-02-27 21:26:44 UTC; Student9
Repository: CRAN
Date/Publication: 2019-03-05 22:20:04 UTC

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New package newsanchor with initial version 0.1.0
Package: newsanchor
Type: Package
Title: Client for the News API
Version: 0.1.0
Authors@R: c(person("Preu", "Frie", email = "fr1e@pm.me", role = c("aut", "pro")), person("Buhl", "Yannik", email = "ybuhl@posteo.de", role = c("aut", "cre")), person("Schulze", "Lars", email = "lars.schulze@hotmail.com", role = c("aut")), person("Dix", "Jan", email = "jan.dix@uni-konstanz.de", role = c("aut", "pro")))
Description: Interface to gather news from the 'News API', based on a multilevel query <https://newsapi.org/>. A personal API key is required.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.2.0)
BugReports: https://github.com/correlaid/newsanchor/issues
LazyData: true
Imports: devtools, httr, jsonlite, tidyr, xml2, lubridate
Suggests: dplyr, knitr, magrittr, rmarkdown, robotstxt, rvest, stringr, testthat, tidytext
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-03-05 21:34:57 UTC; Yannik B
Author: Preu Frie [aut, pro], Buhl Yannik [aut, cre], Schulze Lars [aut], Dix Jan [aut, pro]
Maintainer: Buhl Yannik <ybuhl@posteo.de>
Repository: CRAN
Date/Publication: 2019-03-05 22:10:11 UTC

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Package midasr updated to version 0.7 with previous version 0.6 dated 2016-08-08

Title: Mixed Data Sampling Regression
Description: Methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras <virmantas.kvedaras@ec.europa.eu>, Vaidotas Zemlys-Balevičius <vaidotas.zemlys@mif.vu.lt>
Maintainer: Vaidotas Zemlys-Balevičius <zemlys@gmail.com>

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Package lme4 updated to version 1.1-21 with previous version 1.1-20 dated 2019-02-04

Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>), Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>), Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>), Rune Haubo Bojesen Christensen [ctb] (<https://orcid.org/0000-0002-4494-3399>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Bin Dai [ctb], Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>), Gabor Grothendieck [ctb], Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>), John Fox [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>

Diff between lme4 versions 1.1-20 dated 2019-02-04 and 1.1-21 dated 2019-03-05

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Package LLSR updated to version 0.0.2.19 with previous version 0.0.2.12 dated 2019-02-15

Title: Data Analysis of Liquid-Liquid Systems using R
Description: Originally design to characterise Aqueous Two Phase Systems, LLSR provide a simple way to analyse experimental data and obtain phase diagram parameters, among other properties, systematically. The package will include (every other update) new functions in order to comprise useful tools in liquid-liquid extraction research.
Author: Diego F Coelho <diegofcoelho@gmail.com> [aut, cre], Pedro Vitor Oliveira Menezes <pedrod841@hotmail.com> [dtc], Carla Corina dos Santos Porto <carlacorina@hotmail.com.br> [dtc], Jon George Huddleston <Jonathan.Huddleston@brunel.ac.uk> [rev], Elias Basile Tambourgi <eliastam@feq.unicamp.br> [rev]
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>

Diff between LLSR versions 0.0.2.12 dated 2019-02-15 and 0.0.2.19 dated 2019-03-05

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Package spMC updated to version 0.3.10 with previous version 0.3.9 dated 2018-02-12

Title: Continuous-Lag Spatial Markov Chains
Description: A set of functions is provided for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields.
Author: Luca Sartore
Maintainer: Luca Sartore <drwolf85@gmail.com>

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Package scifigure updated to version 0.2 with previous version 0.1.1 dated 2017-07-19

Title: Visualize 'Reproducibility' and 'Replicability' in a Comparison of Scientific Studies
Description: Users may specify what fundamental qualities of a new study have or have not changed in an attempt to reproduce or replicate an original study. A comparison of the differences is visualized. Visualization approach follows 'Patil', 'Peng', and 'Leek' (2016) <doi:10.1101/066803>.
Author: Prasad Patil [aut, cre], Gehlenborg Nils [ctb], Muschelli John [ctb], Leek Jeff [aut]
Maintainer: Prasad Patil <prpatil42@gmail.com>

Diff between scifigure versions 0.1.1 dated 2017-07-19 and 0.2 dated 2019-03-05

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Package CEGO updated to version 2.3.0 with previous version 2.2.0 dated 2017-07-12

Title: Combinatorial Efficient Global Optimization
Description: Model building, surrogate model based optimization and Efficient Global Optimization in combinatorial or mixed search spaces.
Author: Martin Zaefferer <mzaefferer@gmail.com>
Maintainer: Martin Zaefferer <mzaefferer@gmail.com>

