Sat, 23 Jun 2018

Package GMDH2 updated to version 1.4 with previous version 1.3 dated 2018-05-15

Title: Binary Classification via GMDH-Type Neural Network Algorithms
Description: Performs binary classification via Group Method of Data Handling (GMDH) - type neural network algorithms. There exist two main algorithms available in GMDH() and dceGMDH() functions. GMDH() performs classification via GMDH algorithm for a binary response and returns important variables. dceGMDH() performs classification via diverse classifiers ensemble based on GMDH (dce-GMDH) algorithm. Also, the package produces a well-formatted table of descriptives for a binary response. Moreover, it produces confusion matrix, its related statistics and scatter plot (2D and 3D) with classification labels of binary classes to assess the prediction performance. All 'GMDH2' functions are designed for a binary response. See Dag O. and Yozgatligil C. (2016, ISSN:2073-4859) and Kondo T. and Ueno J. (2016, ISSN:1349-4198) for the details of GMDH algorithms.
Author: Osman Dag [aut, cre], Erdem Karabulut [aut], Reha Alpar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

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Package clipr updated to version 0.4.1 with previous version 0.4.0 dated 2017-11-03

Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.
Author: Matthew Lincoln [aut, cre], Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>

Diff between clipr versions 0.4.0 dated 2017-11-03 and 0.4.1 dated 2018-06-23

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Package replyr updated to version 0.9.6 with previous version 0.9.5 dated 2018-05-20

Title: Patches to Use 'dplyr' on Remote Data Sources
Description: Patches to use 'dplyr' on remote data sources ('SQL' databases, 'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning user code works similarly on all such sources, without needing per-source adaption). Due to the fluctuating nature of 'dplyr'/'dbplyr'/'rlang' 'APIs' this package is going into maintenance mode. Most of the 'replyr' functions are already done better by one of the non-monolithic replacement packages: 'wrapr', 'seplyr', 'rquery', or 'cdata'.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package mosaicData updated to version 0.17.0 with previous version 0.16.0 dated 2018-01-28

Title: Project MOSAIC Data Sets
Description: Data sets from Project MOSAIC (<http://mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan <kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Package seplyr updated to version 0.5.6 with previous version 0.5.5 dated 2018-03-13

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

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Package schumaker updated to version 1.1 with previous version 1.0 dated 2017-05-20

Title: Schumaker Shape-Preserving Spline
Description: This is a shape preserving spline <doi:10.1137/0720057> which is guaranteed to be monotonic and concave or convex if the data is monotonic and concave or convex. It does not use any optimisation and is therefore quick and smoothly converges to a fixed point in economic dynamics problems including value function iteration. It also automatically gives the first two derivatives of the spline and options for determining behaviour when evaluated outside the interpolation domain.
Author: Stuart Baumann [aut, cre], Margaryta Klymak[aut]
Maintainer: Stuart Baumann <Stuart@StuartBaumann.com>

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Package MPTinR updated to version 1.11.0 with previous version 1.10.3 dated 2015-07-27

Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre], David Kellen [aut], Quentin Gronau [aut], Christian Mueller [ctb], Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>

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Package RZooRoH updated to version 0.1.1 with previous version 0.1.0 dated 2018-06-19

Title: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>

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Package rtdists updated to version 0.8-3 with previous version 0.8-1 dated 2017-12-23

Title: Response Time Distributions
Description: Provides response time distributions (density/PDF, distribution function/CDF, quantile function, and random generation): (a) Ratcliff diffusion model (Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C code by Andreas and Jochen Voss and (b) linear ballistic accumulator (LBA; Brown & Heathcote, 2008, <doi:10.1016/j.cogpsych.2007.12.002>) with different distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>), Scott Brown [aut], Matthew Gretton [aut], Andrew Heathcote [aut], Andreas Voss [ctb], Jochen Voss [ctb], Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann+rtdists@gmail.com>

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Package ddalpha updated to version 1.3.4 with previous version 1.3.3 dated 2018-04-30

Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut], Rainer Dyckerhoff [aut], Stanislav Nagy [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>

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Package trtf updated to version 0.3-2 with previous version 0.3-1 dated 2018-04-23

Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with corresponding random forest for conditional transformation models as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>) and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package TMB updated to version 1.7.14 with previous version 1.7.13 dated 2018-03-22

Title: Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
Description: With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines 'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph], Brad Bell [cph], Hans Skaug [ctb], Arni Magnusson [ctb], Casper Berg [ctb], Anders Nielsen [ctb], Martin Maechler [ctb], Theo Michelot [ctb], Mollie Brooks [ctb], Alex Forrence [ctb], Christoffer Moesgaard Albertsen [ctb], Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>

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Package zeitgebr updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-18

Title: Analysis of Circadian Behaviours
Description: Use behavioural variables to compute period, rhythmicity and other circadian parameters. Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>), Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>), and autocorrelation-based periodograms.
Author: Quentin Geissmann [aut, cre], Luis Garcia [aut]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>

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Package pcr updated to version 1.1.1 with previous version 1.1.0 dated 2017-11-20

Title: Analyzing Real-Time Quantitative PCR Data
Description: Calculates the amplification efficiency and curves from real-time quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative expression from PCR data using the double delta CT and the standard curve methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for statistical significance using two-group tests and linear regression Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>

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Package plotROC updated to version 2.2.1 with previous version 2.2.0 dated 2017-08-09

Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.
Author: Michael C. Sachs [aut, cre], Robert W. Corty [ctb]
Maintainer: Michael C. Sachs <sachsmc@gmail.com>

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Package heatmaply updated to version 0.15.0 with previous version 0.14.1 dated 2018-02-01

Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Jonathan Sidi [ctb] (https://github.com/yonicd), Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package makedummies updated to version 1.1.1 with previous version 1.1 dated 2018-04-06

Title: Create Dummy Variables from Categorical Data
Description: Create dummy variables from categorical data. This package can convert categorical data (factor and ordered) into dummy variables and handle multiple columns simultaneously. This package enables to select whether a dummy variable for base group is included (for principal component analysis/factor analysis) or excluded (for regression analysis) by an option.
Author: Toshiaki Ara [aut, cre]
Maintainer: Toshiaki Ara <toshiaki.ara@gmail.com>

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Package ggdistribute updated to version 1.0.2 with previous version 1.0.1 dated 2018-05-30

Title: A 'ggplot2' Extension for Plotting Unimodal Distributions
Description: The 'ggdistribute' package is an extension for plotting posterior or other types of unimodal distributions that require overlaying information about a distribution's intervals. It makes use of the 'ggproto' system to extend 'ggplot2', providing additional "geoms", "stats", and "positions." The extensions integrate with existing 'ggplot2' layer elements.
Author: Joseph M. Burling [aut, cre]
Maintainer: Joseph M. Burling <josephburling@gmail.com>

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Package vetr updated to version 0.2.5 with previous version 0.2.4 dated 2018-03-28

Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects meet structural requirements, and auto-composing error messages when they do not.
Author: Brodie Gaslam [aut, cre], Paxdiablo [cph] (Hash table implementation in src/pfhash.h), R Core Team [cph] (Used/adapted several code snippets from R sources, see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>

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Package robustbase updated to version 0.93-1 with previous version 0.93-0 dated 2018-04-24

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre], Peter Rousseeuw [ctb] (Qn and Sn), Christophe Croux [ctb] (Qn and Sn), Valentin Todorov [aut] (most robust Cov), Andreas Ruckstuhl [aut] (nlrob, anova, glmrob), Matias Salibian-Barrera [aut] (lmrob orig.), Tobias Verbeke [ctb, fnd] (mc, adjbox), Manuel Koller [aut] (mc, lmrob, psi-func.), Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob), Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package ggpubr updated to version 0.1.7 with previous version 0.1.6 dated 2017-11-14

Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package droptest updated to version 0.1.1 with previous version 0.1.0 dated 2018-05-22

Title: Simulates LOX Drop Testing
Description: Generates simulated data representing the LOX drop testing process (also known as impact testing). A simulated process allows for accelerated study of test behavior. Functions are provided to simulate trials, test series, and groups of test series. Functions for creating plots specific to this process are also included. Test attributes and criteria can be set arbitrarily. This work is not endorsed by or affiliated with NASA. See "ASTM G86-17, Standard Test Method for Determining Ignition Sensitivity of Materials to Mechanical Impact in Ambient Liquid Oxygen and Pressurized Liquid and Gaseous Oxygen Environments" <doi:10.1520/G0086-17>.
Author: Chad Ross [aut, cre]
Maintainer: Chad Ross <chad.ross@gmail.com>

