Tue, 19 Feb 2019

Package robCompositions updated to version 2.0.10 with previous version 2.0.9 dated 2018-11-08

Title: Robust Estimation for Compositional Data
Description: Methods for analysis of compositional data including robust methods, imputation, methods to replace rounded zeros, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.
Author: Matthias Templ [aut, cre], Karel Hron [aut], Peter Filzmoser [aut], Petra Kynclova [ctb], Jan Walach [ctb], Veronika Pintar [ctb], Jiajia Chen [ctb], Dominika Miksova [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between robCompositions versions 2.0.9 dated 2018-11-08 and 2.0.10 dated 2019-02-19

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Package ssizeRNA updated to version 1.3.1 with previous version 1.2.9 dated 2017-01-09

Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Maintainer: Ran Bi <biranpier@gmail.com>

Diff between ssizeRNA versions 1.2.9 dated 2017-01-09 and 1.3.1 dated 2019-02-19

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Package sampleSelection updated to version 1.2-2 with previous version 1.2-0 dated 2017-12-07

Title: Sample Selection Models
Description: Two-step and maximum likelihood estimation of Heckman-type sample selection models: standard sample selection models (Tobit-2), endogenous switching regression models (Tobit-5), sample selection models with binary dependent outcome variable, interval regression with sample selection (only ML estimation), and endogenous treatment effects models.
Author: Arne Henningsen [aut, cre], Ott Toomet [aut], Sebastian Petersen [ctb]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between sampleSelection versions 1.2-0 dated 2017-12-07 and 1.2-2 dated 2019-02-19

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Package geonames updated to version 0.999 with previous version 0.998 dated 2014-12-19

Title: Interface to the "Geonames" Spatial Query Web Service
Description: The web service at <https://www.geonames.org/> provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.
Author: Barry Rowlingson
Maintainer: Barry Rowlingson <b.rowlingson@gmail.com>

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Package ssh updated to version 0.4 with previous version 0.3 dated 2018-10-07

Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between ssh versions 0.3 dated 2018-10-07 and 0.4 dated 2019-02-19

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Package bupaR updated to version 0.4.2 with previous version 0.4.1 dated 2018-07-01

Title: Business Process Analysis in R
Description: Comprehensive Business Process Analysis toolkit. Creates S3-class for event log objects, and related handler functions. Imports related packages for filtering event data, computation of descriptive statistics, handling of 'Petri Net' objects and visualization of process maps. See also packages 'edeaR','processmapR', 'eventdataR' and 'processmonitR'.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>

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Package rockchalk updated to version 1.8.140 with previous version 1.8.129 dated 2018-11-09

Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation of regression analysis. These functions are used to produce the statistics lectures in <http://pj.freefaculty.org/guides>. Includes regression diagnostics, regression tables, and plots of interactions and "moderator" variables. The emphasis is on "mean-centered" and "residual-centered" predictors. The vignette 'rockchalk' offers a fairly comprehensive overview. The vignette 'Rstyle' has advice about coding in R. The package title 'rockchalk' refers to our school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre], Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>

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Package perturbR updated to version 0.1.3 with previous version 0.1.2 dated 2018-07-27

Title: Random Perturbation of Count Matrices
Description: The perturbR() function incrementally perturbs network edges (using the rewireR function)and compares the resulting community detection solutions from the rewired networks with the solution found for the original network. These comparisons aid in understanding the stability of the original solution. The package requires symmetric, weighted (specifically, count) matrices/networks.
Author: KM Gates [aut, cre], Zachary Fisher [aut], Cara Arizmendi [aut]
Maintainer: KM Gates <gateskm@email.unc.edu>

Diff between perturbR versions 0.1.2 dated 2018-07-27 and 0.1.3 dated 2019-02-19

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Package idealstan updated to version 0.7.0 with previous version 0.5.1 dated 2018-12-06

Title: Generalized IRT Ideal Point Models with 'Stan'
Description: Offers item-response theory (IRT) ideal-point estimation for binary, ordinal, counts and continuous responses with time-varying and missing-data inference. Full and approximate Bayesian sampling with 'Stan' (www.mc-stan.org).
Author: Robert Kubinec [aut, cre], Jonah Gabry [ctb], Ben Goodrich [ctb], Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7@nyu.edu>

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Package relMix updated to version 1.3 with previous version 1.2.3 dated 2017-04-03

Title: Relationship Inference for DNA Mixtures
Description: Makes relationship inference involving DNA mixtures with unknown profiles.
Author: Guro Dorum, Elias Hernandis, Navreet Kaur, Thore Egeland
Maintainer: Guro Dorum <guro.dorum@gmail.com>

Diff between relMix versions 1.2.3 dated 2017-04-03 and 1.3 dated 2019-02-19

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Package haven updated to version 2.1.0 with previous version 2.0.0 dated 2018-11-21

Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between haven versions 2.0.0 dated 2018-11-21 and 2.1.0 dated 2019-02-19

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More information about haven at CRAN
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Package divDyn updated to version 0.7.1 with previous version 0.7.0 dated 2019-01-08

Title: Diversity Dynamics using Fossil Sampling Data
Description: Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Author: Adam T. Kocsis, John Alroy, Carl J. Reddin, Wolfgang Kiessling
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>

Diff between divDyn versions 0.7.0 dated 2019-01-08 and 0.7.1 dated 2019-02-19

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Package CB2 updated to version 1.1 with previous version 1.0 dated 2019-02-11

Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2018) <doi:10.1101/309302> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>

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Package ellipsis updated to version 0.1.0 with previous version 0.0.2 dated 2019-01-09

Title: Tools for Working with ...
Description: In S3 generics, it's useful to take ... so that methods can have additional argument. But this flexibility comes at a cost: misspelled arguments will be silently ignored. The ellipsis packages is an experiment that allows a generic to warn if any arguments passed in ... are not used.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between ellipsis versions 0.0.2 dated 2019-01-09 and 0.1.0 dated 2019-02-19

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Package afex updated to version 0.23-0 with previous version 0.22-1 dated 2018-09-24

Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), automatically aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot() provides a high-level interface for interaction or one-way plots using ggplot2, combining raw data and model estimates. afex uses type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>), Ben Bolker [aut], Jake Westfall [aut], Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>), Søren Højsgaard [ctb], John Fox [ctb], Michael A. Lawrence [ctb], Ulf Mertens [ctb], Jonathon Love [ctb], Russell Lenth [ctb], Rune Haubo Bojesen Christensen [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>

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Mon, 18 Feb 2019

Package windfarmGA updated to version 2.2.1 with previous version 1.2.1 dated 2018-03-24

Title: Genetic Algorithm for Wind Farm Layout Optimization
Description: The genetic algorithm is designed to optimize small wind farms with irregular shapes. The algorithm works with a fixed amount of turbines, a fixed rotor radius and a mean wind speed value for every incoming wind direction. If required, it can include a terrain effect model which downloads an 'SRTM' elevation model automatically and loads a Corine Land Cover raster, which has to be downloaded previously. Further information can be found in the description of the function 'windfarmGA'. To start an optimization run, either the function 'windfarmGA' or 'genAlgo' can be used. The function 'windfarmGA' checks the user inputs interactively and then runs the function 'genAlgo'. If the input parameters are already known, an optimization can be run directly via the function 'genAlgo'. Their output is identical.
Author: Sebastian Gatscha
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>

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Package tidygraph updated to version 1.1.2 with previous version 1.1.1 dated 2018-11-20

Title: A Tidy API for Graph Manipulation
Description: A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between tidygraph versions 1.1.1 dated 2018-11-20 and 1.1.2 dated 2019-02-18

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Package shinyWidgets updated to version 0.4.5 with previous version 0.4.4 dated 2018-11-05

Title: Custom Inputs Widgets for Shiny
Description: Some custom inputs widgets to use in Shiny applications, like a toggle switch to replace checkboxes. And other components to pimp your apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], David Granjon [aut] (jQuery Knob shiny interface & sliders appearance), Ian Fellows [ctb] (Methods for mutating vertical tabs & updateMultiInput), Wil Davis [ctb] (numericRangeInput function), SnapAppointments [cph] (bootstrap-select), Mattia Larentis [ctb, cph] (Bootstrap Switch), Emanuele Marchi [ctb, cph] (Bootstrap Switch), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Flatlogic [cph] (Awesome Bootstrap Checkbox), mouse0270 [ctb, cph] (Material Design Switch), Tristan Edwards [ctb, cph] (SweetAlert), Fabian Lindfors [ctb, cph] (multi.js), Anthony Terrien [ctb, cph] (jQuery Knob), Daniel Eden [ctb, cph] (animate.css), Ganapati V S [ctb, cph] (bttn.css), Brian Grinstead [ctb, cph] (Spectrum), Lokesh Rajendran [ctb, cph] (pretty-checkbox), Leon Gersen [ctb, cph] (wnumb & noUiSlider), Timofey Marochkin [ctb, cph] (air-datepicker), Tobias Ahlin [ctb, cph] (CSS spin)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package nonmem2R updated to version 0.2.1 with previous version 0.1.10 dated 2018-09-26

Title: Loading NONMEM Output Files with Functions for Visual Predictive Checks (VPC) and Goodness of Fit (GOF) Plots
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/solutions/nonmem/>) and PSN (Perl-speaks-NONMEM, <https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>

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Package ggsn updated to version 0.5.0 with previous version 0.4.0 dated 2017-03-20

Title: North Symbols and Scale Bars for Maps Created with 'ggplot2' or 'ggmap'
Description: Adds north symbols (18 options) and scale bars in kilometers, meters, nautical miles, or statue miles, to maps in geographic or metric coordinates created with 'ggplot2' or 'ggmap'.
Author: Oswaldo Santos Baquero [aut, cre]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>

Diff between ggsn versions 0.4.0 dated 2017-03-20 and 0.5.0 dated 2019-02-18

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Package modelr updated to version 0.1.4 with previous version 0.1.3 dated 2019-02-05

Title: Modelling Functions that Work with the Pipe
Description: Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between modelr versions 0.1.3 dated 2019-02-05 and 0.1.4 dated 2019-02-18

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Package flexmix updated to version 2.3-15 with previous version 2.3-14 dated 2017-04-28