Diff between CEGO versions 2.2.0 dated 2017-07-12 and 2.3.0 dated 2019-03-05

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Package bnlearn updated to version 4.4.1 with previous version 4.4 dated 2018-10-16

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development snapshots with the latest bugfixes are available from <http://www.bnlearn.com>.
Author: Marco Scutari [aut, cre], Robert Ness [ctb]
Maintainer: Marco Scutari <marco.scutari@gmail.com>

Diff between bnlearn versions 4.4 dated 2018-10-16 and 4.4.1 dated 2019-03-05

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Package automagic updated to version 0.5.1 with previous version 0.3 dated 2017-02-26

Title: Automagically Document and Install Packages Necessary to Run R Code
Description: Parse R code in a given directory for R packages and attempt to install them from CRAN or GitHub. Optionally use a dependencies file for tighter control over which package versions to install.
Author: Cole Brokamp [aut, cre], Steph Locke [ctb]
Maintainer: Cole Brokamp <cole.brokamp@gmail.com>

Diff between automagic versions 0.3 dated 2017-02-26 and 0.5.1 dated 2019-03-05

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Package firebehavioR updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-26

Title: Prediction of Wildland Fire Behavior and Hazard
Description: Fire behavior prediction models, including the Scott & Reinhardt's (2001) Rothermel Wildland Fire Modelling System <DOI:10.2737/RMRS-RP-29> and Alexander et al.'s (2006) Crown Fire Initiation & Spread model <DOI:10.1016/j.foreco.2006.08.174>. Also contains sample datasets, estimation of fire behavior prediction model inputs (e.g., fuel moisture, canopy characteristics, wind adjustment factor), results visualization, and methods to estimate fire weather hazard.
Author: Justin Ziegler [aut, cre]
Maintainer: Justin Ziegler <Justin.Ziegler@colostate.edu>

Diff between firebehavioR versions 0.1.1 dated 2018-10-26 and 0.1.2 dated 2019-03-05

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New package SongEvo with initial version 1.0.0
Package: SongEvo
Title: An Individual-Based Model of Bird Song Evolution
Version: 1.0.0
Authors@R: c( person("Raymond", "Danner", email = "dannerR@uncw.edu", role = c("aut", "cre")), person("Elizabeth", "Derryberry", role = "aut"), person("Graham", "Derryberry", role = "aut"), person("Julie", "Danner", role = "aut"), person("David", "Luther", role = "aut"))
BugReports: https://github.com/raydanner/SongEvo/issues
Description: Simulates the cultural evolution of quantitative traits of bird song. 'SongEvo' is an individual- (agent-) based model. 'SongEvo' is spatially-explicit and can be parameterized with, and tested against, measured song data. Functions are available for model implementation, sensitivity analyses, parameter optimization, model validation, and hypothesis testing.
Depends: R (>= 3.1.0)
Imports: boot, geosphere, lattice, sp
Suggests: reshape2, Hmisc, knitr, rmarkdown
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-03-02 20:00:19 UTC; dannerr
Author: Raymond Danner [aut, cre], Elizabeth Derryberry [aut], Graham Derryberry [aut], Julie Danner [aut], David Luther [aut]
Maintainer: Raymond Danner <dannerR@uncw.edu>
Repository: CRAN
Date/Publication: 2019-03-05 19:10:09 UTC

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Package precrec updated to version 0.10 with previous version 0.9.1 dated 2017-08-23

Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between precrec versions 0.9.1 dated 2017-08-23 and 0.10 dated 2019-03-05

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Package trackeR updated to version 1.3.0 with previous version 1.2.0 dated 2018-10-12

Title: Infrastructure for Running, Cycling and Swimming Data from GPS-Enabled Tracking Devices
Description: Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>), Hannah Frick [aut] (<https://orcid.org/0000-0002-6049-5258>), Robin Hornak [aut]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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More information about trackeR at CRAN
Permanent link

New package POINT with initial version 1.1
Package: POINT
Type: Package
Title: Protein Structure Guided Local Test
Version: 1.1
Date: 2019-03-02
Author: Rachel Marceau West, Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Description: Provides an implementation of a rare variant association test that utilizes protein tertiary structure to increase signal and to identify likely causal variants. Performs structure-guided collapsing, which leads to local tests that borrow information from neighboring variants on a protein and that provide association information on a variant-specific level. For details of the implemented method see West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S-M., Wagner M. J., Buse, J. B., Motsinger-Reif, A., Fourches, D., and Tzeng, J-Y. (2019) <doi:10.1371/journal.pcbi.1006722>.
License: GPL-2
Depends: methods, stats, rARPACK, Matrix, CompQuadForm
NeedsCompilation: no
Encoding: UTF-8
RoxygenNote: 6.1.1
Collate: 'A_Kernel.R' 'A_BurdenKernel.R' 'A_LinearKernel.R' 'A_PolyKernel.R' 'B_PvMethod.R' 'B_PvMethod_Davies.R' 'B_PvMethod_Liu.R' 'C_BinomialTrait.R' 'C_GaussianTrait.R' 'D_NullResult.R' 'calcLocalKernel.R' 'distanceMatrix.R' 'mainCode.R' 'point.R' 'pvResamp.R'
Packaged: 2019-03-02 18:00:39 UTC; sthollow
Repository: CRAN
Date/Publication: 2019-03-05 18:50:03 UTC