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Fri, 22 Jun 2018

Package reprex updated to version 0.2.0 with previous version 0.1.2 dated 2018-01-26

Title: Prepare Reproducible Example Code via the Clipboard
Description: Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as <https://stackoverflow.com> and <https://github.com>, or in email. The user's clipboard is the default source of input code and the default target for rendered output. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.
Author: Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), David Robinson [aut], Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package groupedSurv updated to version 1.0.2 with previous version 1.0.1 dated 2018-05-15

Title: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function
Description: These 'Rcpp'-based functions compute the efficient score statistics for grouped time-to-event data (Prentice and Gloeckler, 1978), with the optional inclusion of baseline covariates. Functions for estimating the parameter of interest and nuisance parameters, including baseline hazards, using maximum likelihood are also provided. A parallel set of functions allow for the incorporation of family structure of related individuals (e.g., trios). Note that the current implementation of the frailty model (Ripatti and Palmgren, 2000) is sensitive to departures from model assumptions, and should be considered experimental. For these data, the exact proportional-hazards-model-based likelihood is computed by evaluating multiple variable integration. The integration is accomplished using the 'Cuba' library (Hahn, 2005), and the source files are included in this package. The maximization process is carried out using Brent's algorithm, with the C++ code file from John Burkardt and John Denker (Brent, 2002).
Author: Jiaxing Lin [aut], Alexander Sibley [aut], Tracy Truong [aut], Kouros Owzar [aut], Zhiguo Li [aut], Yu Jiang [ctb], Janice McCarthy [ctb], Andrew Allen [ctb]
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>

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Package BayLum updated to version 0.1.2 with previous version 0.1.1 dated 2017-09-07

Title: Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating
Description: Bayesian analysis of luminescence data and 14C age estimate. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.
Author: Claire Christophe [aut], Anne Philippe [aut, cre], Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>), Guillaume Guerin [aut] (<https://orcid.org/0000-0001-6298-5579>)
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>

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Package subscreen updated to version 1.0.0 with previous version 0.2.2 dated 2017-07-19

Title: Systematic Screening of Study Data for Subgroup Effects
Description: Identifying outcome relevant subgroups has now become as simple as possible! The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation. The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup. The diagram may show thousands of them. The position of the dot in the diagram is determined by the sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore, the diagram shows the line of no effect and the overall study results. For small subgroups, which are found on the left side of the plot, larger random deviations from the mean study effect are expected, while for larger subgroups only small deviations from the study mean can be expected to be chance findings. So for a study with no conspicuous subgroup effects, the dots in the figure are expected to form a kind of funnel. Any deviations from this funnel shape hint to conspicuous subgroups.
Author: Bodo Kirsch, Susanne Lippert, Thomas Schmelter, Christoph Muysers, Hermann Kulmann
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>

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Package sdcTable updated to version 0.23 with previous version 0.22.8 dated 2017-07-29

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>

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Package RStoolbox updated to version 0.2.3 with previous version 0.2.1 dated 2018-04-09

Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as calculating spectral indices, principal component transformation, unsupervised and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut], Ned Horning [aut], Jakob Schwalb-Willmann [aut], Robert J. Hijmans [ctb]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>

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Package mombf updated to version 2.1.2 with previous version 2.1.1 dated 2018-05-08

Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation for non-local and some conjugate priors. Bayes factors for regression and mixtures. Routines to sample, evaluate prior densities, distributions and quantiles.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>

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Package doRNG updated to version 1.7.1 with previous version 1.6.6 dated 2017-04-10

Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>]. It enables to easily convert standard %dopar% loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>

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Package crunch updated to version 1.23.0 with previous version 1.22.0 dated 2018-05-02

Title: Crunch.io Data Tools
Description: The Crunch.io service <http://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Author: Neal Richardson [aut, cre], Jonathan Keane [aut], Gordon Shotwell [aut]
Maintainer: Neal Richardson <neal@crunch.io>

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Package CodeDepends updated to version 0.6.0 with previous version 0.5-3 dated 2017-05-29

Title: Analysis of R Code for Reproducible Research and Code Comprehension
Description: Tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.
Author: Duncan Temple Lang, Roger Peng, Deborah Nolan, Gabriel Becker
Maintainer: Gabriel Becker <becker.gabriel@gene.com>

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Package alr3 updated to version 2.0.8 with previous version 2.0.7 dated 2018-04-11

Title: Data to Accompany Applied Linear Regression 3rd Edition
Description: Data files and a few functions used in the textbook S. Weisberg (2005), 'Applied Linear Regression,' 3rd edition, Wiley are presented. This package depends on the car package. Many functions formerly in alr3 have been renamed and now reside in car. Data files have been lightly modified to make some data columns row labels. Many of these files are also in the newer alr4 package.
Author: Sanford Weisberg <sandy@umn.edu>
Maintainer: Sanford Weisberg <sandy@umn.edu>

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Package RanglaPunjab updated to version 2.3.1 with previous version 1.1.1 dated 2018-05-28

Title: Displays Palette of 5 Colors
Description: Displays palette of 5 colors based on photos depicting the unique and vibrant culture of Punjab in Northern India. Since Punjab translates to ``Land of 5 Rivers'' there are 5 colors per palette. If users need more than 5 colors, they can merge 2 to 3 palettes to create their own color-combination, or they can cherry-pick their own custom colors. Users can view up to 3 palettes together. Users can also list all the palette choices. And last but not least, users can see the photo that inspired a particular palette.
Author: Sonia Ahluwalia [aut, cre]
Maintainer: Sonia Ahluwalia <sonia.bhar.ahluwalia@gmail.com>

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Package wallace updated to version 1.0.5 with previous version 1.0.4 dated 2018-02-12

Title: A Modular Platform for Reproducible Modeling of Species Niches and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre], Bruno Vilela [aut], Matthew E. Aiello-Lammens [aut], Robert Muscarella [aut], Cory Merow [aut], Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>

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Package tram updated to version 0.2-2 with previous version 0.2-1 dated 2018-04-23

Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package mlt.docreg updated to version 1.0-1 with previous version 1.0-0 dated 2018-03-08

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package SSLASSO updated to version 1.1 with previous version 0.0-1 dated 2017-09-21

Title: The Spike-and-Slab LASSO
Description: Efficient coordinate ascent algorithm for fitting regularization paths for linear models penalized by Spike-and-Slab LASSO. Rockova and George (2018) <doi:10.1080/01621459.2016.1260469>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gmoran@wharton.upenn.edu>

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Package rgdal updated to version 1.3-3 with previous version 1.3-2 dated 2018-06-08

Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Tim Keitt [aut], Barry Rowlingson [aut, ctb], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Even Rouault [cph, ctb], Frank Warmerdam [cph, ctb], Jeroen Ooms [ctb], Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package DendroSync updated to version 0.1.1 with previous version 0.1.0 dated 2017-05-22

Title: A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies
Description: Provides functions for the calculation and plotting of synchrony in tree growth from tree-ring width chronologies (TRW index). It combines variance-covariance (VCOV) mixed modelling with functions that quantify the degree to which the TRW chronologies contain a common temporal signal. It also implements temporal trends in spatial synchrony using a moving window. These methods can also be used with other kind of ecological variables that have temporal autocorrelation corrected.
Author: Josu G. Alday, Tatiana A. Shestakova, Victor Resco de Dios, Jordi Voltas
Maintainer: Josu G. Alday <josucham@gmail.com>

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Package CopulaREMADA updated to version 1.1 with previous version 1.0 dated 2016-09-13

Title: Copula Mixed Effect Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies
Description: It has functions to implement the copula mixed models for multivariate meta-analysis of diagnostic test accuracy studies.
Author: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>

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Package BHTSpack updated to version 0.4 with previous version 0.3 dated 2018-06-14