Title: Flexible Mixture Modeling
Description: A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
Author: Bettina Gruen [aut, cre] (<https://orcid.org/0000-0001-7265-4773>), Friedrich Leisch [aut] (<https://orcid.org/0000-0001-7278-1983>), Deepayan Sarkar [ctb] (<https://orcid.org/0000-0003-4107-1553>), Frederic Mortier [ctb], Nicolas Picard [ctb] (<https://orcid.org/0000-0001-5548-9171>)
Maintainer: Bettina Gruen <Bettina.Gruen@jku.at>

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Package nonneg.cg updated to version 0.1.1 with previous version 0.1 dated 2019-01-27

Title: Non-Negative Conjugate-Gradient Minimizer
Description: Minimize a differentiable function subject to all the variables being non-negative (i.e. >= 0), using a Conjugate-Gradient algorithm based on a modified Polak-Ribiere-Polyak formula as described in (Li, Can, 2013, <https://www.hindawi.com/journals/jam/2013/986317/abs/>).
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package libcoin updated to version 1.0-3 with previous version 1.0-2 dated 2018-12-13

Title: Linear Test Statistics for Permutation Inference
Description: Basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999) <http://epub.wu.ac.at/102/>. This package must not be used by end-users. CRAN package 'coin' implements all user interfaces and is ready to be used by anyone.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between libcoin versions 1.0-2 dated 2018-12-13 and 1.0-3 dated 2019-02-18

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More information about libcoin at CRAN
Permanent link

Package poplite updated to version 0.99.21 with previous version 0.99.19 dated 2017-10-12

Title: Tools for Simplifying the Population and Querying of SQLite Databases
Description: Provides objects and accompanying methods which facilitates populating and querying SQLite databases.
Author: Daniel Bottomly [cre, aut], Shannon McWeeney [aut], Beth Wilmot [aut]
Maintainer: Daniel Bottomly <bottomly@ohsu.edu>

Diff between poplite versions 0.99.19 dated 2017-10-12 and 0.99.21 dated 2019-02-18

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More information about poplite at CRAN
Permanent link

Package rayshader updated to version 0.10.0 with previous version 0.5.1 dated 2018-09-11

Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing, spherical texture mapping, lambertian reflectance, and ambient occlusion to produce hillshades of elevation matrices. Includes water detection and layering functions, programmable color palette generation, several built-in textures, 2D and 3D plotting options, and the ability to export 3D maps to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

Diff between rayshader versions 0.5.1 dated 2018-09-11 and 0.10.0 dated 2019-02-18

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More information about rayshader at CRAN
Permanent link

Package lwgeom updated to version 0.1-6 with previous version 0.1-5 dated 2018-12-07

Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/svn-trunk/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Colin Rundel [ctb], Andy Teucher [ctb], liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between lwgeom versions 0.1-5 dated 2018-12-07 and 0.1-6 dated 2019-02-18

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Package SAM updated to version 1.1.0 with previous version 1.0.5 dated 2014-02-12

Title: Sparse Additive Modelling
Description: Computationally efficient tools for high dimensional predictive modeling (regression and classification). SAM is short for sparse additive modeling, and adopts the computationally efficient basis spline technique. We solve the optimization problems by various computational algorithms including the block coordinate descent algorithm, fast iterative soft-thresholding algorithm, and newton method. The computation is further accelerated by warm-start and active-set tricks.
Author: Haoming Jiang, Yukun Ma, Xinyu Fei, Tuo Zhao, Xingguo Li, Han Liu, and Kathryn Roeder
Maintainer: Haoming Jiang <jianghm.ustc@gmail.com>

Diff between SAM versions 1.0.5 dated 2014-02-12 and 1.1.0 dated 2019-02-18

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More information about SAM at CRAN
Permanent link

Package dkanr updated to version 0.1.3 with previous version 0.1.2 dated 2018-07-12

Title: Client for the 'DKAN' API
Description: Provides functions to facilitate access to the 'DKAN' API (<https://dkan.readthedocs.io/en/latest/apis/index.html>), including the 'DKAN' REST API (metadata), and the 'DKAN' datastore API (data). Includes functions to list, create, retrieve, update, and delete datasets and resources nodes. It also includes functions to search and retrieve data from the 'DKAN' datastore.
Author: Tony Fujs [aut, cre], Meera Desai [aut], Karthik Ramanathan [aut]
Maintainer: Tony Fujs <tonyfujs@gmail.com>

Diff between dkanr versions 0.1.2 dated 2018-07-12 and 0.1.3 dated 2019-02-18

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Package RandomFields updated to version 3.3.1 with previous version 3.3 dated 2019-02-14

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.3 dated 2019-02-14 and 3.3.1 dated 2019-02-18

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More information about RandomFields at CRAN
Permanent link

Package geometry updated to version 0.4.0 with previous version 0.3-6 dated 2015-09-09

Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Author: Jean-Romain Roussel [cph, ctb] (wrote tsearch function with QuadTrees), C. B. Barber [cph], Kai Habel [cph, aut], Raoul Grasman [cph, aut], Robert B. Gramacy [cph, aut], Pavlo Mozharovskyi [cph, aut], David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>

Diff between geometry versions 0.3-6 dated 2015-09-09 and 0.4.0 dated 2019-02-18

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Package zCompositions updated to version 1.2.0 with previous version 1.1.2 dated 2018-11-06

Title: Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets.
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>

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Package catlearn updated to version 0.6.1 with previous version 0.6 dated 2018-07-17

Title: Formal Psychological Models of Categorization and Learning
Description: Formal psychological models of categorization and learning, independently-replicated data sets against which to test them, and simulation archives.
Author: Andy Wills, Lenard Dome, Charlotte Edmunds, Garrett Honke, Angus Inkster, René Schlegelmilch, Stuart Spicer
Maintainer: Andy Wills <andy@willslab.co.uk>

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Package VGAM updated to version 1.1-1 with previous version 1.0-6 dated 2018-08-18

Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

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Package maptools updated to version 0.9-5 with previous version 0.9-4 dated 2018-09-19

Title: Tools for Handling Spatial Objects
Description: Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', 'RArcInfo', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Nicholas Lewin-Koh [aut], Edzer Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb], Nick Bearman [ctb], Hans-Jörg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan [ctb], German Carrillo [ctb], Stéphane Dray [ctb], David Forrest [ctb], Michael Friendly [ctb], Patrick Giraudoux [ctb], Duncan Golicher [ctb], Virgilio Gómez Rubio [ctb], Patrick Hausmann [ctb], Karl Ove Hufthammer [ctb], Thomas Jagger [ctb], Kent Johnson [ctb], Sebastian Luque [ctb], Don MacQueen [ctb], Andrew Niccolai [ctb], Edzer Pebesma [ctb], Oscar Perpiñán Lamigueiro [ctb], Ethan Plunkett [ctb], Tom Short [ctb], Greg Snow [ctb], Ben Stabler [ctb], Murray Stokely [ctb], Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between maptools versions 0.9-4 dated 2018-09-19 and 0.9-5 dated 2019-02-18

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Package tsibble updated to version 0.7.0 with previous version 0.6.2 dated 2018-12-12

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage temporal data in a data-centric format, which is built on top of the 'tibble'. The 'tsibble' aims at easily manipulating and analysing temporal data, including counting and filling in time gaps, aggregate over calendar periods, performing rolling window calculations, and etc.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>

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Package Spectrum updated to version 0.3 with previous version 0.2 dated 2019-02-11

Title: Versatile Ultra-Fast Spectral Clustering for Single and Multi-View Data
Description: A versatile ultra-fast spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens local connections in dense regions in the graph. For integrating multi-view data and reducing noise we use a recently developed tensor product graph data integration and diffusion system. 'Spectrum' contains two techniques for finding the number of clusters (K); the classical eigengap method and a novel multimodality gap procedure. The multimodality gap analyses the distribution of the eigenvectors of the graph Laplacian to decide K and tune the kernel. 'Spectrum' is suited for clustering a wide range of complex data.
Author: Christopher R John, David Watson
Maintainer: Christopher R John <chris.r.john86@gmail.com>

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Package SDLfilter updated to version 1.2.0 with previous version 1.1.1 dated 2018-06-20

Title: Filtering Satellite-Derived Locations
Description: Functions to filter GPS and/or Argos locations. The provided filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as proposed in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>.
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <takahiro.shimada@my.jcu.edu.au>

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Package ggstatsplot updated to version 0.0.9 with previous version 0.0.8 dated 2019-01-07

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It is targeted primarily at behavioral sciences community to provide a one-line code to generate information-rich plots for statistical analysis. of continuous (violin plots, scatterplots, histograms) or categorical (pie and bar charts) data. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Chuck Powell [aut, ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package cchs updated to version 0.4.1 with previous version 0.4.0 dated 2017-08-26

Title: Cox Model for Case-Cohort Data with Stratified Subcohort-Selection
Description: Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones
Maintainer: E. Jones <edmundjones79@gmail.com>

Diff between cchs versions 0.4.0 dated 2017-08-26 and 0.4.1 dated 2019-02-18

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Package openVA updated to version 1.0.8 with previous version 1.0.7 dated 2018-09-13

Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@gmail.com>

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Package JuliaCall updated to version 0.16.4 with previous version 0.16.2 dated 2019-01-02

Title: Seamless Integration Between R and 'Julia'
Description: Provides an R interface to 'Julia', which is a high-level, high-performance dynamic programming language for numerical computing, see <https://julialang.org/> for more information. It provides a high-level interface as well as a low-level interface. Using the high level interface, you could call any 'Julia' function just like any R function with automatic type conversion. Using the low level interface, you could deal with C-level SEXP directly while enjoying the convenience of using a high-level programming language like 'Julia'.
Author: Changcheng Li [aut, cre], Randy Lai [ctb], Dmitri Grominski [ctb], Nagi Teramo [ctb]
Maintainer: Changcheng Li <cxl508@psu.edu>

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Sun, 17 Feb 2019

Package LPCM updated to version 0.46-1 with previous version 0.45-0 dated 2015-09-22

Title: Local Principal Curve Methods
Description: Fitting multivariate data patterns with local principal curves, including tools for data compression (projection) and measuring goodness-of-fit; with some additional functions for mean shift clustering.
Author: Jochen Einbeck and Ludger Evers
Maintainer: Jochen Einbeck <jochen.einbeck@durham.ac.uk>

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Package funtimes updated to version 6.0 with previous version 5.0 dated 2018-02-04

Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich [aut, cre], Yulia R. Gel [aut], Calvin Chu [ctb], Xin Huang [ctb], Ethan D. Schaeffer [ctb], Srishti Vishwakarma [ctb], Xingyu Wang [ctb]
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>

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Package survELtest updated to version 1.0.1 with previous version 1.0.0 dated 2018-11-16

Title: Comparing Multiple Survival Functions with Crossing Hazards in R
Description: Contains routines for computing the one-sided/two-sided integrated/maximally selected EL statistics for simultaneous testing, the one-sided/two-sided EL tests for pointwise testing, and an initial test that precedes one-sided testing to exclude the possibility of crossings or alternative orderings.
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>

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Package rqdatatable updated to version 1.1.3 with previous version 1.1.2 dated 2018-12-17

Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package tableone updated to version 0.10.0 with previous version 0.9.3 dated 2018-04-29

Title: Create 'Table 1' to Describe Baseline Characteristics
Description: Creates 'Table 1', i.e., description of baseline patient characteristics, which is essential in every medical research. Supports both continuous and categorical variables, as well as p-values and standardized mean differences. Weighted data are supported via the 'survey' package. See 'github' for a screen cast. 'tableone' was inspired by descriptive statistics functions in 'Deducer' , a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida [cre, aut] (<https://orcid.org/0000-0002-2030-3549>), Jonathan J Chipman [ctb], Justin Bohn [ctb], Lucy DAgostino McGowan [ctb], Malcolm Barrett [ctb], Rune Haubo B Christensen [ctb], gbouzill [ctb]
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>

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Package ThreeArmedTrials updated to version 1.0-3 with previous version 1.0-0 dated 2016-05-17

Title: Design and Analysis of Clinical Non-Inferiority or Superiority Trials with Active and Placebo Control
Description: Design and analyze three-arm non-inferiority or superiority trials which follow a gold-standard design, i.e. trials with an experimental treatment, an active, and a placebo control. Method for the following distributions are implemented: Poisson (Mielke and Munk (2009) <arXiv:0912.4169>), negative binomial (Muetze et al. (2016) <doi:10.1002/sim.6738>), normal (Pigeot et al. (2003) <doi:10.1002/sim.1450>; Hasler et al. (2009) <doi:10.1002/sim.3052>), binary (Friede and Kieser (2007) <doi:10.1002/sim.2543>), nonparametric (Muetze et al. (2017) <doi:10.1002/sim.7176>), exponential (Mielke and Munk (2009) <arXiv:0912.4169>).
Author: Tobias Mütze [aut, cre] (<https://orcid.org/0000-0002-4111-1941>), Tim Friede [ctb]
Maintainer: Tobias Mütze <tobias.muetze@outlook.com>

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Package MSPRT updated to version 2.0 with previous version 1.0 dated 2018-09-17

Title: Modified Sequential Probability Ratio Test (MSPRT)
Description: A modified SPRT (MSPRT) can be designed and implemented with the help of this package. In a MSPRT design, (i) the maximum sample size of an experiment is fixed prior to the start of an experiment; (ii) the alternative hypothesis used to define the rejection region of the test is derived from the size of the test (Type I error), the maximum available sample size (N), and (iii) the targeted Type 2 error (equals to 1 minus the power) is also prespecified. Given these values, the MSPRT is defined in a manner very similar to Wald's initial proposal. This test can reduce the average sample size required to perform statistical hypothesis tests at the specified level of significance and power. This package implements one-sample proportion tests, one-sample Z-tests, one-sample T-tests, two-sample Z-tests and two-sample T-tests. A user guidance for this package is provided here. One can also refer to the supplemental information for the same.
Author: Sandipan Pramanik [aut, cre], Valen E. Johnson [aut], Anirban Bhattacharya [aut]
Maintainer: Sandipan Pramanik <sandy@stat.tamu.edu>

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Package BAwiR updated to version 1.2 with previous version 1.1.3 dated 2018-09-24

Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly web scraping and visualization. Data were obtained from <http://www.euroleague.net/>, <http://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions of their respectives robots.txt files, when available. Tools for visualization include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games and maps of nationalities.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

Diff between BAwiR versions 1.1.3 dated 2018-09-24 and 1.2 dated 2019-02-17

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Package sloop updated to version 1.0.1 with previous version 1.0.0 dated 2018-10-30

Title: Helpers for 'OOP' in R
Description: A collection of helper functions designed to help you to better understand object oriented programming in R, particularly using 'S3'.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package congressbr updated to version 0.2.0 with previous version 0.1.8 dated 2019-01-29

Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/> respectively.
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>

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Package quadprogXT updated to version 0.0.4 with previous version 0.0.3 dated 2018-05-22

Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre]
Maintainer: Bob Harlow <rharlow86@gmail.com>

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Package forcats updated to version 0.4.0 with previous version 0.3.0 dated 2018-02-19

Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package pivottabler updated to version 1.1.0 with previous version 1.0.0 dated 2018-10-17

Title: Create Pivot Tables in R
Description: Create regular pivot tables with just a few lines of R. More complex pivot tables can also be created, e.g. pivot tables with irregular layouts, multiple calculations and/or derived calculations based on multiple data frames. Pivot tables are constructed using R only and can be written to a range of output formats (plain text, 'HTML', 'Latex' and 'Excel'), including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>

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Package foghorn updated to version 1.1.0 with previous version 1.0.2 dated 2018-04-14

Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results in your R terminal.
Author: Francois Michonneau [aut, cre], Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

Diff between foghorn versions 1.0.2 dated 2018-04-14 and 1.1.0 dated 2019-02-17

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Package nasapower updated to version 1.0.7 with previous version 1.0.5 dated 2019-02-02

Title: NASA POWER API Client
Description: Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 1/2 by 1/2 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>), Hazel Kavili [rev], Alison Boyer [rev]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>

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Package AGread updated to version 0.2.0 with previous version 0.1.2 dated 2018-04-19

Title: Read Data Files from ActiGraph Monitors
Description: Standardize the process of bringing various modes of output files into R. For more information, see: <https://actigraph.desk.com/customer/en/portal/articles/2515800-what-do-the-different-mode-numbers-mean-in-a-csv-or-dat-file->. Additionally, processes are provided to read and minimally pre- process raw data from primary accelerometer and inertial measurement unit files, as well as binary .gt3x files. ActiGraph monitors are used to estimate physical activity outcomes via body-worn sensors that measure (e.g.) acceleration or rotational velocity.
Author: Paul R. Hibbing [aut, cre], Vincent T. van Hees [ctb], Samuel R. LaMunion [ctb]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>

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Sat, 16 Feb 2019

Package netgwas updated to version 1.8.1 with previous version 1.7.0 dated 2018-08-13

Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. We use conditional independence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <arXiv:1710.01063>. NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>

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Package optionstrat updated to version 1.1.0 with previous version 1.0.0 dated 2018-12-09

Title: Utilizes the Black-Scholes Option Pricing Model to Perform Strategic Option Analysis and Plot Option Strategies
Description: Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.
Author: John T. Buynak [aut, cre]
Maintainer: John T. Buynak <jbuynak94@gmail.com>

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Package matsbyname updated to version 0.4.10 with previous version 0.4.9 dated 2019-01-25

Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>

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Package ezpickr updated to version 1.0.1 with previous version 1.0.0 dated 2019-02-02

Title: Import Various Data File Types as a Rectangular Form Using a File Picker Dialogue Box
Description: Easy data importing for the most frequently used file formats in a 'tibble' form.
Author: JooYoung Seo [aut, cre], Soyoung Choi [aut], hyun seung Lee [ctb], Jonghoen Kim [ctb]
Maintainer: JooYoung Seo <jooyoung@psu.edu>

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Package SignifReg updated to version 1.1 with previous version 1.0 dated 2017-02-01

Title: Consistent Significance Controlled Variable Selection in Linear Regression
Description: Provide consistent significance controlled variable selection procedure with different directions (forward, backward, stepwise) based on diverse criteria (Mallows' Cp, AIC, BIC, adjusted r-square, p-value). The algorithm selects a final model with only significant variables based on a correction choice of False Discovery Rate, Bonferroni, or no correction.
Author: Jongwook Kim, Adriano Zanin Zambom
Maintainer: Jongwook Kim <jongwook226@gmail.com>

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Package ROI.plugin.neos updated to version 0.3-1 with previous version 0.3-0 dated 2018-06-19

Title: 'NEOS' Plug-in for the 'R' Optimization Interface
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package with a connection to the 'neos' server. 'ROI' optimization problems can be directly be sent to the 'neos' server and solution obtained in the typical 'ROI' style.
Author: Ronald Hochreiter [aut], Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>

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Package hoa updated to version 2.1.4.1 with previous version 2.1.4 dated 2015-08-11

Title: Higher Order Likelihood Inference
Description: Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).
Author: R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Alex-Antoine Fortin <alex@fortin.bio>

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Package ipcwswitch updated to version 1.0.2 with previous version 1.0.1 dated 2018-11-16

Title: Inverse Probability of Censoring Weights to Deal with Treatment Switch in Randomized Clinical Trials
Description: Contains functions for formatting clinical trials data and implementing inverse probability of censoring weights to handle treatment switches when estimating causal treatment effect in randomized clinical trials.
Author: Nathalie Graffeo [aut, cre], Aurelien Latouche [aut], Sylvie Chevret [aut]
Maintainer: Nathalie Graffeo <nathalie.graffeo@univ-amu.fr>

Diff between ipcwswitch versions 1.0.1 dated 2018-11-16 and 1.0.2 dated 2019-02-16

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Package rPref updated to version 1.3 with previous version 1.2 dated 2016-12-18

Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict partial order. This especially includes the computation of the Pareto frontier, also known as (Top-k) Skyline operator (see Börzsönyi, et al. (2001) <doi:10.1109/ICDE.2001.914855>), and some generalizations known as database preferences (see Kießling (2002) <doi:10.1016/B978-155860869-6/50035-4>).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>

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Package WRSS updated to version 2.2 with previous version 2.1 dated 2019-01-21

Title: Water Resources System Simulator
Description: Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems. 'WRSS' proposes functions and methods for construction, simulation and analysis of primary storage and hydropower water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
Author: Rezgar Arabzadeh; Parisa Aberi; Kaveh Panaghi; Shahab Araghinejad; Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>