More information about POINT at CRAN
Permanent link

Package mongolite updated to version 2.0.1 with previous version 2.0 dated 2018-08-09

Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), MongoDB, Inc [cph] (Bundled mongo-c-driver, see AUTHORS file)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between mongolite versions 2.0 dated 2018-08-09 and 2.0.1 dated 2019-03-05

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New package KATforDCEMRI with initial version 1.0
Package: KATforDCEMRI
Type: Package
Title: Kinetic Analysis and Visualization of DCE-MRI Data
Version: 1.0
Date: 2019-03-01
Authors@R: c(person("Gregory Z.", "Ferl", role = c("aut", "cre"), email = "ferl.gregory@gene.com"), person("Georges", "Hankov", role = "aut", email = "georges.hankov@roche.com"))
Depends: R (>= 2.11.0)
Imports: locfit, R.matlab, matlab
Description: Provides kinetic analysis of Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) data. Includes tools for fitting the Tofts (described in Tofts, Kermode (1991) <DOI:10.1002/mrm.1910170208>) and extended Tofts (described in Tofts et al. (1999) <https://www.ncbi.nlm.nih.gov/pubmed/10508281>) mathematical models to dynamic (signal vs. time) data associated with each voxel of an image and a Graphical User Inferface (GUI) for visualization and exploration of fitted model parameters over the volume of the image.
License: LGPL-3
Copyright: (C) 2019 Genentech, Inc.
LazyLoad: yes
LazyData: yes
NeedsCompilation: no
Packaged: 2019-03-03 02:21:03 UTC; ferlg
Author: Gregory Z. Ferl [aut, cre], Georges Hankov [aut]
Maintainer: Gregory Z. Ferl <ferl.gregory@gene.com>
Repository: CRAN
Date/Publication: 2019-03-05 18:30:11 UTC

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Package formatR updated to version 1.6 with previous version 1.5 dated 2017-04-25

Title: Format R Code Automatically
Description: Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package (see tidy_app()).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Eugene Ha [ctb], Kohske Takahashi [ctb], Ed Lee [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between formatR versions 1.5 dated 2017-04-25 and 1.6 dated 2019-03-05

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Package dvmisc updated to version 1.1.3 with previous version 1.1.2 dated 2018-02-05

Title: Convenience Functions, Moving Window Statistics, and Graphics
Description: Contains functions that do something convenient (e.g. create BMI categories), functions for calculating moving-window statistics efficiently, and functions for generating various figures (e.g. histograms with fitted probability mass/density function).
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>

Diff between dvmisc versions 1.1.2 dated 2018-02-05 and 1.1.3 dated 2019-03-05

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Package chillR updated to version 0.70.15 with previous version 0.70.14 dated 2019-02-15

Title: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi.org/10.1016/j.scienta.2012.07.011>). 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi.org/10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, 'chillR' contains a function for interpolating hourly temperature records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

Diff between chillR versions 0.70.14 dated 2019-02-15 and 0.70.15 dated 2019-03-05

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Package sonicLength updated to version 1.4.6 with previous version 1.4.4 dated 2014-08-23

Title: Estimating Abundance of Clones from DNA Fragmentation Data
Description: Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.
Author: Charles Berry <ccberry@ucsd.edu>
Maintainer: Charles Berry <ccberry@ucsd.edu>

Diff between sonicLength versions 1.4.4 dated 2014-08-23 and 1.4.6 dated 2019-03-05

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Package OBsMD updated to version 5.0 with previous version 3.0 dated 2018-06-01

Title: Objective Bayesian Model Discrimination in Follow-Up Designs
Description: Implements the objective Bayesian methodology proposed in Consonni and Deldossi in order to choose the optimal experiment that better discriminate between competing models. G.Consonni, L. Deldossi (2014) Objective Bayesian Model Discrimination in Follow-up Experimental Designs, Test. <DOI:10.1007/s11749-015-0461-3>.
Author: Laura Deldossi and Marta Nai Ruscone based on Daniel Meyer's code (2016)
Maintainer: Marta Nai Ruscone <mnairuscone@liuc.it>