Title: Bayesian Multi-Plate High-Throughput Screening of Compounds
Description: Can be used for joint identification of candidate compound hits from multiple assays, in drug discovery. This package implements the framework of I. D. Shterev, D. B. Dunson, C. Chan and G. D. Sempowski. "Bayesian Multi-Plate High-Throughput Screening of Compounds", Scientific Reports 8 (1), 9551. This project was funded by the Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN272201400054C entitled "Adjuvant Discovery For Vaccines Against West Nile Virus and Influenza", awarded to Duke University and lead by Drs. Herman Staats and Soman Abraham.
Author: Ivo D. Shterev [aut, cre], David B. Dunson [aut], Cliburn Chan [aut], Gregory D. Sempowski [aut]
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>

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Package KnowBR updated to version 1.8 with previous version 1.7 dated 2018-04-10

Title: Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases
Description: It uses species accumulation curves and diverse estimators to assess, at the same time, the levels of survey coverage in multiple geographic cells of a size defined by the user or polygons. It also enables the geographical depiction of observed species richness, survey effort and completeness values including a background with administrative areas.
Author: Cástor Guisande González and Jorge M. Lobo
Maintainer: Cástor Guisande González <castor@uvigo.es>

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Package configr updated to version 0.3.3 with previous version 0.3.2.2 dated 2018-05-06

Title: An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

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Package validate updated to version 0.2.5 with previous version 0.2.4 dated 2018-03-28

Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront data with them and analyze or visualize the results. The package supports rules that are per-field, in-record, cross-record or cross-dataset. Rules can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut], Edwin de Jonge [aut], Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package heatwaveR updated to version 0.3.0 with previous version 0.2.7 dated 2018-05-30

Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb] (<https://orcid.org/0000-0002-0705-1287>), Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>

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Package RcmdrPlugin.temis updated to version 0.7.10 with previous version 0.7.9 dated 2017-07-11

Title: Graphical Integrated Text Mining Solution
Description: An 'R Commander' plug-in providing an integrated solution to perform a series of text mining tasks such as importing and cleaning a corpus, and analyses like terms and documents counts, vocabulary tables, terms co-occurrences and documents similarity measures, time series analysis, correspondence analysis and hierarchical clustering. Corpora can be imported from spreadsheet-like files, directories of raw text files, 'Twitter' queries, as well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and 'Alceste' files.
Author: Milan Bouchet-Valat [aut, cre], Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

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Package protViz updated to version 0.3.1 with previous version 0.2.45 dated 2017-11-17

Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Description: Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>), Jonas Grossmann [aut] (<https://orcid.org/0000-0002-6899-9020>), Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

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Package mlt updated to version 1.0-2 with previous version 1.0-1 dated 2018-04-20

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package lcmm updated to version 1.7.9 with previous version 1.7.8 dated 2017-05-29

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

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Package robcbi updated to version 1.1-2 with previous version 1.1.1 dated 2018-05-09

Title: Conditionally Unbiased Bounded Influence Estimates
Description: Conditionally unbiased bounded influence estimates as described in Kuensch et al. (1989) <doi:10.1080/01621459.1989.10478791> in three special cases of the generalized linear model: Bernoulli, Binomial, and Poisson distributed responses.
Author: Alfio Marazzi <Alfio.Marazzi@chuv.ch>
Maintainer: A. Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>

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Package mosum updated to version 1.2.0 with previous version 1.1 dated 2018-04-05

Title: Moving Sum Based Procedures for Changes in the Mean
Description: Implementations of MOSUM-based statistical procedures and algorithms for detecting multiple changes in the mean. This comprises the MOSUM procedure for estimating multiple mean changes from Eichinger and Kirch (2018) <doi:10.3150/16-BEJ887> and the multiscale algorithmic extensions from Cho and Kirch (2018+).
Author: Alexander Meier [aut], Haeran Cho [aut, cre], Claudia Kirch [aut]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>

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Package acebayes updated to version 1.5 with previous version 1.4.1 dated 2017-07-13

Title: Optimal Bayesian Experimental Design using the ACE Algorithm
Description: Optimal Bayesian experimental design using the approximate coordinate exchange (ACE) algorithm.
Author: Antony M. Overstall, David C. Woods & Maria Adamou
Maintainer: Antony M. Overstall <A.M.Overstall@soton.ac.uk>

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Package AssetCorr updated to version 1.0.1 with previous version 1.0.0 dated 2018-06-06

Title: Estimating Asset Correlations from Default Data
Description: Functions for the estimation of intra- and inter-cohort correlations in the Vasicek credit portfolio model. For intra-cohort correlations, the package covers the two method of moments estimators of Gordy (2000) <doi:10.1016/S0378-4266(99)00054-0>, the method of moments estimator of Lucas (1995) <http://jfi.iijournals.com/content/4/4/76> and a Binomial approximation extension of this approach. Moreover, the maximum likelihood estimators of Gordy and Heitfield (2010) <http://elsa.berkeley.edu/~mcfadden/e242_f03/heitfield.pdf> and Duellmann and Gehde-Trapp (2004) <http://hdl.handle.net/10419/19729> are implemented. For inter-cohort correlations, the method of moments estimator of Bluhm and Overbeck (2003) <doi:10.1007/978-3-642-59365-9_2>/Bams et al. (2016) <https://ssrn.com/abstract=2676595> is provided and the maximum likelihood estimators comprise the approaches of Gordy and Heitfield (2010)/Kalkbrener and Onwunta (2010) <ISBN: 978-1906348250> and Pfeuffer et al. (2018). Bootstrap and Jackknife procedures for bias correction are included as well as the method of moments estimator of Frei and Wunsch (2018) <doi:10.21314/JCR.2017.231> for auto-correlated time series.
Author: Maximilian Nagl [aut,cre], Yevhen Havrylenko [aut], Marius Pfeuffer [aut], Kevin Jakob [aut], Matthias Fischer [aut], Daniel Roesch [aut]
Maintainer: Maximilian Nagl <maximilian.nagl@ur.de>

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Package statnet.common updated to version 4.1.4 with previous version 4.1.2 dated 2018-06-05

Title: Common R Scripts and Utilities Used by the Statnet Project Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre], Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>

Diff between statnet.common versions 4.1.2 dated 2018-06-05 and 4.1.4 dated 2018-06-22

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Package bisoreg updated to version 1.5 with previous version 1.4 dated 2015-03-19

Title: Bayesian Isotonic Regression with Bernstein Polynomials
Description: Provides functions for fitting Bayesian monotonic regression models to data.
Author: S. McKay Curtis <s.mckay.curtis@gmail.com>
Maintainer: S. McKay Curtis <s.mckay.curtis@gmail.com>

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Package s20x updated to version 3.1-27 with previous version 3.1-26 dated 2017-12-07

Title: Functions for University of Auckland Course STATS 201/208 Data Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Ben Stevenson, Chris Wild
Maintainer: James Curran <j.curran@auckland.ac.nz>

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Package cbinom updated to version 1.2 with previous version 1.1 dated 2018-06-10

Title: Continuous Analog of a Binomial Distribution
Description: Implementation of the d/p/q/r family of functions for a continuous analog to the standard discrete binomial with continuous size parameter and continuous support with x in [0, size + 1], following Ilienko (2013) <arXiv:1303.5990>.
Author: Dan Dalthorp
Maintainer: Dan Dalthorp <ddalthorp@usgs.gov>

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Package mcmcplots updated to version 0.4.3 with previous version 0.4.2 dated 2015-03-19

Title: Create Plots from MCMC Output
Description: Functions for convenient plotting and viewing of MCMC output.
Author: S. McKay Curtis [aut, cre], Ilya Goldin [ctb], Evangelos Evangelou [ctb], 'sumtxt' from GitHub [ctb]
Maintainer: S. McKay Curtis <s.mckay.curtis@gmail.com>

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Package hexSticker updated to version 0.4.4 with previous version 0.4.3 dated 2018-03-04

Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre], Laurent Gatto [ctb], Johannes Rainer [ctb], Sebastian Gibb [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package Delaporte updated to version 6.2.0 with previous version 6.1.0 dated 2017-08-12

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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Thu, 21 Jun 2018

Package fastDummies updated to version 1.2.0 with previous version 1.1.0 dated 2018-03-03

Title: Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre], Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

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Package LEGIT updated to version 1.2.2 with previous version 1.2.1 dated 2018-02-07

Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where G is a weighted sum of genetic variants (genetic score) and E is a weighted sum of environments (environmental score) using the alternating optimization algorithm by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly enhanced predictive power over traditional GxE models which include only a single genetic variant and a single environmental exposure. Although this approach was originally made for GxE modelling, it is flexible and does not require the use of genetic and environmental variables. It can also handle more than 2 latent variables (rather than just G and E) and 3-way interactions or more. The LEGIT model produces highly interpretable results and is very parameter-efficient thus it can even be used with small sample sizes (n < 250). Tools to determine the type of interaction (vantage sensitivity, diathesis-stress or differential susceptibility), with any number of genetic variants or environments, are available <arXiv:1712.04058>.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>