Diff between WRSS versions 2.1 dated 2019-01-21 and 2.2 dated 2019-02-16

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Package areaplot updated to version 1.2-1 with previous version 1.2-0 dated 2017-10-18

Title: Plot Stacked Areas and Confidence Bands as Filled Polygons
Description: Plot stacked areas and confidence bands as filled polygons, or add polygons to existing plots. A variety of input formats are supported, including vectors, matrices, data frames, formulas, etc.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>

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Fri, 15 Feb 2019

Package ggmcmc updated to version 1.2 with previous version 1.1.1 dated 2019-01-23

Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of Markov Chain Monte Carlo simulations, as well as for graphically display results from full MCMC analysis. The package also facilitates the graphical interpretation of models by providing flexible functions to plot the results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>

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Package FNN updated to version 1.1.3 with previous version 1.1.2.2 dated 2018-12-10

Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford (cover tree library), Sunil Arya and David Mount (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>

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Package chillR updated to version 0.70.14 with previous version 0.70.12 dated 2018-12-18

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>

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Package psychmeta updated to version 2.3.1 with previous version 2.3.0 dated 2019-01-09

Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre], Brenton M. Wiernik [aut], Michael T. Brannick [ctb] (Testing), Jack Kostal [ctb] (Code for reshape_mat2dat function), Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots), John Sakaluk [ctb] (Code for funnel and forest plots), Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>

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Package neo4r updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-27

Title: A 'Neo4J' Driver
Description: A Modern and Flexible 'Neo4J' Driver, allowing you to query data on a 'Neo4J' server and handle the results in R. It's modern in the sense it provides a driver that can be easily integrated in a data analysis workflow, especially by providing an API working smoothly with other data analysis and graph packages. It's flexible in the way it returns the results, by trying to stay as close as possible to the way 'Neo4J' returns data. That way, you have the control over the way you will compute the results. At the same time, the result is not too complex, so that the "heavy lifting" of data wrangling is not left to the user.
Author: Colin Fay [cre, aut] (<https://orcid.org/0000-0001-7343-1846>), ThinkR [cph], Neo4J [spn]
Maintainer: Colin Fay <contact@colinfay.me>

Diff between neo4r versions 0.1.0 dated 2019-01-27 and 0.1.1 dated 2019-02-15

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Package gganimate updated to version 1.0.1 with previous version 1.0.0 dated 2019-01-02

Title: A Grammar of Animated Graphics
Description: The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.
Author: Thomas Lin Pedersen [aut, cre], David Robinson [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package finalfit updated to version 0.9.0 with previous version 0.8.9 dated 2018-12-18

Title: Quickly Create Elegant Regression Results Tables and Plots when Modelling
Description: Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre], Tom Drake [aut], Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>

Diff between finalfit versions 0.8.9 dated 2018-12-18 and 0.9.0 dated 2019-02-15

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 R/ff_interaction.R                                                                 |    2 
 R/ff_label.R                                                                       |    1 
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 R/or_plot.R                                                                        |    7 
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 R/surv_plot.R                                                                      |    2 
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Package ruler updated to version 0.2.0 with previous version 0.1.4 dated 2018-12-05

Title: Tidy Data Validation Reports
Description: Tools for creating data validation pipelines and tidy reports. This package offers a framework for exploring and validating data frame like objects using 'dplyr' grammar of data manipulation.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package rotl updated to version 3.0.7 with previous version 3.0.6 dated 2019-01-20

Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Author: Francois Michonneau [aut, cre] (<https://orcid.org/0000-0002-9092-966X>), Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>), David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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Package ahpsurvey updated to version 0.4.0 with previous version 0.3.0 dated 2018-12-17

Title: Analytic Hierarchy Process for Survey Data
Description: The Analytic Hierarchy Process is a versatile multi-criteria decision-making tool introduced by Saaty (1987) <doi:10.1016/0270-0255(87)90473-8> that allows decision-makers to weigh attributes and evaluate alternatives presented to them. This package provides a consistent methodology for researchers to reformat data and run analytic hierarchy process in R on data that are formatted using the survey data entry mode. It is optimized for performing the analytic hierarchy process with many decision-makers, and provides tools and options for researchers to aggregate individual preferences and test multiple options. It also allows researchers to quantify, visualize and correct for inconsistency in the decision-maker's comparisons.
Author: Frankie Cho [aut, cre]
Maintainer: Frankie Cho <htcho@connect.hku.hk>

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Package BDgraph updated to version 2.55 with previous version 2.54 dated 2019-01-21

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Letac et al. (2018) <arXiv:1706.04416>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>, Ernst Wit [aut], Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

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Package MATA updated to version 0.4 with previous version 0.3 dated 2015-04-18

Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals, which are constructed using single-model estimators and model weights. See Turek and Fletcher (2012) <doi:10.1016/j.csda.2012.03.002> for details.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>

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Package MachineShop updated to version 1.2.0 with previous version 1.1.0 dated 2019-01-23

Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package walker updated to version 0.2.4 with previous version 0.2.3-1 dated 2018-11-09

Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression coefficients can vary over time as random walks. Gaussian, Poisson, and binomial observations are supported. The Markov chain Monte Carlo computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling. For non-Gaussian models, walker uses the importance sampling type estimators based on approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package visdat updated to version 0.5.3 with previous version 0.5.2 dated 2018-12-10

Title: Preliminary Visualisation of Data
Description: Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>), Sean Hughes [rev] (<https://orcid.org/0000-0002-9409-9405>, Sean Hughes reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Mara Averick [rev] (Mara Averick reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Stuart Lee [ctb], Earo Wang [ctb], Nic Crane [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>

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Package scopr updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-29

Title: Read Ethoscope Data
Description: Handling of behavioural data from the Ethoscope platform (Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>). Ethoscopes (<http://gilestrolab.github.io/ethoscope/>) are an open source/open hardware framework made of interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables such as xy coordinates, dimensions and speed. This package is part of the rethomics framework <http://rethomics.github.io/>.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>

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Package rwty updated to version 1.0.2 with previous version 1.0.1 dated 2016-06-22

Title: R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Description: Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment.
Author: Dan Warren [aut, cre], Anthony Geneva [aut], Rob Lanfear [aut], Luke Harmon [ctb], April Wright [ctb], Diego Mallo [ctb], Klaus Schliep [ctb]
Maintainer: Dan Warren <dan.l.warren@gmail.com>

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Package readxl updated to version 1.3.0 with previous version 1.2.0 dated 2018-12-19

Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded 'libxls' C library <https://github.com/evanmiller/libxls> and '.xlsx' via the embedded 'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package purrrlyr updated to version 0.0.4 with previous version 0.0.3 dated 2018-05-29

Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and 'purrr' that formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre], Hadley Wickham [ctb], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package jstable updated to version 0.7.9 with previous version 0.7.7 dated 2019-02-03

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Anpanman [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package irg updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-04

Title: Instantaneous Rate of Green Up
Description: Fits a double logistic function to NDVI time series and calculates instantaneous rate of green (IRG) according to methods described in Bischoff et al. (2012) <doi:10.1086/667590>.
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>

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Package dplyr updated to version 0.8.0.1 with previous version 0.8.0 dated 2019-02-14

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package stats19 updated to version 0.2.0 with previous version 0.1.1 dated 2019-01-17

Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The data are provided as 'CSV' files with detailed road safety data about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979, the types (including make and model) of vehicles involved and the consequential casualties. The statistics relate only to personal casualties on public roads that are reported to the police, and subsequently recorded, using the 'STATS19' accident reporting form. See the Department for Transportation website <https://data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more information on these data.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Malcolm Morgan [aut], Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>), Mark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>), David Ranzolin [rev], Adam Sparks [rev, ctb] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package naniar updated to version 0.4.2 with previous version 0.4.1 dated 2018-11-20

Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. 'naniar' provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of 'ggplot2' and tidy data.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>), Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>), Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>), Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>), Mitchell O'Hara-Wild [ctb], Jim Hester [ctb], Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>

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Package jskm updated to version 0.3.0 with previous version 0.2.7 dated 2019-02-01

Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Anpanman [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package dbhydroR updated to version 0.2-7 with previous version 0.2-6 dated 2018-07-19

Title: 'DBHYDRO' Hydrologic and Water Quality Data
Description: Client for programmatic access to the South Florida Water Management District's 'DBHYDRO' database at <https://www.sfwmd.gov/science-data/dbhydro>, with functions for accessing hydrologic and water quality data.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package castor updated to version 1.3.5 with previous version 1.3.4 dated 2018-08-16

Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

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Package udpipe updated to version 0.8.1 with previous version 0.8 dated 2018-12-09

Title: Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <http://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph], BNOSAC [cph], Institute of Formal and Applied Linguistics, Faculty of Mathematics and Physics, Charles University in Prague, Czech Republic [cph], Milan Straka [ctb, cph], Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>

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Package Rmosek updated to version 1.3.2 with previous version 1.3.1 dated 2019-01-23

Title: The R to MOSEK Optimization Interface
Description: This is a generic meta-package designed to make the optimization facilities of MOSEK available from the R-language. The interface supports large-scale optimization of many kinds: Mixed-integer and continuous linear, second-order cone, exponential cone and power cone optimization, as well as continuous semidefinite optimization. Rmosek and the R-language are open-source projects. MOSEK is a proprietary product, but unrestricted trial and academic licenses are available.
Author: MOSEK ApS
Maintainer: Henrik A. Friberg <haf@mosek.com>

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Package LLSR updated to version 0.0.2.12 with previous version 0.0.2.6 dated 2019-01-14

Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and provide a simple way to obtain its parameters, producing a simplified report. Designed initially to analyse Aqueous Two-Phases Systems, the package will include (every other update) new functions in order to comprise useful tools in liquid-liquid analysis.
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>

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Package bcmaps updated to version 0.18.0 with previous version 0.17.1 dated 2018-03-14

Title: Map Layers and Spatial Utilities for British Columbia
Description: Provides access to various spatial layers for B.C., such as administrative boundaries, natural resource management boundaries, etc. All layers are imported from the 'bcmapsdata' package as 'sf' or 'Spatial' objects through function calls in this package. All layers are in B.C. 'Albers' equal-area projection <http://spatialreference.org/ref/epsg/nad83-bc-albers/>, which is the B.C. government standard.
Author: Andy Teucher [aut, cre], Stephanie Hazlitt [aut], Sam Albers [aut], Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>