Diff between OBsMD versions 3.0 dated 2018-06-01 and 5.0 dated 2019-03-05

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Package Rd2roxygen updated to version 1.8 with previous version 1.7 dated 2018-08-02

Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an Rd file to a list, create the 'roxygen' documentation and update the original R script (e.g. the one containing the definition of the function) accordingly. This package also provides utilities that can help developers build packages using 'roxygen' more easily. The 'formatR' package can be used to reformat the R code in the examples sections so that the code will be more readable.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)
Maintainer: Yihui Xie <xie@yihui.name>

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New package SHT with initial version 0.1.0
Package: SHT
Type: Package
Title: Statistical Hypothesis Testing Toolbox
Version: 0.1.0
Date: 2019-02-28
Authors@R: c(person("Kyoungjae","Lee",role="aut",email="leekjstat@gmail.com"),person("Lizhen", "Lin", role = "aut", email="lizhen.lin@nd.edu"),person("Hyungmin", "Park", role = "aut", email="hmpark0702@korea.ac.kr"),person("Kisung", "You", role = c("aut", "cre"),email = "ksyou496@gmail.com",comment=c(ORCID="0000-0002-8584-459X")))
Description: We provide a collection of statistical hypothesis testing procedures ranging from classical to modern methods for non-trivial settings such as high-dimensional scenario. For the general treatment of statistical hypothesis testing, see the book by Lehmann and Romano (2005) <doi:10.1007/0-387-27605-X>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: Rcpp, Rdpack, stats, utils, fastclime, pracma
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.1.1
RdMacros: Rdpack
URL: https://github.com/kisungyou/SHT
NeedsCompilation: yes
Packaged: 2019-02-27 19:41:29 UTC; kisung
Author: Kyoungjae Lee [aut], Lizhen Lin [aut], Hyungmin Park [aut], Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <ksyou496@gmail.com>
Repository: CRAN
Date/Publication: 2019-03-05 15:30:02 UTC

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Package radiant.multivariate updated to version 0.9.9 with previous version 0.9.7 dated 2018-10-06

Title: Multivariate Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Multivariate menu includes interfaces for perceptual mapping, factor analysis, cluster analysis, and conjoint analysis. The application extends the functionality in radiant.data.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.multivariate versions 0.9.7 dated 2018-10-06 and 0.9.9 dated 2019-03-05

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 NEWS.md                                  |   15 ++++
 R/aaa.R                                  |    2 
 R/conjoint.R                             |   12 +--
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 R/hclus.R                                |    2 
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 R/mds.R                                  |    2 
 R/pre_factor.R                           |   25 +++----
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 R/radiant.R                              |   16 +++-
 inst/app/tools/analysis/conjoint_ui.R    |  101 +++++++++++++++++--------------
 inst/app/tools/analysis/full_factor_ui.R |   91 ++++++++++++++++-----------
 inst/app/tools/analysis/kclus_ui.R       |   62 +++++++------------
 inst/app/tools/analysis/pre_factor_ui.R  |   36 +++++------
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 inst/app/tools/help/conjoint.md          |    2 
 inst/app/tools/help/full_factor.md       |    2 
 inst/app/tools/help/hclus.md             |    2 
 inst/app/tools/help/kclus.md             |    2 
 inst/app/tools/help/mds.md               |    2 
 inst/app/tools/help/pre_factor.md        |    2 
 inst/app/tools/help/prmap.md             |    2 
 man/plot.full_factor.Rd                  |    5 +
 man/radiant.multivariate.Rd              |    7 +-
 man/radiant.multivariate_viewer.Rd       |    7 +-
 man/radiant.multivariate_window.Rd       |    7 +-
 28 files changed, 335 insertions(+), 255 deletions(-)

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Package PoisBinOrd updated to version 1.4 with previous version 1.3 dated 2018-01-03

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, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>

Diff between PoisBinOrd versions 1.3 dated 2018-01-03 and 1.4 dated 2019-03-05

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 16 files changed, 569 insertions(+), 594 deletions(-)

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Package PoisBinNonNor updated to version 1.3 with previous version 1.2 dated 2018-01-03

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, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>

Diff between PoisBinNonNor versions 1.2 dated 2018-01-03 and 1.3 dated 2019-03-05

 DESCRIPTION                  |   12 ++---
 MD5                          |    8 +--
 R/fleishman.coef.R           |   76 +++++++++++++++++----------------
 man/PoisBinNonNor-package.Rd |   96 +++++++++++++++++++++---------------------
 man/fleishman.coef.Rd        |   98 +++++++++++++++++++++----------------------
 5 files changed, 148 insertions(+), 142 deletions(-)