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Package gnm updated to version 1.1-0 with previous version 1.0-8 dated 2015-04-22

Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Author: Heather Turner [aut, cre] (<https://orcid.org/0000-0002-1256-3375>), David Firth [aut] (<https://orcid.org/0000-0003-0302-2312>), Brian Ripley [ctb], Bill Venables [ctb], Douglas M. Bates [ctb], Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Heather Turner <ht@heatherturner.net>

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Package BUCSS updated to version 1.0.0 with previous version 0.0.2 dated 2017-04-10

Title: Bias and Uncertainty Corrected Sample Size
Description: Implements a method of correcting for publication bias and uncertainty when planning sample sizes in a future study from an original study. See Anderson, Kelley, & Maxwell (2017; Psychological Science, 28, 1547-1562).
Author: Samantha F. Anderson <samantha.f.anderson@asu.edu>, Ken Kelley <kkelley@nd.edu>
Maintainer: Ken Kelley <kkelley@nd.edu>

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Package shinyhelper updated to version 0.3.0 with previous version 0.2.0 dated 2018-06-07

Title: Easily Add Markdown Help Files to 'shiny' App Elements
Description: Creates a lightweight way to add markdown helpfiles to 'shiny' apps, using modal dialog boxes, with no need to observe each help button separately.
Author: Chris Thom [aut, cre]
Maintainer: Chris Thom <christopher.w.thom@outlook.com>

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Package RQEntangle updated to version 0.1.1 with previous version 0.1.0 dated 2018-05-27

Title: Quantum Entanglement of Bipartite System
Description: It computes the Schmidt decomposition of bipartite quantum systems, discrete or continuous, and their respective entanglement metrics. See Artur Ekert, Peter L. Knight (1995) <doi:10.1119/1.17904> for more details.
Author: Kwan-Yuet Ho [aut, cre]
Maintainer: Kwan-Yuet Ho <stephenhky@yahoo.com.hk>

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Package rnn updated to version 0.8.1 with previous version 0.8.0 dated 2016-09-11

Title: Recurrent Neural Network
Description: Implementation of a Recurrent Neural Network in R.
Author: Bastiaan Quast [aut, cre], Dimitri Fichou [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>

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Package qrng updated to version 0.0-5 with previous version 0.0-4 dated 2018-06-15

Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in high dimensions.
Author: Marius Hofert [aut, cre], Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

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Package warbleR updated to version 1.1.14 with previous version 1.1.13 dated 2018-05-18

Title: Streamline Bioacoustic Analysis
Description: A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository 'Xeno-Canto' <http://xeno-canto.org/>, manipulating sound files, detecting acoustic signals, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>

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Package TSPred updated to version 4.0 with previous version 3.0.2 dated 2017-04-05

Title: Functions for Benchmarking Time Series Prediction
Description: Functions for time series preprocessing, decomposition, prediction and accuracy assessment using automatic linear modelling. The generated linear models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Author: Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ), Eduardo Ogasawara [ths] (CEFET/RJ)
Maintainer: Rebecca Pontes Salles <rebeccapsalles@acm.org>

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Package sigmoid updated to version 0.3.0 with previous version 0.2.1 dated 2017-03-14

Title: Sigmoid Functions for Machine Learning
Description: Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>

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Package rAmCharts updated to version 2.1.8 with previous version 2.1.7 dated 2018-05-25

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>

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 rAmCharts-2.1.8/rAmCharts/R/chart_amPie.R                                                        |   18 
 rAmCharts-2.1.8/rAmCharts/R/chart_amPlot.R                                                       |   21 
 rAmCharts-2.1.8/rAmCharts/R/chart_amRadar.R                                                      |   20 
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 rAmCharts-2.1.8/rAmCharts/R/chart_amWaterfall.R                                                  |   17 
 rAmCharts-2.1.8/rAmCharts/R/chart_amWind.R                                                       |   18 
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Package NonCompart updated to version 0.4.3 with previous version 0.4.2 dated 2018-05-17

Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) Use of CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package mlrMBO updated to version 1.1.2 with previous version 1.1.1 dated 2018-01-02

Title: Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions
Description: Flexible and comprehensive R toolbox for model-based optimization ('MBO'), also known as Bayesian optimization. It implements the Efficient Global Optimization Algorithm and is designed for both single- and multi- objective optimization with mixed continuous, categorical and conditional parameters. The machine learning toolbox 'mlr' provide dozens of regression learners to model the performance of the target algorithm with respect to the parameter settings. It provides many different infill criteria to guide the search process. Additional features include multi-point batch proposal, parallel execution as well as visualization and sophisticated logging mechanisms, which is especially useful for teaching and understanding of algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that single components can be easily replaced or adapted by the user for specific use cases.
Author: Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Jakob Richter [aut, cre] (<https://orcid.org/0000-0003-4481-5554>), Jakob Bossek [aut] (<https://orcid.org/0000-0002-4121-4668>), Daniel Horn [aut], Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Janek Thomas [aut] (<https://orcid.org/0000-0003-4511-6245>)
Maintainer: Jakob Richter <code@jakob-r.de>

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Package iilasso updated to version 0.0.2 with previous version 0.0.1 dated 2018-04-16

Title: Independently Interpretable Lasso
Description: Efficient algorithms for fitting linear / logistic regression model with Independently Interpretable Lasso. Takada, M., Suzuki, T., & Fujisawa, H. (2018). Independently Interpretable Lasso: A New Regularizer for Sparse Regression with Uncorrelated Variables. AISTATS. <http://proceedings.mlr.press/v84/takada18a/takada18a.pdf>.
Author: Masaaki Takada
Maintainer: Masaaki Takada <tkdmah@gmail.com>

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Package googleAuthR updated to version 0.6.3 with previous version 0.6.2 dated 2017-11-14

Title: Authenticate and Create Google APIs
Description: Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>), Jennifer Bryan [ctb], Johann deBoer [ctb], Neal Richardson [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

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Package echo.find updated to version 1.1.1 with previous version 1.0.1 dated 2018-05-29

Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators (ECHO)
Description: Provides a function (echo_find()) designed to find rhythms from data using extended harmonic oscillators. For more information, see H. De los Santos et al. (2017) <doi:10.1145/3107411.3107420> .
Author: Hannah De los Santos [aut, cre], Emily Collins [aut], Jonathan Shewchuk [ctb], E.F. Harding [ctb], Kristin Bennett [aut], Jennifer Hurley [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>

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Package clickR updated to version 0.4.05 with previous version 0.3.64 dated 2018-04-21

Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis, fixing data errors in numerical, factor and date variables and creating report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

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Package cartogram updated to version 0.1.0 with previous version 0.0.3 dated 2018-05-22

Title: Create Cartograms with R
Description: Construct continuous and non-contiguous area cartograms.
Author: Sebastian Jeworutzki [aut, cre] (<https://orcid.org/0000-0002-2671-5253>), Timothee Giraud [ctb], Nicolas Lambert [ctb], Roger Bivand [cph], Edzer Pebesma [cph], Jakub Nowosad [ctb] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Sebastian Jeworutzki <sebastian.jeworutzki@ruhr-uni-bochum.de>

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Package BDgraph updated to version 2.51 with previous version 2.50 dated 2018-05-20

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Provides 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> and 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 [ctb], Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

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Package BAMBI updated to version 2.0.0 with previous version 1.2.1 dated 2018-04-20

Title: Bivariate Angular Mixture Models
Description: Fit (using Bayesian methods) and simulate mixtures of univariate and bivariate angular distributions. Chakraborty and Wong (2017) <arXiv:1708.07804> .
Author: Saptarshi Chakraborty, Samuel W.K. Wong
Maintainer: Saptarshi Chakraborty <chakra.saptarshi@gmail.com>

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Package tidyxl updated to version 1.0.3 with previous version 1.0.1 dated 2018-03-26