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Package AzureStor updated to version 2.0.0 with previous version 1.0.0 dated 2018-12-25

Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS).
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package BacArena updated to version 1.8 with previous version 1.7 dated 2018-05-09

Title: Modeling Framework for Cellular Communities in their Environments
Description: Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.
Author: Eugen Bauer [aut], Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>

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Package SqlRender updated to version 1.6.0 with previous version 1.5.3 dated 2018-11-23

Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle', 'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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Package QuantumOps updated to version 2.4 with previous version 2.3 dated 2019-01-30

Title: Performs Common Linear Algebra Operations Used in Quantum Computing
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of arbitrarily sized kets, bras, matrices and implements quantum gates, inner products, and tensor products. Contains all commonly used quantum gates, creates arbitrarily controlled versions of all gates, and can simulate complete or partial measurements of kets. Implements modular arithmetic commonly found in quantum algorithms and can convert functions into equivalent quantum gates. It can also simulate larger applications, including the Quantum Fourier Transform developed by Shor (1999), Shor's algorithm which factors numbers up to 21, Grover's algorithm (1996), and the training of a quantum neural network developed by Schuld (2018) which can classify the MNIST dataset.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>

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Package GWmodel updated to version 2.0-8 with previous version 2.0-7 dated 2019-02-02

Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>

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Thu, 14 Feb 2019

Package cdata updated to version 1.0.6 with previous version 1.0.5 dated 2019-01-20

Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 . Works on in-memory data or on remote data using 'rquery' and the 'DBI' database interface.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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More information about cdata at CRAN
Permanent link

Package triangle updated to version 0.12 with previous version 0.11 dated 2017-10-02

Title: Provides the Standard Distribution Functions for the Triangle Distribution
Description: Provides the "r, q, p, and d" distribution functions for the triangle distribution.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>

Diff between triangle versions 0.11 dated 2017-10-02 and 0.12 dated 2019-02-14

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More information about triangle at CRAN
Permanent link

Package RandomFieldsUtils updated to version 0.5.1 with previous version 0.5 dated 2019-02-10

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFieldsUtils versions 0.5 dated 2019-02-10 and 0.5.1 dated 2019-02-14

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More information about RandomFieldsUtils at CRAN
Permanent link

Package RandomFields updated to version 3.3 with previous version 3.1.50 dated 2017-04-17

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

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More information about RandomFields at CRAN
Permanent link

Package dplyr updated to version 0.8.0 with previous version 0.7.8 dated 2018-11-10

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between dplyr versions 0.7.8 dated 2018-11-10 and 0.8.0 dated 2019-02-14

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Package R.utils updated to version 2.8.0 with previous version 2.7.0 dated 2018-08-27

Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package GMCM updated to version 1.3.1 with previous version 1.3.0 dated 2018-12-15

Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>

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Package rquery updated to version 1.3.1 with previous version 1.3.0 dated 2019-01-29

Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package R6 updated to version 2.4.0 with previous version 2.3.0 dated 2018-10-04

Title: Encapsulated Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>

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Package icr updated to version 0.5.9 with previous version 0.5.8 dated 2018-10-21

Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder reliability coefficient alpha and bootstrapped uncertainty estimates (Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb] (author of the C++ RNG code)
Maintainer: Alexander Staudt <staudtlex@live.de>

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Package brglm2 updated to version 0.5.1 with previous version 0.5.0 dated 2019-02-06

Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>), Kjell Konis [ctb], Euloge Clovis Kenne Pagui [ctb], Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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Package GetDFPData updated to version 1.5 with previous version 1.4 dated 2019-01-12

Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.bmfbovespa.com.br/en_us/products/listed-equities-and-derivatives/equities/listed-companies.htm>. These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package qrandom updated to version 1.1 with previous version 1.0 dated 2019-01-10

Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API. The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies. By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers. The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793> and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>. The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package vardpoor updated to version 0.14.0 with previous version 0.12.0 dated 2018-09-20

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearization of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>

Diff between vardpoor versions 0.12.0 dated 2018-09-20 and 0.14.0 dated 2019-02-14

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Package popkin updated to version 1.1.2 with previous version 1.0.5 dated 2018-01-26

Title: Estimate Kinship and FST under Arbitrary Population Structure
Description: Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Author: Alejandro Ochoa [aut, cre], John D. Storey [aut]
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>

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Package EBPRS updated to version 1.1.2 with previous version 1.0.1 dated 2018-11-03

Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <shuangsong0110@163.com>

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Package monotonicity updated to version 1.2 with previous version 1.1 dated 2018-05-23

Title: Test for Monotonicity in Expected Asset Returns, Sorted by Portfolios
Description: Test for monotonicity in financial variables sorted by portfolios. It is conventional practice in empirical research to form portfolios of assets ranked by a certain sort variable. A t-test is then used to consider the mean return spread between the portfolios with the highest and lowest values of the sort variable. Yet comparing only the average returns on the top and bottom portfolios does not provide a sufficient way to test for a monotonic relation between expected returns and the sort variable. This package provides nonparametric tests for the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010) <doi:10.1016/j.jfineco.2010.06.006> and compares the proposed results with extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequality tests through empirical applications and simulations.
Author: Siegfried Köstlmeier [aut, cre, trl] (<https://orcid.org/0000-0002-7221-6981>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

Diff between monotonicity versions 1.1 dated 2018-05-23 and 1.2 dated 2019-02-14

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Package workflowr updated to version 1.2.0 with previous version 1.1.1 dated 2018-07-06

Title: A Framework for Reproducible and Collaborative Data Science
Description: Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.
Author: John Blischak [aut, cre] (<https://orcid.org/0000-0003-2634-9879>), Peter Carbonetto [aut] (<https://orcid.org/0000-0003-1144-6780>), Matthew Stephens [aut] (<https://orcid.org/0000-0001-5397-9257>), Luke Zappia [ctb] (Instructions for hosting with GitLab), Pierre Formont [ctb] (Support for hosting with Shiny Server), Tim Trice [ctb] (Instructions for sharing common code)
Maintainer: John Blischak <jdblischak@uchicago.edu>

Diff between workflowr versions 1.1.1 dated 2018-07-06 and 1.2.0 dated 2019-02-14

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Package spongebob updated to version 0.3.0 with previous version 0.2.0 dated 2019-01-24

Title: SpongeBob-Case Converter : spOngEboB-CASe CoNVertOR
Description: Convert character strings to Mocking SpongeBob case <https://knowyourmeme.com/memes/mocking-spongebob> and show them off in fun ways. coNvErt CharACtER strInGs to MOckiNG spOngEbOb caSE <https://knowyourmeme.com/memes/mocking-spongebob> aND shOw tHem OFf IN Fun WayS.
Author: Jay Qi [aut, cre]
Maintainer: Jay Qi <jayqi.opensource@gmail.com>

Diff between spongebob versions 0.2.0 dated 2019-01-24 and 0.3.0 dated 2019-02-14

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Package rmytarget updated to version 2.1.3 with previous version 2.1.1 dated 2019-01-03

Title: Load Data from 'MyTarget API v2'
Description: Allows work with 'MyTarget API v2' <https://target.my.com/doc/apiv2/ru/detailed.html> and load data by ads, campaigns, agency clients and statistic from your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package popEpi updated to version 0.4.6 with previous version 0.4.5 dated 2018-05-16

Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models, rates, mean survival times, relative survival, and standardized incidence and mortality ratios (SIRs/SMRs), all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.
Author: Joonas Miettinen [aut, cre], Matti Rantanen [aut], Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>

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Package graphTweets updated to version 0.5.1 with previous version 0.5.0 dated 2018-08-25

Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets, also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>

Diff between graphTweets versions 0.5.0 dated 2018-08-25 and 0.5.1 dated 2019-02-14

 DESCRIPTION  |   17 ++++++++---------
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Package BoltzMM updated to version 0.1.4 with previous version 0.1.3 dated 2019-01-10

Title: Boltzmann Machines with MM Algorithms
Description: Provides probability computation, data generation, and model estimation for fully-visible Boltzmann machines. It follows the methods described in Nguyen and Wood (2016a) <doi:10.1162/NECO_a_00813> and Nguyen and Wood (2016b) <doi:10.1109/TNNLS.2015.2425898>.
Author: Andrew Thomas Jones, Hien Duy Nguyen, and Jessica Juanita Bagnall
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>

Diff between BoltzMM versions 0.1.3 dated 2019-01-10 and 0.1.4 dated 2019-02-14

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Package SQRL updated to version 0.6.2 with previous version 0.6.1 dated 2019-02-01

Title: Database Query Interfaces
Description: Facilitates interaction with 'ODBC' data sources.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>

Diff between SQRL versions 0.6.1 dated 2019-02-01 and 0.6.2 dated 2019-02-14

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Package AzureContainers updated to version 1.0.1 with previous version 1.0.0 dated 2018-12-25

Title: Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure'
Description: An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/overview/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'kubectl' and 'helm' commandline tools are provided.
Author: Hong Ooi [aut, cre], Bill Liang [ctb] (Assistance debugging MMLS on Kubernetes), Ramkumar Chandrasekaran [ctb] (Original blog article on Dockerising MMLS), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Wed, 13 Feb 2019

Package ordinalCont updated to version 2.0.1 with previous version 2.0.0 dated 2018-11-21

Title: Ordinal Regression Analysis for Continuous Scales
Description: A regression framework for response variables which are continuous self-rating scales such as the Visual Analog Scale (VAS) used in pain assessment, or the Linear Analog Self-Assessment (LASA) scales in quality of life studies. These scales measure subjects' perception of an intangible quantity, and cannot be handled as ratio variables because of their inherent non-linearity. We treat them as ordinal variables, measured on a continuous scale. A function (the g function) connects the scale with an underlying continuous latent variable. The link function is the inverse of the CDF of the assumed underlying distribution of the latent variable. A variety of link functions are currently implemented.
Author: Maurizio Manuguerra [aut, cre], Gillian Heller [aut]
Maintainer: Maurizio Manuguerra <maurizio.manuguerra@mq.edu.au>

Diff between ordinalCont versions 2.0.0 dated 2018-11-21 and 2.0.1 dated 2019-02-13

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Package RAMClustR updated to version 1.0.4 with previous version 1.0.0 dated 2019-01-18