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New package MultiRobust with initial version 1.0.0
Package: MultiRobust
Type: Package
Title: Multiply Robust Methods for Missing Data Problems
Version: 1.0.0
Author: Shixiao Zhang and Peisong Han
Maintainer: Shixiao Zhang <praetere@gmail.com>
Description: Multiply robust estimation for population mean (Han and Wang 2013) <doi:10.1093/biomet/ass087>, regression analysis (Han 2014) <doi:10.1080/01621459.2014.880058> (Han 2016) <doi:10.1111/sjos.12177> and quantile regression (Han et al. 2019) <doi:10.1111/rssb.12309>.
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.1.1
Imports: stats
Suggests: MASS, SuppDists, quantreg
NeedsCompilation: no
Packaged: 2019-02-27 19:38:29 UTC; Administrator
Repository: CRAN
Date/Publication: 2019-03-05 15:30:07 UTC

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New package leafsync with initial version 0.1.0
Package: leafsync
Type: Package
Title: Small Multiples for Leaflet Web Maps
Version: 0.1.0
Authors@R: c( person("Tim", "Appelhans", role = c("aut", "cre"), email = "tim.appelhans@gmail.com"), person("Kenton", "Russell", role = c("aut")), person("Jan Pieter", "Wagmeester", role = c("ctb"), comment = "Leaflet.Sync plugin") )
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Description: Create small multiples of several leaflet web maps with (optional) synchronised panning and zooming control. When syncing is enabled all maps respond to mouse actions on one map. This allows side-by-side comparisons of different attributes of the same geometries. Syncing can be adjusted so that any combination of maps can be synchronised.
License: MIT + file LICENSE
URL: https://github.com/r-spatial/leafsync
BugReports: https://github.com/r-spatial/leafsync/issues
Depends: R (>= 3.1.0), methods
Imports: htmltools (>= 0.3), htmlwidgets, leaflet (>= 2.0.1)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2019-02-27 17:09:11 UTC; timpanse
Author: Tim Appelhans [aut, cre], Kenton Russell [aut], Jan Pieter Wagmeester [ctb] (Leaflet.Sync plugin)
Repository: CRAN
Date/Publication: 2019-03-05 15:10:03 UTC

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New package insight with initial version 0.1.2
Package: insight
Type: Package
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.
Version: 0.1.2
Date: 2019-02-27
Authors@R: c(person("Daniel", "Lüdecke", role = c("aut", "cre"), email = "d.luedecke@uke.de", comment = c(ORCID = "0000-0002-8895-3206")), person("Dominique", "Makowski", role = c("aut", "ctb"), email = "dom.makowski@gmail.com", comment = c(ORCID = "0000-0001-5375-9967")))
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
License: GPL-3
URL: https://easystats.github.io/insight/
BugReports: https://github.com/easystats/insight/issues
Depends: R (>= 3.0), stats
Suggests: AER, betareg, brms, coxme, gam, gamm4, gee, GLMMadaptive, glmmTMB, gmnl, lfe, MASS, MCMCglmm, mlogit, lme4, mgcv, nnet, nlme, ordinal, plm, pscl, rstanarm, splines, survey, survival, truncreg, testthat, VGAM
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-27 18:07:47 UTC; Daniel
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>)
Repository: CRAN
Date/Publication: 2019-03-05 15:20:07 UTC

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Package GPSCDF updated to version 0.1.1 with previous version 0.1.0 dated 2019-02-28

Title: Generalized Propensity Score Cumulative Distribution Function
Description: Implements the generalized propensity score cumulative distribution function proposed by Greene (2017) <https://digitalcommons.library.tmc.edu/dissertations/AAI10681743/>. A single scalar balancing score is calculated for any generalized propensity score vector with three or more treatments. This balancing score is used for propensity score matching and stratification in outcome analyses when analyzing either ordinal or multinomial treatments.
Author: Derek W. Brown [aut, cre], Thomas J. Greene [aut], Stacia M. DeSantis [aut]
Maintainer: Derek W. Brown <derek9@gwu.edu>

Diff between GPSCDF versions 0.1.0 dated 2019-02-28 and 0.1.1 dated 2019-03-05

 DESCRIPTION               |   20 ++++++++++----------
 MD5                       |    6 +++---
 R/GPSCDF.R                |    9 +++------
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 4 files changed, 18 insertions(+), 23 deletions(-)

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Package DJL updated to version 2.9.2 with previous version 2.9.1 dated 2019-02-11

Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the Econometrics & Technometrics. Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>