Title: Read Untidy Excel Files
Description: Imports non-tabular from Excel files into R. Exposes cell content, position and formatting in a tidy structure for further manipulation. Tokenizes Excel formulas. Supports '.xlsx' and '.xlsm' via the embedded 'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Does not support '.xlsb' or '.xls'.
Author: Duncan Garmonsway [aut, cre], Hadley Wickham [ctb] (Author of included readxl fragments), Jenny Bryan [ctb] (Author of included readxl fragments), RStudio [cph] (Copyright holder of included readxl fragments), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code)
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>

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Package staRdom updated to version 1.0.8 with previous version 1.0.5 dated 2018-05-02

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], Nora Maria Zechmeister [ctb], Christoph Zechmeister [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>

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Package SimilaR updated to version 1.0.2 with previous version 1.0.1 dated 2018-04-12

Title: R Source Code Similarity Evaluation
Description: An Implementation of a novel method to determine similarity of R functions based on program dependence graphs, see Bartoszuk, Gagolewski (2017) <doi:10.1109/FUZZ-IEEE.2017.8015582>. Possible use cases include plagiarism detection among students' homework assignments.
Author: Maciej Bartoszuk [aut, cre], Marek Gagolewski [aut]
Maintainer: Maciej Bartoszuk <bartoszuk@rexamine.com>

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Package RCzechia updated to version 1.2.6 with previous version 1.2.5 dated 2018-06-18

Title: Spatial Objects of the Czech Republic
Description: Administrative regions, rivers and water bodies of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>

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Package googleLanguageR updated to version 0.2.0 with previous version 0.1.1 dated 2017-11-16

Title: Call Google's 'Natural Language' API, 'Cloud Translation' API, 'Cloud Speech' API and 'Cloud Text-to-Speech' API
Description: Call 'Google Cloud' machine learning APIs for text and speech tasks. Call the 'Cloud Translation' API <https://cloud.google.com/translate/> for detection and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language/> to analyse text for sentiment, entities or syntax, the 'Cloud Speech' API <https://cloud.google.com/speech/> to transcribe sound files to text and the 'Cloud Text-to-Speech' API <https://cloud.google.com/text-to-speech/> to turn text into sound files.
Author: Mark Edmondson [aut, cre], Neal Richardson [rev] (Neal reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/127>), Julia Gustavsen [rev] (Julia reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/127>)
Maintainer: Mark Edmondson <r@sunholo.com>

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Package forecast updated to version 8.4 with previous version 8.3 dated 2018-04-11

Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>), George Athanasopoulos [aut], Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>), Gabriel Caceres [aut], Leanne Chhay [aut], Mitchell O'Hara-Wild [aut], Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>), Slava Razbash [aut], Earo Wang [aut], Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>), R Core Team [ctb, cph], Ross Ihaka [ctb, cph], Daniel Reid [ctb], David Shaub [ctb], Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>), Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

Diff between forecast versions 8.3 dated 2018-04-11 and 8.4 dated 2018-06-21

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Package docopulae updated to version 0.3.5 with previous version 0.3.4 dated 2018-06-19

Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>

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Package thinkr updated to version 0.13 with previous version 0.11 dated 2018-02-20

Title: Tools for Cleaning Up Messy Files
Description: Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.
Author: Vincent Guyader [aut, cre]
Maintainer: Vincent Guyader <vincent@thinkr.fr>

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Package graphframes updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-06

Title: Interface for 'GraphFrames'
Description: A 'sparklyr' <https://spark.rstudio.com/> extension that provides an R interface for 'GraphFrames' <https://graphframes.github.io/>. 'GraphFrames' is a package for 'Apache Spark' that provides a DataFrame-based API for working with graphs. Functionality includes motif finding and common graph algorithms, such as PageRank and Breadth-first search.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>

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More information about graphframes at CRAN
Permanent link

Package civis updated to version 1.5.0 with previous version 1.4.0 dated 2018-05-06

Title: R Client for the 'Civis data science API'
Description: A set of tools around common workflows and a convenient interface to make 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]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>

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More information about civis at CRAN
Permanent link

Package choroplethr updated to version 3.6.2 with previous version 3.6.1 dated 2017-04-16

Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps.
Author: Ari Lamstein <ari@lamsteinconsulting.com>[cre, aut], Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>

Diff between choroplethr versions 3.6.1 dated 2017-04-16 and 3.6.2 dated 2018-06-21

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More information about choroplethr at CRAN
Permanent link

Package CATkit updated to version 3.3.2 with previous version 3.2.3 dated 2018-01-03

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

Diff between CATkit versions 3.2.3 dated 2018-01-03 and 3.3.2 dated 2018-06-21

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Permanent link

Package BinQuasi updated to version 0.1-5 with previous version 0.1-3 dated 2018-04-03

Title: Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood
Description: Identify peaks in ChIP-seq data with biological replicates using a one-sided quasi-likelihood ratio test in quasi-Poisson or quasi-negative binomial models.
Author: Emily Goren [aut, cre], Steve Lund [aut] (The author of the QuasiSeq package, from which all functions were modified to produce this package.), Long Qu [aut] (The author of the QuasiSeq package, from which all functions were modified to produce this package.), Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified slightly leading to glm.fit3 in this package.), Daniel Gerhard [aut] (The author of mcprofile::orglm.fit, which was modified slightly and used under the same name in this package.), R Core Team [aut] (The author of stats::glm.fit, which was modified slightly leading to glm.fit3 in this package.)
Maintainer: Emily Goren <emily.goren@gmail.com>

Diff between BinQuasi versions 0.1-3 dated 2018-04-03 and 0.1-5 dated 2018-06-21

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More information about BinQuasi at CRAN
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Wed, 20 Jun 2018

Package Gmisc updated to version 1.6.2 with previous version 1.6.1 dated 2018-04-21

Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories, flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>

Diff between Gmisc versions 1.6.1 dated 2018-04-21 and 1.6.2 dated 2018-06-20

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More information about Gmisc at CRAN
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Package smicd updated to version 1.0.1 with previous version 1.0.0 dated 2018-06-12

Title: Statistical Methods for Interval Censored Data
Description: Functions that provide statistical methods for interval censored (grouped) data. The package supports the estimation of linear and linear mixed regression models with interval censored dependent variables. Parameter estimates are obtained by a stochastic expectation maximization algorithm. Furthermore, the package enables the direct (without covariates) estimation of statistical indicators from interval censored data via an iterative kernel density algorithm. Survey and Organisation for Economic Co-operation and Development (OECD) weights can be included into the direct estimation (see, Groß, M., U. Rendtel, T. Schmid, S. Schmon, and N. Tzavidis (2017) <doi:10.1111/rssa.12179>).
Author: Paul Walter
Maintainer: Paul Walter <paul.walter@fu-berlin.de>

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Package rEDM updated to version 0.7.1 with previous version 0.6.9 dated 2017-12-04

Title: Applications of Empirical Dynamic Modeling from Time Series
Description: A new implementation of EDM algorithms based on research software previously developed for internal use in the Sugihara Lab (UCSD/SIO). Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described in Sugihara et al. (2012) <DOI:10.1126/science.1227079> and multiview embedding as described in Ye & Sugihara (2016) <DOI:10.1126/science.aag0863>.
Author: Hao Ye [aut, cre], Adam Clark [aut], Ethan Deyle [aut], Steve Munch [aut], Jun Cai [ctb], Jane Cowles [ctb], Yair Daon [ctb], Andrew Edwards [ctb], Oliver Keyes [ctb], James Stagge [ctb], Masayuki Ushio [ctb], Ethan White [ctb], George Sugihara [ctb, ccp]
Maintainer: Hao Ye <hao.ye@weecology.org>

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Package VarSelLCM updated to version 2.1.2 with previous version 2.1.1 dated 2018-04-12

Title: Variable Selection for Model-Based Clustering of Mixed-Type Data Set with Missing Values
Description: Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering (see reference here <doi:10.1007/s11222-016-9670-1>). Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.
Author: Matthieu Marbac and Mohammed Sedki
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>

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Package modifiedmk updated to version 1.1.0 with previous version 0.1.2 dated 2018-03-03