Title: Mass Spectrometry Metabolomics Feature Clustering and Interpretation
Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectromery <DOI: 10.1021/ac501530d> data.
Author: Corey D. Broeckling, Fayyaz Afsar, Steffan Neumann, Asa Ben-Hur, Jessica Prenni.
Maintainer: "Broeckling,Corey" <Corey.Broeckling@ColoState.EDU>

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Package xROI updated to version 0.9.13 with previous version 0.9.11 dated 2018-11-12

Title: Delineate Region of Interests (ROI's) and Extract Time-Series Data from Digital Repeat Photography Images
Description: Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
Author: Bijan Seyednasrollah, Thomas Milliman, Andrew D. Richardson
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>

Diff between xROI versions 0.9.11 dated 2018-11-12 and 0.9.13 dated 2019-02-13

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Package SoyNAM updated to version 1.6 with previous version 1.5 dated 2018-10-01

Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB). See <doi.org/10.1534/g3.118.200332> and <doi.org/10.1534/g3.117.300300>. BLUP function formats data for genome-wide prediction and association analysis.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, Rouf Mian, Reka Howard, George Graef, Randall Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah McHale, Perry Cregan, Qijian Song, Miguel Lopez, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between SoyNAM versions 1.5 dated 2018-10-01 and 1.6 dated 2019-02-13

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Package paletteer updated to version 0.2.1 with previous version 0.2.0 dated 2019-02-04

Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This packages aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>

Diff between paletteer versions 0.2.0 dated 2019-02-04 and 0.2.1 dated 2019-02-13

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Package NAM updated to version 1.7 with previous version 1.6.5 dated 2019-02-11

Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between NAM versions 1.6.5 dated 2019-02-11 and 1.7 dated 2019-02-13

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Package lcc updated to version 1.0.1 with previous version 1.0 dated 2018-11-16

Title: Longitudinal Concordance Correlation
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Author: Thiago de Paula Oliveira [aut, cre], Rafael de Andrade Moral [aut], John Hinde [aut], Silvio Sandoval Zocchi [ctb], Clarice Garcia Borges Demetrio [ctb]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@usp.br>

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Package ethnobotanyR updated to version 0.1.4 with previous version 0.1.3 dated 2019-01-21

Title: Calculate Quantitative Ethnobotany Indices
Description: Calculate common quantitative ethnobotany indices to assess the cultural significance of plant species based on informant consensus. The package closely follows the paper by Tardio and Pardo-de-Santayana (2008). Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <doi:10.1007/s12231-007-9004-5>.
Author: Cory Whitney
Maintainer: Cory Whitney <whitney.cory@gmail.com>

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Package logmult updated to version 0.7.1 with previous version 0.7.0 dated 2018-10-19

Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart. Functions allow computing the intrinsic association coefficient (and therefore the Altham index), including via the Bayes shrinkage estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Author: Milan Bouchet-Valat [aut, cre], Heather Turner [ctb], Michael Friendly [ctb], Jim Lemon [cph], Gabor Csardi [cph]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

Diff between logmult versions 0.7.0 dated 2018-10-19 and 0.7.1 dated 2019-02-13

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 16 files changed, 122 insertions(+), 71 deletions(-)

More information about logmult at CRAN
Permanent link

Package stringi updated to version 1.3.1 with previous version 1.2.4 dated 2018-07-20

Title: Character String Processing Facilities
Description: Fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the 'ICU' (International Components for Unicode) library, the package provides 'R' users with platform-independent functions known to 'Java', 'Perl', 'Python', 'PHP', and 'Ruby' programmers. Available features include: pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, and many more.
Author: Marek Gagolewski [aut, cre], Bartek Tartanus [ctb], and other contributors (stringi source code); IBM, Unicode, Inc., and other contributors (ICU4C source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>

Diff between stringi versions 1.2.4 dated 2018-07-20 and 1.3.1 dated 2019-02-13

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More information about stringi at CRAN
Permanent link

Package igraph updated to version 1.2.4 with previous version 1.2.3 dated 2019-02-10

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between igraph versions 1.2.3 dated 2019-02-10 and 1.2.4 dated 2019-02-13

 DESCRIPTION            |   12 
 MD5                    |   22 
 configure              |   18 
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 src/Makevars.win       |    2 
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 12 files changed, 1842 insertions(+), 1602 deletions(-)

More information about igraph at CRAN
Permanent link

Package bWGR updated to version 1.6 with previous version 1.5.7 dated 2019-02-05

Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM or Gibbs sampling, with optional kernel term and sampling techniques as described by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between bWGR versions 1.5.7 dated 2019-02-05 and 1.6 dated 2019-02-13

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Permanent link

Package staRdom updated to version 1.0.12 with previous version 1.0.8 dated 2018-06-21

Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre], Daniel Graeber [aut, ctb], Stefan Preiner [ctb], Renata Pinto [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>

Diff between staRdom versions 1.0.8 dated 2018-06-21 and 1.0.12 dated 2019-02-13

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 staRdom-1.0.12/staRdom/README                                      |   35 
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Package rehh updated to version 2.0.4 with previous version 2.0.3 dated 2019-02-04

Title: Searching for Footprints of Selection using "Extended Haplotype Homozygosity" Based Tests
Description: Population genetic data in form of "Single Nucleotide Polymorphisms" (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. The concept of an "Extended Haplotype Homozygosity" (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several derived statistics designed for whole genome scans. The package provides functions to compute three of these, namely: "iHS" (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting selection within a single population as well as "Rsb" (Tang 2007) <doi:10.1371/journal.pbio.0050171> and "XP-EHH" (Sabeti 2007) <doi:10.1038/nature06250> to detect (differential) selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@inra.fr>

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Package ISOcodes updated to version 2019.02.13 with previous version 2018.06.29 dated 2018-06-30

Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes. Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.
Author: Christian Buchta [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package crseEventStudy updated to version 1.1 with previous version 1.0 dated 2018-11-15

Title: A Robust and Powerful Test of Abnormal Stock Returns in Long-Horizon Event Studies
Description: Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this package provides their standardized test for abnormal returns in long-horizon event studies. The methods used improve the major weaknesses of size, power, and robustness of long-run statistical tests described in Kothari/Warner (2007) <doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted by their statistical precision (i.e., standard deviation), resulting in abnormal standardized returns. This procedure efficiently captures the heteroskedasticity problem. Clustering techniques following Cameron et al. (2011) <10.1198/jbes.2010.07136> are adopted for computing cross-sectional correlation robust standard errors. The statistical tests in this package therefore accounts for potential biases arising from returns' cross-sectional correlation, autocorrelation, and volatility clustering without power loss.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Seppo Pynnonen [aut]
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package auth0 updated to version 0.1.1 with previous version 0.1.0 dated 2018-11-02

Title: Secure Authentication in Shiny with Auth0
Description: Uses Auth0 API (see <https://auth0.com> for more information) to use a simple and secure authentication system. It provides tools to log in and out a shiny application using social networks or a list of e-mails.
Author: Julio Trecenti [cre], Daniel Falbel [aut], José Jesus [ctb]
Maintainer: Julio Trecenti <julio.trecenti@gmail.com>

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Package rbacon updated to version 2.3.7 with previous version 2.3.6 dated 2019-01-17

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>

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Package qsub updated to version 1.1.0 with previous version 1.0.3 dated 2018-07-30

Title: Running Commands Remotely on 'Gridengine' Clusters
Description: Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package antaresRead updated to version 2.2.3 with previous version 2.2.2 dated 2019-01-21

Title: Import, Manipulate and Explore the Results of an 'Antares' Simulation
Description: Import, manipulate and explore results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here : <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>.
Author: Jalal-Edine ZAWAM [aut], Frederic Breant [aut, cre], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], RTE [cph]
Maintainer: Frederic Breant <frederic.breant@rte-france.com>

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Package rosr updated to version 0.0.4 with previous version 0.0.3 dated 2019-02-12

Title: Create Reproducible Research Projects
Description: Creates reproducible academic projects with integrated academic elements, including datasets, references, codes, images, manuscripts, dissertations, slides and so on. These elements are well connected so that they can be easily synchronized and updated.
Author: Peng Zhao [aut, cre]
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package DSsim updated to version 1.1.4 with previous version 1.1.3 dated 2018-06-27

Title: Distance Sampling Simulations
Description: Performs distance sampling simulations.It repeatedly generates instances of a user defined population within a given survey region, generates realisations of a survey design (currently these must be generated using Distance software in advance <http://distancesampling.org/>) and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This will allow users to select survey designs which will give them the best accuracy and precision given their expectations about population distribution. Any uncertainty in population distribution or population parameters can be included by running the different survey designs for a number of different population descriptions. An example simulation can be found in the help file for make.simulation.
Author: Laura Marshall <lhm@st-and.ac.uk>
Maintainer: Laura Marshall <lhm@st-and.ac.uk>

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Package carbonate updated to version 0.1.2 with previous version 0.1.1 dated 2019-01-17

Title: Interact with 'carbon.js'
Description: Create beautiful images of source code using 'carbon.js'<https://carbon.now.sh/about>.
Author: Jonathan Sidi [aut, cre] (<https://orcid.org/0000-0002-4222-1819>)
Maintainer: Jonathan Sidi <yonicd@gmail.com>

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Package ALA4R updated to version 1.6.2 with previous version 1.6.0 dated 2018-05-22

Title: Atlas of Living Australia (ALA) Data and Resources in R
Description: The Atlas of Living Australia (ALA) provides tools to enable users of biodiversity information to find, access, combine and visualise data on Australian plants and animals; these have been made available from <http://ala.org.au/>. ALA4R provides a subset of the tools to be directly used within R. It enables the R community to directly access data and resources hosted by the ALA.
Author: Peggy Newman [aut, cre], Ben Raymond [aut], Jeremy VanDerWal [aut], Lee Belbin [aut], Michael Sumner [ctb], Tom August [ctb], John Baumgartner [ctb]
Maintainer: Peggy Newman <peggy.newman@csiro.au>

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Package qgraph updated to version 1.6.1 with previous version 1.6 dated 2019-01-24

Title: Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre], Giulio Costantini [aut], Jonas Haslbeck [aut], Angelique O. J. Cramer [ctb], Lourens J. Waldorp [ctb], Verena D. Schmittmann [ctb], Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