Diff between DJL versions 2.9.1 dated 2019-02-11 and 2.9.2 dated 2019-03-05

 DESCRIPTION      |    8 -
 MD5              |   10 +-
 NEWS             |   11 ++
 R/DJL-internal.R |  250 +++++++++++++++++++++++++++----------------------------
 R/roc.hdf.R      |    2 
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 6 files changed, 146 insertions(+), 137 deletions(-)

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New package Rraven with initial version 1.0.5
Type: Package
Package: Rraven
Title: Connecting R and 'Raven' Sound Analysis Software
Version: 1.0.5
Date: 2019-03-04
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Description: A tool to exchange data between R and 'Raven' sound analysis software <http://www.birds.cornell.edu/brp/raven/RavenOverview.html> (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
License: GPL (>= 2)
Imports: pbapply, warbleR, utils, stats
Depends: R (>= 3.2.1)
LazyData: TRUE
URL: https://github.com/maRce10/Rraven
BugReports: https://github.com/maRce10/Rraven/issues
NeedsCompilation: no
Suggests: knitr, vegan, dplyr, kableExtra
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Packaged: 2019-03-04 17:05:35 UTC; m
Repository: CRAN
Authors@R: person("Marcelo", "Araya-Salas", role = c("aut", "cre"), email = "araya-salas@cornell.edu")
Date/Publication: 2019-03-05 15:00:03 UTC

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Package registry updated to version 0.5-1 with previous version 0.5 dated 2017-12-03

Title: Infrastructure for R Package Registries
Description: Provides a generic infrastructure for creating and using registries.
Author: David Meyer
Maintainer: David Meyer <David.Meyer@R-project.org>

Diff between registry versions 0.5 dated 2017-12-03 and 0.5-1 dated 2019-03-05

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Package proxy updated to version 0.4-23 with previous version 0.4-22 dated 2018-04-08

Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre], Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>

Diff between proxy versions 0.4-22 dated 2018-04-08 and 0.4-23 dated 2019-03-05

 DESCRIPTION           |    6 +++---
 MD5                   |   12 ++++++------
 R/registry.R          |    6 +++---
 build/vignette.rds    |binary
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 7 files changed, 30 insertions(+), 20 deletions(-)

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New package folderfun with initial version 0.1.1
Package: folderfun
Version: 0.1.1
Date: 2019-02-26
Title: Creates and Manages Folder Functions for Portable Large-Scale R Analysis
Description: If you find yourself working on multiple different projects in R, you'll want a series of folders pointing to raw data, processed data, plot results, intermediate table outputs, etc. This package makes it easier to do that by providing a quick and easy way to create and use functions for project-level directories.
Authors@R: c( person(given=c("Nathan", "C."), "Sheffield", email = "nathan@code.databio.org", role=c("aut", "cre")), person("Michal", "Stolarczyk", email="mjs5kd@virginia.edu", role="ctb"), person("Vince", "Reuter", email="vince.reuter@gmail.com", role="ctb"))
Depends: R (> 3.0)
Suggests: knitr, testthat
VignetteBuilder: knitr
License: BSD_2_clause + file LICENSE
Encoding: UTF-8
RoxygenNote: 6.1.1
URL: http://code.databio.org/folderfun
BugReports: http://github.com/databio/folderfun
NeedsCompilation: no
Packaged: 2019-02-28 16:56:22 UTC; nsheff
Author: Nathan C. Sheffield [aut, cre], Michal Stolarczyk [ctb], Vince Reuter [ctb]
Maintainer: Nathan C. Sheffield <nathan@code.databio.org>
Repository: CRAN
Date/Publication: 2019-03-05 14:30:07 UTC

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Package CopulaCenR updated to version 1.0.0 with previous version 0.1.0 dated 2019-03-04

Title: Copula-Based Regression Models for Bivariate Censored Data
Description: Copula-based regression models for bivariate censored data, including bivariate right-censored data and bivariate interval-censored data. Currently supports Clayton, Gumbel, Frank, Joe, AMH and Copula2 copula models. For marginal models, it supports parametric (Weibull, Loglogistic, Gompertz), weakly-parametric piecewise-constant hazards (only for bivariate right-censored) and semiparametric transformation (only for bivariate interval-censored data) models. Includes methods for convenient prediction and plotting. Also provides a bivariate time-to-event simulation function. Method details can be found in Sun et.al. (2018) < doi:10.1007/s10985-018-09459-5> and Sun et.al (2019) <arXiv:1901.01918>.
Author: Tao Sun, Ying Ding
Maintainer: Tao Sun <tao.sun@pitt.edu>

Diff between CopulaCenR versions 0.1.0 dated 2019-03-04 and 1.0.0 dated 2019-03-05

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Package SMITIDvisu updated to version 0.0.4 with previous version 0.0.3 dated 2019-02-18