Title: Modified Mann Kendall Trend Tests
Description: Power of non-parametric Mann-Kendall test is highly influenced by serially correlated data. To address this issue, original time-series may be modified by the following approaches namely Prewhitening (PW), Trend Free Prewhitening (TFPW) and Modified Mann-Kendall tests through variance correction approach by calculating effective sample size. Yue, S., & Wang, C. Y. (2002) <doi:10.1029/2001WR000861>. Yue, S., Pilon, P., Phinney, B., & Cavadias, G. (2002) <doi:10.1002/hyp.1095>. Hamed, K. H., & Ramachandra Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>. Yue, S., & Wang, C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>. Önöz, B., & Bayazit, M. (2012) <doi:10.1002/hyp.8438>.
Author: Sandeep Kumar Patakamuri [aut, cre], Nicole O'Brien [ctb]
Maintainer: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>

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Package hsdar updated to version 0.7.1 with previous version 0.7.0 dated 2017-12-14

Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut], Hanna Meyer [aut], Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>

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Package mortAAR updated to version 1.0.1 with previous version 1.0.0 dated 2017-10-20

Title: Analysis of Archaeological Mortality Data
Description: A collection of functions for the analysis of archaeological mortality data (on the topic see e.g. Chamberlain 2006 <https://books.google.de/books?id=nG5FoO_becAC&lpg=PA27&ots=LG0b_xrx6O&dq=life%20table%20archaeology&pg=PA27#v=onepage&q&f=false>). It takes demographic data in different formats and displays the result in a standard life table as well as plots the relevant indices (percentage of deaths, survivorship, probability of death, life expectancy, percentage of population).
Author: Nils Mueller-Scheessel [aut, cre, cph], Martin Hinz [aut], Clemens Schmid [aut], Christoph Rinne [aut], Daniel Knitter [aut], Wolfgang Hamer [aut], Dirk Seidensticker [aut], Franziska Faupel [aut], Carolin Tietze [aut], Nicole Grunert [aut]
Maintainer: Nils Mueller-Scheessel <nils.mueller-scheessel@ufg.uni-kiel.de>

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Package ggpol updated to version 0.0.2 with previous version 0.0.1 dated 2018-04-26

Title: Visualizing Social Science Data with 'ggplot2'
Description: A 'ggplot2' extension for implementing parliament charts and several other useful visualizations.
Author: Frederik Tiedemann [aut, cre]
Maintainer: Frederik Tiedemann <fj.tiedemann@googlemail.com>

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Package rsimsum updated to version 0.3.3 with previous version 0.3.1 dated 2018-04-04

Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (See White I.R., 2010 <http://www.stata-journal.com/article.html?article=st0200>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Ian R. White [aut]
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>

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Package womblR updated to version 1.0.3 with previous version 1.0.2 dated 2017-09-12

Title: Spatiotemporal Boundary Detection Model for Areal Unit Data
Description: Implements a spatiotemporal boundary detection model with a dissimilarity metric for areal data with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget), probit or Tobit link and spatial correlation is introduced at each time point through a conditional autoregressive (CAR) prior. Temporal correlation is introduced through a hierarchical structure and can be specified as exponential or first-order autoregressive. Full details of the package can be found in the accompanying vignette. Furthermore, the details of the package can be found in the corresponding paper on arXiv by Berchuck et al (2018): "Diagnosing Glaucoma Progression with Visual Field Data Using a Spatiotemporal Boundary Detection Method", <arXiv:1805.11636>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>

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Package sjmisc updated to version 2.7.3 with previous version 2.7.2 dated 2018-05-06

Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a 'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package fluxweb updated to version 0.1.1 with previous version 0.1.0 dated 2018-03-09

Title: Estimate Energy Fluxes in Food Webs
Description: Compute energy fluxes in trophic networks, from resources to their consumers, and can be applied to systems ranging from simple two-species interactions to highly complex food webs. It implements the approach described in Gauzens et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also used to calculate equilibrium stability.
Author: Benoit Gauzens
Maintainer: Benoit Gauzens <benoit.gauzens@gmail.com>

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Package projections updated to version 0.3.0 with previous version 0.1.1 dated 2018-05-29

Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R0 in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>.
Author: Thibaut Jombart [aut, cre], Pierre Nouvellet [aut], Sangeeta Bhatia [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

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Package SDLfilter updated to version 1.1.1 with previous version 1.1.0 dated 2018-04-27

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 imputeTS updated to version 2.7 with previous version 2.6 dated 2018-03-20

Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time series. Offers several imputation functions and missing data plots. Available imputation algorithms include: 'Mean', 'LOCF', 'Interpolation', 'Moving Average', 'Seasonal Decomposition', 'Kalman Smoothing on Structural Time Series models', 'Kalman Smoothing on ARIMA models'.
Author: Steffen Moritz [aut, cre, cph] (<https://orcid.org/0000-0002-0085-1804>)
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

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Package randomizeBE updated to version 0.3-4 with previous version 0.3-3 dated 2017-03-22

Title: Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>

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Package MortalityLaws updated to version 1.4.0 with previous version 1.3.0 dated 2018-01-11

Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct full and abridge life tables given various input indices. A mortality law is a parametric function that describes the dying-out process of individuals in a population during a significant portion of their life spans. For a comprehensive review of the most important mortality laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>. An elegant function for downloading data from Human Mortality Database <http://www.mortality.org> is provided as well.
Author: Marius D. Pascariu [aut, cre], Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>

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Package vertexenum updated to version 1.0.2 with previous version 1.0.1 dated 2015-07-17

Title: Vertex Enumeration of Polytopes
Description: When given a description of a polyhedral set by a system of linear inequalities Ax <= b, produce the list of the vertices of the set.
Author: Robert Robere
Maintainer: Robert Robere <robere@cs.toronto.edu>

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Package emojifont updated to version 0.5.2 with previous version 0.5.1 dated 2017-11-02

Title: Emoji and Font Awesome in Graphics
Description: An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Claus Thorn Ekstrøm [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package visualFields updated to version 0.5.4 with previous version 0.4.3 dated 2016-01-16

Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch <ivan.marin.franch@gmail.com>
Maintainer: Ivan Marin-Franch <ivan.marin.franch@gmail.com>

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Package momentuHMM updated to version 1.4.2 with previous version 1.4.1 dated 2018-05-21

Title: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. These include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>

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Package mice updated to version 3.1.0 with previous version 3.0.0 dated 2018-05-25

Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.
Author: Stef van Buuren [aut, cre], Karin Groothuis-Oudshoorn [aut], Alexander Robitzsch [ctb], Gerko Vink [ctb], Lisa Doove [ctb], Shahab Jolani [ctb], Rianne Schouten [ctb], Philipp Gaffert [ctb], Florian Meinfelder [ctb], Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>

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Package docxtools updated to version 0.1.3 with previous version 0.1.2 dated 2018-06-14

Title: Tools for R Markdown to Docx Documents
Description: A set of helper functions for using R Markdown to create documents in docx format, especially documents for use in a classroom or workshop setting.
Author: Richard Layton [aut, cre]
Maintainer: Richard Layton <graphdoctor@gmail.com>

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Package bfw updated to version 0.1.0 with previous version 0.0.1 dated 2018-06-15

Title: Bayesian Framework for Computational Modeling
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>), the present package aim to provide a framework for conducting Bayesian analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>). The initial version include several modules for conducting Bayesian equivalents of chi-squared tests, analysis of variance (ANOVA), multiple (hierarchical) regression, softmax regression, and for fitting data (e.g., structural equation modeling).
Author: Øystein Olav Skaar [aut, cre]
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>

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Package anipaths updated to version 0.9.6 with previous version 0.9.3 dated 2018-02-21

Title: Animation of Observed Trajectories Using Spline-Based Interpolation
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf
Maintainer: Henry Scharf <henry.scharf@colostate.edu>

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Package rtweet updated to version 0.6.7 with previous version 0.6.0 dated 2017-11-16

Title: Collecting Twitter Data
Description: An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: <https://developer.twitter.com/en/docs>.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>

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Package ncar updated to version 0.4.0 with previous version 0.3.9 dated 2018-05-11

Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method 5) Produce pdf, rtf, text report files. * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package future.apply updated to version 1.0.0 with previous version 0.2.0 dated 2018-05-01

Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Author: Henrik Bengtsson [aut, cre, cph], R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package ecm updated to version 3.1.0 with previous version 3.0.0 dated 2017-12-20

Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>

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Tue, 19 Jun 2018

Package recommenderlab updated to version 0.2-3 with previous version 0.2-2 dated 2017-04-05

Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop recommender algorithms including UBCF, IBCF, FunkSVD and association rule-based algorithms.
Author: Michael Hahsler [aut, cre, cph], Bregt Vereet [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package convey updated to version 0.2.1 with previous version 0.2.0 dated 2017-04-17