Diff between qgraph versions 1.6 dated 2019-01-24 and 1.6.1 dated 2019-02-13

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Package philentropy updated to version 0.3.0 with previous version 0.2.0 dated 2018-05-22

Title: Similarity and Distance Quantification Between Probability Functions
Description: Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>

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Package spdep updated to version 1.0-2 with previous version 0.8-1 dated 2018-11-21

Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I', 'APLE', 'Gearys C', 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' Index, 'Getis/Ord' G and multicoloured join count statistics, local 'Moran's I' and 'Getis/Ord' G, 'saddlepoint' approximations, exact tests for global and local 'Moran's I' and 'LOSH' local indicators of spatial heteroscedasticity; and functions for estimating spatial simultaneous 'autoregressive' ('SAR') lag, error, general nested spatial and 'SARAR' models using maximum likelihood and 'MCMC', impact measures for lag, spatial 'Durbin', 'SLX', spatial 'Durbin' error, 'SARAR' and 'GNS' models, weighted and 'unweighted' 'SAR' and 'CAR' spatial regression models, semi-parametric and Moran 'eigenvector' spatial filtering, 'GM SAR' error models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Micah Altman [ctb], Luc Anselin [ctb], Renato Assunção [ctb], Olaf Berke [ctb], Andrew Bernat [ctb], Guillaume Blanchet [ctb], Eric Blankmeyer [ctb], Marilia Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb], Carsten Dormann [ctb], Stéphane Dray [ctb], Virgilio Gómez-Rubio [ctb], Martin Gubri [ctb], Rein Halbersma [ctb], Elias Krainski [ctb], Pierre Legendre [ctb], Nicholas Lewin-Koh [ctb], Angela Li [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Abhirup Mallik [ctb, trl], Giovanni Millo [ctb], Werner Mueller [ctb], Hisaji Ono [ctb], Pedro Peres-Neto [ctb], Gianfranco Piras [ctb], Markus Reder [ctb], Michael Tiefelsdorf [ctb], René Westerholt [ctb], Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package mri updated to version 1.0.0 with previous version 0.1.1 dated 2015-07-22

Title: Modified Rand and Wallace Indices
Description: Provides modified Rand and Wallace indices for comparing two partitions, which are usually obtained on two different sets of units with a non-empty intercept. Splitting and merging of clusters have a different affects on the value of the indices.
Author: Marjan Cugmas [aut, cre]
Maintainer: Marjan Cugmas <marjan.cugmas@fdv.uni-lj.si>

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Package isqg updated to version 1.2 with previous version 1.1 dated 2018-05-08

Title: In Silico Quantitative Genetics
Description: Accomplish high performance simulations in quantitative genetics. The molecular genetic components are represented by R6/C++ classes and methods. Mimic the meiosis recombination and de novo genetic variability by means a count-location process (Karlin & Liberman, 1978) <doi:10.1073/pnas.75.12.6332>. The core computational algorithm is implemented using 'Boost' dynamic bitsets (Schaling, 2014) [ISBN:978-1937434366]. A mix between low and high level interfaces provides great flexibility and allows user defined extensions and a wide range of applications.
Author: Fernando H. Toledo [aut, cre], International Maize and Wheat Improvement Center [cph]
Maintainer: Fernando H. Toledo <f.toledo@cgiar.org>

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Package wru updated to version 0.1-8 with previous version 0.1-7 dated 2017-09-01

Title: Who are You? Bayesian Prediction of Racial Category Using Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation, and other attributes, such as gender and age. The method utilizes the Bayes' Rule to compute the posterior probability of each racial category for any given individual. The package implements methods described in Imai and Khanna (2015) "Improving Ecological Inference by Predicting Individual Ethnicity from Voter Registration Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut]
Maintainer: Kabir Khanna <kabirkhanna@gmail.com>

Diff between wru versions 0.1-7 dated 2017-09-01 and 0.1-8 dated 2019-02-13

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Package qs updated to version 0.13.1 with previous version 0.12 dated 2019-02-08

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk. This package makes use of the 'zstd' library for compression and decompression. 'zstd' is created by Yann Collet and owned by Facebook, Inc.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep structures)
Maintainer: Travers Ching <traversc@gmail.com>

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Package HierDpart updated to version 0.3.5 with previous version 0.2.0 dated 2019-01-31

Title: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems
Description: Miscellaneous R functions for calculating and decomposing hierarchical diversity metrics, including hierarchical allele richness (q=0), hierarchical exponential Shannon entropy (q=1), hierarchical heterozygosity (q=2) and genetic differentiation (Fst and Delta D). This package allows you to analyse spatial structured genetic data or species data under a unifying framework (Gaggiotti, O. E. et al, 2018, Evol Appl, 11:1176-1193; <DOI:10.1111/eva.12593>), which partitions diversity and differentiation into any hierarchical levels. It helps you easily structure and format your data. It produces diversity profiles (q=0,1,2), hierarchical diversities and differentiation, as well as the the correlation between geographic distance and genetic differentiation.
Author: Xinghu Qin
Maintainer: Xinghu Qin <qinxinghu@gmail.com>

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Package staplr updated to version 2.9.0 with previous version 2.2.0 dated 2018-05-08

Title: A Toolkit for PDF Files
Description: Provides function to manipulate PDF files: fill out PDF forms; merge multiple PDF files into one; remove selected pages from a file; rename multiple files in a directory; rotate entire pdf document; rotate selected pages of a pdf file; Select pages from a file; splits single input PDF document into individual pages; splits single input PDF document into parts from given points.
Author: Priyanga Dilini Talagala [aut, cre], Ogan Mancarci [aut], Daniel Padfield [aut], Granville Matheson [aut]
Maintainer: Priyanga Dilini Talagala <dilini.talagala@monash.edu>

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Package rlmDataDriven updated to version 0.2.0 with previous version 0.1.0 dated 2018-09-17

Title: Robust Regression with Data Driven Tuning Parameter
Description: Data driven approach for robust regression estimation in homoscedastic and heteroscedastic context. See Wang et al. (2007), <doi:10.1198/106186007X180156> regarding homoscedastic framework.
Author: You-Gan Wang
Maintainer: The package maintainer <you-gan.wang@qut.edu.au>

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Package PlayerRatings updated to version 1.0-2 with previous version 1.0-1 dated 2016-01-04

Title: Dynamic Updating Methods for Player Ratings Estimation
Description: Implements schemes for estimating player or team skill based on dynamic updating. Implemented methods include Elo, Glicko and Stephenson. Contains pdf documentation of a reproducible analysis using approximately two million chess matches.
Author: Alec Stephenson and Jeff Sonas.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>

Diff between PlayerRatings versions 1.0-1 dated 2016-01-04 and 1.0-2 dated 2019-02-13

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Package funModeling updated to version 1.7 with previous version 1.6.8 dated 2018-07-31

Title: Exploratory Data Analysis and Data Preparation Tool-Box Book
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<http://livebook.datascienceheroes.com/>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas [aut, cre]
Maintainer: Pablo Casas <pcasas.biz@gmail.com>

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Tue, 12 Feb 2019

Package randnet updated to version 0.2 with previous version 0.1 dated 2017-09-17

Title: Random Network Model Selection and Parameter Tuning
Description: Model selection and parameter tuning procedures for a class of random network models. The model selection can be done by a general cross-validation framework called ECV from Li et. al. (2016) <arXiv:1612.04717> . Several other model-based and task-specific methods are also included, such as NCV from Chen and Lei (2016) <arXiv:1411.1715>, likelihood ratio method from Wang and Bickel (2015) <arXiv:1502.02069>, spectral methods from Le and Levina (2015) <arXiv:1507.00827>. Many network analysis methods are also implemented, such as the regularized spectral clustering (Amini et. al. 2013 <doi:10.1214/13-AOS1138>) and its degree corrected version and graphon neighborhood smoothing (Zhang et. al. 2015 <arXiv:1509.08588>).
Author: Tianxi Li, Elizaveta Levina, Ji Zhu
Maintainer: Tianxi Li <tianxili@umich.edu>

Diff between randnet versions 0.1 dated 2017-09-17 and 0.2 dated 2019-02-12

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Package civis updated to version 1.6.1 with previous version 1.5.1 dated 2018-08-15

Title: R Client for the 'Civis data science API'
Description: A convenient interface for making requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut], Keith Ingersoll [aut], Bill Lattner [ctb], Anh Le [ctb], Michelangelo D'Agostino [ctb], Sam Weiss [ctb], Stephen Hoover [ctb], Danning Chen [ctb], Elizabeth Sander [ctb], Madison Hobbs [ctb], Anna Bladey [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>

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Package evaluate updated to version 0.13 with previous version 0.12 dated 2018-10-09

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package CornerstoneR updated to version 1.1.1 with previous version 1.1.0 dated 2019-02-12

Title: Collection of Scripts for Interface Between 'Cornerstone' and 'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'. --- The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>) is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster. The engineers incorporate intensified hands-on statistics into their projects. They benefit from an intuitive and uniquely designed graphical Workmap concept: you design experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon, immediately, interactively, and without any programming. --- While 'Cornerstone's' interface to the statistical programming language 'R' has been available since version 6.0, the latest interface with 'R' is even much more efficient. 'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the standard 'Cornerstone' GUI. Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R' routines, immediately and without the need to deal with programming code. --- Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel (<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>

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Package bnpsd updated to version 1.0.4 with previous version 1.0.1 dated 2018-01-16

Title: Simulate Genotypes from the BN-PSD Admixture Model
Description: The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Author: Alejandro Ochoa [aut, cre], John D. Storey [aut]
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>

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Package GUTS updated to version 1.1.0 with previous version 1.0.4 dated 2017-10-10

Title: Fast Calculation of the Likelihood of a Stochastic Survival Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch>, Sören Vogel <soeren.vogel@posteo.ch>, Oliver Jakoby <oliver.jakoby@rifcon.de> and Alexander Singer <alexander.singer@rifcon.de>
Maintainer: Oliver Jakoby <oliver.jakoby@rifcon.de>

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Package gridSVG updated to version 1.7-0 with previous version 1.6-0 dated 2017-10-29

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

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Package Delaporte updated to version 7.0.0 with previous version 6.3.0 dated 2018-11-21

Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

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Package ufs updated to version 0.2.0 with previous version 0.1.0 dated 2019-01-16