Title: Visualize Data for Host and Viral Population from 'SMITIDstruct' using HTMLwidgets
Description: Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using HTMLwidgets. It mainly using D3JS javascript framework.
Author: Jean-Francois Rey [aut, cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>

Diff between SMITIDvisu versions 0.0.3 dated 2019-02-18 and 0.0.4 dated 2019-03-05

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 MD5                              |   22 +++++++++++-----------
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 R/data-format.R                  |   29 ++++++++++++++++++++++++-----
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 man/transmissionTree.Rd          |    2 +-
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Package SMITIDstruct updated to version 0.0.4 with previous version 0.0.3 dated 2019-02-01

Title: Data Structure and Manipulations Tool for Host and Viral Population
Description: Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.
Author: Jean-Francois Rey [aut, cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>

Diff between SMITIDstruct versions 0.0.3 dated 2019-02-01 and 0.0.4 dated 2019-03-05

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 MD5                         |   29 +++++++++++-----
 NAMESPACE                   |    8 ++++
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More information about SMITIDstruct at CRAN
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Package RAppArmor updated to version 3.1 with previous version 3.0 dated 2019-02-26

Title: Bindings to AppArmor and Security Related Linux Tools
Description: Bindings to kernel methods for enforcing security restrictions. AppArmor can apply mandatory access control (MAC) policies on a given task (process) via security profiles with detailed ACL definitions. In addition this package implements bindings for setting process resource limits (rlimit), uid, gid, affinity and priority. The high level R function 'eval.secure' builds on these methods to perform dynamic sandboxing: it evaluates a single R expression within a temporary fork which acts as a sandbox by enforcing fine grained restrictions without affecting the main R process. A portable version of this function is now available in the 'unix' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between RAppArmor versions 3.0 dated 2019-02-26 and 3.1 dated 2019-03-05

 DESCRIPTION |   12 +++++++-----
 MD5         |    6 +++---
 NEWS        |    5 +++++
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 4 files changed, 17 insertions(+), 10 deletions(-)

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Permanent link

Package radiant.model updated to version 0.9.9 with previous version 0.9.7 dated 2018-10-06

Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic regression, naive Bayes, neural networks, classification and regression trees, model evaluation, collaborative filtering, decision analysis, and simulation. The application extends the functionality in radiant.data.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.model versions 0.9.7 dated 2018-10-06 and 0.9.9 dated 2019-03-05

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 radiant.model-0.9.9/radiant.model/R/deprecated.R                          |    5 
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 radiant.model-0.9.9/radiant.model/R/evalreg.R                             |   47 +
 radiant.model-0.9.9/radiant.model/R/logistic.R                            |   97 ++-
 radiant.model-0.9.9/radiant.model/R/nb.R                                  |   24 
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Package ClinReport updated to version 0.9.1.10 with previous version 0.9.1.8 dated 2019-02-27

Title: Statistical Reporting in Clinical Trials
Description: It enables to create easily formatted statistical tables in 'Microsoft Word' documents in pretty formats according to 'clinical standards'. It can be used also outside the scope of clinical trials, for any statistical reporting in 'Word'. Descriptive tables for quantitative statistics (mean, median, max etc..) and/or qualitative statistics (frequencies and percentages) are available and formatted tables of Least Square Means of Linear Models, Linear Mixed Models and Generalized Linear Mixed Models coming from emmeans() function are also available. The package works with 'officer' and 'flextable' packages to export the outputs into 'Microsoft Word' documents.
Author: Jean-Francois Collin
Maintainer: Jean-Francois Collin <jfcollin@live.fr>

Diff between ClinReport versions 0.9.1.8 dated 2019-02-27 and 0.9.1.10 dated 2019-03-05

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Package prcbench updated to version 0.8 with previous version 0.7.3 dated 2017-04-20

Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating precision-recall curves under various conditions.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between prcbench versions 0.7.3 dated 2017-04-20 and 0.8 dated 2019-03-05

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Package multcomp updated to version 1.4-10 with previous version 1.4-8 dated 2017-11-08

Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>), Frank Bretz [aut], Peter Westfall [aut], Richard M. Heiberger [ctb], Andre Schuetzenmeister [ctb], Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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New package credentials with initial version 1.0
Package: credentials
Type: Package
Title: Tools for Managing SSH and Git Credentials
Version: 1.0
Authors@R: person("Jeroen", "Ooms", role = c("aut", "cre"), email = "jeroen@berkeley.edu", comment = c(ORCID = "0000-0002-4035-0289"))
Description: Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.
License: MIT + file LICENSE
SystemRequirements: git (optional)
Encoding: UTF-8
Imports: openssl (>= 1.2), sys (>= 2.1), curl, jsonlite, askpass
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2019-02-20 10:50:31 UTC; jeroen
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Repository: CRAN
Date/Publication: 2019-03-05 13:00:07 UTC