Title: Income Concentration Analysis with Complex Survey Samples
Description: Variance estimation on indicators of income concentration and poverty using complex sample survey designs. Wrapper around the survey package.
Author: Djalma Pessoa [aut, cre], Anthony Damico [aut], Guilherme Jacob [aut]
Maintainer: Djalma Pessoa <pessoad@gmail.com>

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Package smapr updated to version 0.1.2 with previous version 0.1.1 dated 2017-10-20

Title: Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
Description: Facilitates programmatic access to NASA Soil Moisture Active Passive (SMAP) data with R. It includes functions to search for, acquire, and extract SMAP data.
Author: Maxwell Joseph [aut, cre], Matthew Oakley [aut], Zachary Schira [aut]
Maintainer: Maxwell Joseph <maxwell.b.joseph@colorado.edu>

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Package arfima updated to version 1.6-7 with previous version 1.6-6 dated 2018-01-06

Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time series, possibly mixed with ARMA, regression, transfer-function components. Exact methods (MLE, forecasting, simulation) are used. Bug reports should be done via GitHub (at <https://github.com/JQVeenstra/arfima>), where the development version of this package lives; it can be installed using devtools.
Author: JQ (Justin) Veenstra [aut, cre], A.I. McLeod [aut]
Maintainer: JQ Veenstra <jqveenstra@gmail.com>

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Package derivmkts updated to version 0.2.3 with previous version 0.2.2.1 dated 2018-04-05

Title: Functions and R Code to Accompany Derivatives Markets
Description: A set of pricing and expository functions that should be useful in teaching a course on financial derivatives.
Author: Robert McDonald [aut, cre, cph]
Maintainer: Robert McDonald <rmcd1024@gmail.com>

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Package httptest updated to version 3.1.0 with previous version 3.0.0 dated 2018-01-16

Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers can be painful. Dealing with authentication, server state, and other complications can make testing seem too costly to bother with. But it doesn't need to be that hard. This package enables one to test all of the logic on the R sides of the API in your package without requiring access to the remote service. Importantly, it provides three contexts that mock the network connection in different ways, as well as testing functions to assert that HTTP requests were---or were not---made. It also allows one to safely record real API responses to use as test fixtures. The ability to save responses and load them offline also enables one to write vignettes and other dynamic documents that can be distributed without access to a live server.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>

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Package spectrolab updated to version 0.0.6 with previous version 0.0.5 dated 2018-06-02

Title: Class and Methods for Hyperspectral Data
Description: Input/Output, processing and visualization of spectra taken with different spectrometers, including SVC (Spectra Vista), ASD and PSR (Spectral Evolution). Implements an S3 class 'spectra' that other packages can build on. Provides methods to access, plot, manipulate, splice sensor overlap, vector normalize and smooth spectra.
Author: Jose Eduardo Meireles [aut, cre], Anna K. Schweiger [aut], Jeannine Cavender-Bares [aut]
Maintainer: Jose Eduardo Meireles <meireles@umn.edu>

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Package spam updated to version 2.2-0 with previous version 2.1-4 dated 2018-04-12

Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64).
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb], Roman Flury [ctb], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

Diff between spam versions 2.1-4 dated 2018-04-12 and 2.2-0 dated 2018-06-19

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Package spam64 updated to version 2.2-0 with previous version 2.1-4 dated 2018-04-12

Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package spam enables the sparse matrix class spam to handle huge sparse matrices with more than 2^31-1 non-zero elements.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb], Roman Flury [ctb], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

Diff between spam64 versions 2.1-4 dated 2018-04-12 and 2.2-0 dated 2018-06-19

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Package cstab updated to version 0.2-2 with previous version 0.2-1 dated 2017-07-04

Title: Selection of Number of Clusters via Normalized Clustering Instability
Description: Selection of the number of clusters in cluster analysis using stability methods.
Author: Jonas M. B. Haslbeck, Dirk U. Wulff
Maintainer: Jonas M. B. Haslbeck <jonas.haslbeck@gmail.com>

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Package umx updated to version 2.8.0 with previous version 2.6.5 dated 2018-04-30

Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models. See '?umx' for help, and file.show(system.file("NEWS", package="umx")) for NEWS.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>

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Package vtreat updated to version 1.2.0 with previous version 1.0.4 dated 2018-05-06

Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. 'vtreat' prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new categorical levels (levels seen during application, but not during training). Reference: "'vtreat': a data.frame Processor for Predictive Modeling", 'Zumel', 'Mount', 2016, DOI:10.5281/zenodo.1173314.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between vtreat versions 1.0.4 dated 2018-05-06 and 1.2.0 dated 2018-06-19

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Package rdiversity updated to version 1.2.1 with previous version 1.2 dated 2018-06-12

Title: Measurement and Partitioning of Similarity-Sensitive Biodiversity
Description: Provides a framework for the measurement and partitioning of the (similarity-sensitive) biodiversity of a metacommunity and its constituent subcommunities. Richard Reeve, et al. (2016) <arXiv:1404.6520v3>.
Author: Sonia Mitchell [aut, cre] (<https://orcid.org/0000-0003-1536-2066>), Richard Reeve [aut] (<https://orcid.org/0000-0003-2589-8091>)
Maintainer: Sonia Mitchell <s.mitchell.2@research.gla.ac.uk>

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Package mfGARCH updated to version 0.1.4 with previous version 0.1.3 dated 2018-05-24

Title: Mixed-Frequency GARCH Models
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: volatility forecasting using multiplicative component GARCH models" by Conrad and Kleen (2018, Working Paper, <doi:10.2139/ssrn.2752354>). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>

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Package docopulae updated to version 0.3.4 with previous version 0.3.3 dated 2016-06-23

Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>

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Package deming updated to version 1.2 with previous version 1.0-1 dated 2014-09-23

Title: Deming, Thiel-Sen and Passing-Bablock Regression
Description: Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>

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Package prodest updated to version 1.0.1 with previous version 0.1.1 dated 2017-07-08

Title: Production Function Estimation
Description: Implements the methods proposed by Olley, G.S. and Pakes, A. (1996) <doi:10.2307/2171831>, Levinsohn, J. and Petrin, A. (2003) <doi:10.1111/1467-937X.00246>, Ackerberg, D.A. and Caves, K. and Frazer, G. (2015) <doi:10.3982/ECTA13408> and Wooldridge, J.M. (2009) <doi:10.1016/j.econlet.2009.04.026> for structural productivity estimation .
Author: Gabriele Rovigatti [aut,cre]
Maintainer: Gabriele Rovigatti <gabriele.rovigatti@gmail.com>

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Package sitar updated to version 1.1.0 with previous version 1.0.10 dated 2017-09-15

Title: Super Imposition by Translation and Rotation Growth Curve Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales. The model was first described by Lindstrom (1995) <doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole et al (2010) <doi:10.1093/ije/dyq115>.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>

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Package PRROC updated to version 1.3.1 with previous version 1.3 dated 2017-04-21

Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau <grau@informatik.uni-halle.de>

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Package RxODE updated to version 0.7.2-5 with previous version 0.7.2-4 dated 2018-06-16

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The VODE and LSODA are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut], Melissa Hallow [aut], Wenping Wang [aut, cre], Zufar Mulyukov [ctb], Justin Wilkins [ctb], Simon Frost [ctb], Heng Li [ctb], Yu Feng [ctb], Alan Hindmarsh [ctb], Linda Petzold [ctb], Ernst Hairer [ctb], Gerhard Wanner [ctb], J Colinge [ctb], Hadley Wickham [ctb], G Grothendieck [ctb], Robert Gentleman [ctb], Ross Ihaka [ctb], R core team [cph], odepack authors [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>

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Permanent link

Package GWSDAT updated to version 3.0.1 with previous version 3.0.0 dated 2017-11-29

Title: GroundWater Spatiotemporal Data Analysis Tool (GWSDAT)
Description: Shiny application for the analysis of groundwater monitoring data, designed to work with simple time-series data for solute concentration and ground water elevation, but can also plot non-aqueous phase liquid (NAPL) thickness if required. Also provides the import of a site basemap in GIS shapefile format.
Author: Wayne W Jones <wayne.w.jones@shell.com>, Andrej Aderhold <andrej.aderhold@protonmail.com>, Ludger Evers <ludger.evers@glasgow.ac.uk>
Maintainer: Andrej Aderhold <andrej.aderhold@protonmail.com>