Title: Quantitative Analysis Made Accessible
Description: This is a new version of the 'userfriendlyscience' package, which has grown a bit unwieldy. Therefore, distinct functionalities are being 'consciously uncoupled' into different packages. This package contains the general-purpose tools and utilities (see the 'behaviorchange' and the 'rosetta' packages for other functionality), and is the most direct 'successor' of the original 'userfriendlyscience' package. For example, this package contains a number of basic functions to create higher level plots, such as diamond plots, to easily plot sampling distributions, to generate confidence intervals, to plan study sample sizes for confidence intervals, and to do some basic operations such as (dis)attenuate effect size estimates.
Author: Gjalt-Jorn Peters [aut, cre, ctb]
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>

Diff between ufs versions 0.1.0 dated 2019-01-16 and 0.2.0 dated 2019-02-12

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Package rAmCharts updated to version 2.1.10 with previous version 2.1.9 dated 2018-11-05

Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it provides a global architecture to generate 'JavaScript' source code for charts. Most of classes in the library have their equivalent in R with S4 classes; for those classes, not all properties have been referenced but can easily be added in the constructors. Complex properties (e.g. 'JavaScript' object) can be passed as named list. See examples at <http://datastorm- open.github.io/introduction_ramcharts/> and <http://www.amcharts.com/> for more information about the library. The package includes the free version of 'AmCharts' Library. Its only limitation is a small link to the web site displayed on your charts. If you enjoy this library, do not hesitate to refer to this page <http://www.amcharts.com/online-store/> to purchase a licence, and thus support its creators and get a period of Priority Support. See also <http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Benoit Thieurmel [aut, cre], Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/), Jeffery Petit [aut, ctb], Elena Salette [aut, ctb], Titouan Robert [aut, ctb]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>

Diff between rAmCharts versions 2.1.9 dated 2018-11-05 and 2.1.10 dated 2019-02-12

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Package jetpack updated to version 0.4.2 with previous version 0.4.1 dated 2018-11-16

Title: A Friendly Package Manager
Description: Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>

Diff between jetpack versions 0.4.1 dated 2018-11-16 and 0.4.2 dated 2019-02-12

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Package CornerstoneR updated to version 1.1.0 with previous version 1.0.1 dated 2018-12-18

Title: Collection of Scripts for Interface Between 'Cornerstone' and 'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'. \cr\cr The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>) is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster. The engineers incorporate intensified hands-on statistics into their projects. They benefit from an intuitive and uniquely designed graphical Workmap concept: you design experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon, immediately, interactively, and without any programming. \cr\cr While 'Cornerstone's' interface to the statistical programming language 'R' has been available since version 6.0, the latest interface with 'R' is even much more efficient. 'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the standard 'Cornerstone' GUI. Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R' routines, immediately and without the need to deal with programming code. \cr\cr Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel (<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>

Diff between CornerstoneR versions 1.0.1 dated 2018-12-18 and 1.1.0 dated 2019-02-12

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Package wdpar updated to version 0.0.2 with previous version 0.0.1 dated 2019-01-11

Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected Areas (WDPA). Data is obtained from Protected Planet <http://protectedplanet.net>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>

Diff between wdpar versions 0.0.1 dated 2019-01-11 and 0.0.2 dated 2019-02-12

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Package vcr updated to version 0.2.6 with previous version 0.2.2 dated 2019-01-13

Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

Diff between vcr versions 0.2.2 dated 2019-01-13 and 0.2.6 dated 2019-02-12

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Package r6extended updated to version 0.1.2 with previous version 0.1.1 dated 2018-01-15

Title: Extension for 'R6' Base Class
Description: Useful methods and data fields to extend the bare bones 'R6' class provided by the 'R6' package - ls-method, hashes, warning- and message-method, general get-method and a debug-method that assigns self and private to the global environment.
Author: Peter Meissner [aut, cre]
Maintainer: Peter Meissner <retep.meissner@gmail.com>

Diff between r6extended versions 0.1.1 dated 2018-01-15 and 0.1.2 dated 2019-02-12

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Package photobiology updated to version 0.9.26 with previous version 0.9.25 dated 2018-12-11

Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima. Conversion between energy- and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package lava updated to version 1.6.5 with previous version 1.6.4 dated 2018-11-25

Title: Latent Variable Models
Description: A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2019) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.
Author: Klaus K. Holst [aut, cre], Brice Ozenne [ctb], Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>

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Package languagelayeR updated to version 1.2.4 with previous version 1.2.3 dated 2018-01-26

Title: Access the 'languagelayer' API
Description: Improve your text analysis with languagelayer <https://languagelayer.com>, a powerful language detection API.
Author: Colin FAY [aut, cre]
Maintainer: Colin FAY <contact@colinfay.me>

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Package hBayesDM updated to version 0.7.2 with previous version 0.7.1 dated 2019-01-21

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 (Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut], Harhim Park [ctb], Jaeyeong Yang [ctb], Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

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Package SSDforR updated to version 1.5.1 with previous version 1.5 dated 2019-01-10

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

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Package datarobot updated to version 2.12.0 with previous version 2.11.0 dated 2019-01-12

Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>

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Package BMTME updated to version 1.0.6 with previous version 1.0.5 dated 2019-02-02

Title: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis
Description: Genomic selection and prediction models with the capacity to use multiple traits and environments, through ready-to-use Bayesian models. It consists a group of functions that help to create regression models for some genomic models proposed by Montesinos-López, et al. (2016) <doi:10.1534/g3.116.032359> also in Montesinos-López et al. (2018) <doi:10.1534/g3.118.200728> and Montesinos-López et al. (2018) <doi:10.2134/agronj2018.06.0362>.
Author: Francisco Javier Luna-Vazquez [aut, cre] (<https://orcid.org/0000-0002-5370-7152>), Fernando H. Toledo [aut], Osval Antonio Montesinos-Lopez [aut] (<https://orcid.org/0000-0002-3973-6547>), Abelardo Montesinos-Lopez [aut], Jose Crossa [aut] (<https://orcid.org/0000-0001-9429-5855>)
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>

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Package hoardeR updated to version 0.9.4-2 with previous version 0.9.4 dated 2019-02-07

Title: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices
Description: Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.
Author: Daniel Fischer [aut, cre], Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>

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Package pubmed.mineR updated to version 1.0.14 with previous version 1.0.13 dated 2018-08-17

Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <http://www.ncbi.nlm.nih.gov/pubmed>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>

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Package DHARMa updated to version 0.2.3 with previous version 0.2.2 dated 2019-01-20

Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (Theoretical Ecology, University of Regensburg, Regensburg, Germany)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

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Mon, 11 Feb 2019

Package tourr updated to version 0.5.6 with previous version 0.5.5 dated 2017-08-02

Title: Implement Tour Methods in R Code
Description: Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Author: Hadley Wickham [aut, ctb], Di Cook [aut, cre], Nick Spyrison [ctb], Ursula Laa [ctb]
Maintainer: Di Cook <dicook@monash.edu>

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Package ktsolve updated to version 1.1.1 with previous version 1.1 dated 2013-09-23

Title: Configurable Function for Solving Families of Nonlinear Equations
Description: This is designed for use with an arbitrary set of equations with an arbitrary set of unknowns. The user selects "fixed" values for enough unknowns to leave as many variables as there are equations, which in most cases means the system is properly defined and a unique solution exists. The function, the fixed values and initial values for the remaining unknowns are fed to a nonlinear backsolver. The original version of "TK!Solver" , now a product of Universal Technical Systems (<https://www.uts.com>) was the inspiration for this function.
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>

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Package IDPmisc updated to version 1.1.19 with previous version 1.1.18 dated 2018-10-02

Title: 'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)'
Description: Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Author: Rene Locher [aut, cre], Andreas Ruckstuhl [ctb]
Maintainer: Rene Locher <rene.locher@zhaw.ch>

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Package forecastHybrid updated to version 4.2.17 with previous version 4.1.16 dated 2018-12-19

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(), thetaf(), nnetar(), stlm(), tbats(), and snaive() can be combined with equal weights, weights based on in-sample errors (introduced by Bates & Granger (1969) <doi:10.1057/jors.1969.103>), or cross-validated weights. Cross validation for time series data with 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 emdbook updated to version 1.3.11 with previous version 1.3.10 dated 2018-05-19

Title: Support Functions and Data for "Ecological Models and Data"
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker [aut, cre], Sang Woo Park [ctb], James Vonesh [dtc], Jacqueline Wilson [dtc], Russ Schmitt [dtc], Sally Holbrook [dtc], James D. Thomson [dtc], R. Scot Duncan [dtc]
Maintainer: Ben Bolker <bolker@mcmaster.ca>

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Package autocogs updated to version 0.1.2 with previous version 0.1.1 dated 2018-09-21

Title: Automatic Cognostic Summaries
Description: Automatically calculates cognostic groups for plot objects and list column plot objects. Results are returned in a nested data frame.
Author: Barret Schloerke [aut], Ryan Hafen [ths, cre]
Maintainer: Ryan Hafen <rhafen@gmail.com>

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Package ctmm updated to version 0.5.5 with previous version 0.5.4 dated 2019-02-08

Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, and Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>

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Package cgmanalysis updated to version 2.2 with previous version 2.1 dated 2018-12-17

Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>), 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>), Diasend (<https://diasend.com//us>), Libre (<https://www.freestylelibre.us/>) or Carelink (<https://www.medtronicdiabetes.com/products/carelink-personal-diabetes-software>) data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry). cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>

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Package HeritSeq updated to version 1.0.1 with previous version 1.0.0 dated 2017-01-04

Title: Heritability of Gene Expression for Next-Generation Sequencing
Description: Statistical framework to analyze heritability of gene expression based on next-generation sequencing data and simulating sequencing reads. Variance partition coefficients (VPC) are computed using linear mixed effects and generalized linear mixed effects models. Compound Poisson and negative binomial models are included. Reference: Rudra, Pratyaydipta, et al. "Model based heritability scores for high-throughput sequencing data." BMC bioinformatics 18.1 (2017): 143.
Author: W. Jenny Shi [aut, cre], Pamela Russell [aut], Pratyaydipta Rudra [aut, cre], Brian Vestal [aut, cre], Katerina Kechris [aut], Laura Saba [aut]
Maintainer: W. Jenny Shi <wjennyshi@gmail.com>

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