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Package bayesdfa updated to version 0.1.2 with previous version 0.1.1 dated 2018-11-09

Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic factor analysis is a dimension reduction tool for multivariate time series. 'bayesdfa' extends conventional dynamic factor models in several ways. First, extreme events may be estimated in the latent trend by modeling process error with a student-t distribution. Second, autoregressive and moving average components can be optionally included. Third, the estimated dynamic factors can be analyzed with hidden Markov models to evaluate support for latent regimes.
Author: Eric J. Ward [aut, cre], Sean C. Anderson [aut], Luis A. Damiano [aut], Mary E. Hunsicker, [ctb], Mike A. Litzow [ctb], Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>

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Package AeRobiology updated to version 1.0.3 with previous version 1.0.2 dated 2019-02-20

Title: A Computational Tool for Aerobiological Data
Description: Different tools for managing aeriobiological databases, elaborating the main calculations and visualization of results. In a first step, data are checked using tools for quality control and all missing gaps are completed. Then, the main parameters of the pollen season are calculated and represented graphically. Multiple graphical tools are available: pollen calendars, phenological plots, time series, tendencies, interactive plots, abundance plots...
Author: Jesús Rojo <Jesus.Rojo@uclm.es>, Antonio Picornell <picornell@uma.es>, Jose Oteros <OterosJose@gmail.com>
Maintainer: "Jose Oteros" <OterosJose@gmail.com>

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New package TooManyCellsR with initial version 0.1.0.0
Package: TooManyCellsR
Title: An R Wrapper for 'TooManyCells'
Version: 0.1.0.0
Author: Gregory W. Schwartz
Maintainer: Gregory W. Schwartz <gsch@pennmedicine.upenn.edu>
Description: An R wrapper for using 'TooManyCells', a command line program for clustering, visualizing, and quantifying cell clade relationships. See <https://gregoryschwartz.github.io/too-many-cells/> for more details.
Imports: Matrix, imager, ggplot2, cowplot, jsonlite
SystemRequirements: 'TooManyCells' (https://github.com/GregorySchwartz/too-many-cells)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-25 15:35:00 UTC; gw
Repository: CRAN
Date/Publication: 2019-03-05 11:20:03 UTC

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Package rindex (with last version 0.12.1) was removed from CRAN

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

2018-08-31 0.12.1
2012-08-24 0.12
2012-08-17 0.11
2009-10-11 0.10
2009-04-15 0.09
2008-08-01 0.08
2007-10-22 0.06
2007-10-21 0.04-1
2007-08-25 0.04

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Package cplm updated to version 0.7-8 with previous version 0.7-7 dated 2018-06-10

Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models based on Zhang, Yanwei (2013) <https://link.springer.com/article/10.1007/s11222-012-9343-7>.
Author: Yanwei (Wayne) Zhang
Maintainer: Yanwei (Wayne) Zhang <actuary_zhang@hotmail.com>

Diff between cplm versions 0.7-7 dated 2018-06-10 and 0.7-8 dated 2019-03-05

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Package EdSurvey (with last version 2.2.1) was removed from CRAN

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

2018-11-19 2.2.1
2018-11-19 2.2.2
2018-05-16 2.0.3
2017-05-04 1.0.6
2017-04-26 1.0.5

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Package ccgarch (with last version 0.2.3) was removed from CRAN

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

2014-03-24 0.2.3
2014-02-20 0.2.2
2013-08-18 0.2.1
2013-01-14 0.2.0-2
2010-03-23 0.2.0
2009-10-18 0.1.9
2009-10-12 0.1.7
2009-08-10 0.1.6
2009-05-29 0.1.4-2
2009-05-11 0.1.4-1
2009-05-04 0.1.3
2009-04-16 0.1.2-2
2008-10-30 0.1.1
2008-09-10 0.1.0

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Package icesVocab (with last version 1.1-3) was removed from CRAN

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

2019-01-15 1.1-3
2016-12-06 1.1-0
2016-12-06 1.1-2

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Package WeMix (with last version 2.1.0) was removed from CRAN

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

2018-09-24 2.1.0
2018-08-14 2.0.0
2018-04-10 1.0.2

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Package icesSAG (with last version 1.3-4) was removed from CRAN

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

2018-05-01 1.3-4
2017-05-07 1.3-2

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Package RTextTools (with last version 1.4.2) was removed from CRAN

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

2014-01-19 1.4.2

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Package maxent (with last version 1.3.3.1) was removed from CRAN

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

2013-11-14 1.3.3.1
2013-04-07 1.3.3

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