Diff between GWSDAT versions 3.0.0 dated 2017-11-29 and 3.0.1 dated 2018-06-19

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Permanent link

Package chinese.misc updated to version 0.1.9 with previous version 0.1.8 dated 2018-02-06

Title: Miscellaneous Tools for Chinese Text Mining and More
Description: Efforts are made to make Chinese text mining easier, faster, and robust to errors. Document term matrix can be generated by only one line of code; detecting encoding, segmenting and removing stop words are done automatically. Some convenient tools are also supplied.
Author: Jiang Wu [aut, cre] (from Capital Normal University)
Maintainer: Jiang Wu <textidea@sina.com>

Diff between chinese.misc versions 0.1.8 dated 2018-02-06 and 0.1.9 dated 2018-06-19

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Permanent link

Package tm updated to version 0.7-4 with previous version 0.7-3 dated 2017-12-06

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] (<https://orcid.org/0000-0001-7656-8338>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>

Diff between tm versions 0.7-3 dated 2017-12-06 and 0.7-4 dated 2018-06-19

 DESCRIPTION             |   15 ++++++++-------
 MD5                     |   18 +++++++++---------
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More information about tm at CRAN
Permanent link

Package drake updated to version 5.2.1 with previous version 5.1.2 dated 2018-04-10

Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://ropensci.github.io/drake/> and the online manual <https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre], Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package BETS updated to version 0.4.4 with previous version 0.4.3 dated 2018-06-05

Title: Brazilian Economic Time Series
Description: It provides access to and information about the most important Brazilian economic time series - from the Getulio Vargas Foundation <http://portal.fgv.br/en>, the Central Bank of Brazil <http://www.bcb.gov.br> and the Brazilian Institute of Geography and Statistics <http://www.ibge.gov.br>. It also presents tools for managing, analysing (e.g. generating dynamic reports with a complete analysis of a series) and exporting these time series.
Author: Pedro Costa Ferreira [aut], Talitha Speranza [aut, cre], Jonatha Costa [aut], Fernando Teixeira [ctb], Daiane Marcolino [ctb]
Maintainer: Talitha Speranza <talitha.speranza@fgv.br>

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Package ggimage updated to version 0.1.7 with previous version 0.1.6 dated 2018-05-27

Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package uptasticsearch updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-13

Title: Get Data Frame Representations of 'Elasticsearch' Results
Description: 'Elasticsearch' is an open-source, distributed, document-based datastore (<https://www.elastic.co/products/elasticsearch>). It provides an 'HTTP' 'API' for querying the database and extracting datasets, but that 'API' was not designed for common data science workflows like pulling large batches of records and normalizing those documents into a data frame that can be used as a training dataset for statistical models. 'uptasticsearch' provides an interface for 'Elasticsearch' that is explicitly designed to make these data science workflows easy and fun.
Author: James Lamb [aut, cre], Nick Paras [aut], Austin Dickey [aut], Michael Frasco [ctb], Weiwen Gu [ctb], Will Dearden [ctb], Uptake Technologies Inc. [cph]
Maintainer: James Lamb <james.lamb@uptake.com>

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Package RItools updated to version 0.1-16 with previous version 0.1-15 dated 2016-05-30

Title: Randomization Inference Tools
Description: Tools for randomization inference.
Author: Jake Bowers <jwbowers@illinois.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, and Ben Hansen <ben.hansen@umich.edu>
Maintainer: Jake Bowers <jwbowers@illinois.edu>

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Package Mcomp updated to version 2.8 with previous version 2.7 dated 2018-01-24

Title: Data from the M-Competitions
Description: The 1001 time series from the M-competition (Makridakis et al. 1982) <DOI:10.1002/for.3980010202> and the 3003 time series from the IJF-M3 competition (Makridakis and Hibon, 2000) <DOI:10.1016/S0169-2070(00)00057-1>.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>), Muhammad Akram [ctb], Christoph Bergmeir [ctb] (<https://orcid.org/0000-0002-3665-9021>), Mitchell O'Hara-Wild [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

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Package EmissV updated to version 0.664.7 with previous version 0.664.5 dated 2018-05-31

Title: Vehicular Emissions by Top-Down Methods
Description: Creates emissions for use in air quality models. Vehicular emissions are estimated by a top-down approach, total emissions are calculated using the statistical description of the fleet of vehicles, the emission is spatially distributed according to satellite images or openstreetmap data <https://www.openstreetmap.org> and then distributed temporarily (Vara-Vela et al., 2016, <doi:10.5194/acp-16-777-2016>).
Author: Daniel Schuch [aut, cre] (<https://orcid.org/0000-0001-5977-4519>), Sergio Ibarra-Espinosa [aut] (<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Daniel Schuch <schuch@usp.br>

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Package effects updated to version 4.0-2 with previous version 4.0-1 dated 2018-03-28

Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Michael Friendly [aut], Jangman Hong [aut], Robert Andersen [ctb], David Firth [ctb], Steve Taylor [ctb], R Core Team [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package CAISEr updated to version 0.3.0 with previous version 0.2.1 dated 2017-10-29

Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms using adequate sample sizes for power and accuracy.
Author: Felipe Campelo [aut, cre], Fernanda Takahashi [aut]
Maintainer: Felipe Campelo <fcampelo@ufmg.br>

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Package brranching updated to version 0.3.0 with previous version 0.2.0 dated 2016-04-14

Title: Fetch 'Phylogenies' from Many Sources
Description: Includes methods for fetching 'phylogenies' from a variety of sources, currently includes 'Phylomatic' (<http://phylodiversity.net/phylomatic>), with more in the future.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Mon, 18 Jun 2018

Package httpuv updated to version 1.4.4.1 with previous version 1.4.3 dated 2018-05-10

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>

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Package growthrates updated to version 0.7.2 with previous version 0.7.1 dated 2017-10-22

Title: Estimate Growth Rates from Experimental Data
Description: A collection of methods to determine growth rates from experimental data, in particular from batch experiments and plate reader trials.
Author: Thomas Petzoldt
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>

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Package choiceDes updated to version 0.9-3 with previous version 0.9-1 dated 2014-11-24

Title: Design Functions for Choice Studies
Description: Design functions for DCMs and other types of choice studies (including MaxDiff and other tradeoffs).
Author: Jack Horne [aut, cre]
Maintainer: Jack Horne <jack@jackhorne.net>

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Package rquery updated to version 0.5.0 with previous version 0.4.3 dated 2018-05-07

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 modeling step, 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 rENA updated to version 0.1.5 with previous version 0.1.4 dated 2018-04-19

Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016) <doi:10.18608/jla.2016.33.3>.
Author: Cody L Marquart [aut, cre], Zachari Swiecki [aut], Wesley Collier [aut], Brendan Eagan [aut], Roman Woodward [aut], David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>

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Package grImport updated to version 0.9-1 with previous version 0.9-0 dated 2013-12-11

Title: Importing Vector Graphics
Description: Functions for converting, importing, and drawing PostScript pictures in R plots.
Author: Paul Murrell [aut, cre], Richard Walton [aut], Simon Potter [ctb]
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>

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Package gamclass updated to version 0.58 with previous version 0.57 dated 2018-04-03

Title: Functions and Data for a Course on Modern Regression and Classification
Description: Functions and data are provided that support a course that emphasizes statistical issues of inference and generalizability. Attention is restricted to a relatively small number of methods, often (misleadingly, in my view) referred to as algorithms.
Author: John Maindonald
Maintainer: John Maindonald <jhmaindonald@gmail.com>

Diff between gamclass versions 0.57 dated 2018-04-03 and 0.58 dated 2018-06-18

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More information about gamclass at CRAN
Permanent link

Package asciiSetupReader updated to version 1.4.0 with previous version 1.2 dated 2017-11-26

Title: Reads 'SPSS' and 'SAS' Files from ASCII Data Files (.txt) and Setup Files (.sps or .sas)
Description: Lets you open an 'SPSS' or 'SAS' data file using a .txt file that has the data and a .sps or .sas file with setup instructions. This will only run in a txt-sps or txt-sas pair in which the setup file contains instructions to open that text file. It will NOT open other text files, .sav, .por, or 'SAS' files.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

Diff between asciiSetupReader versions 1.2 dated 2017-11-26 and 1.4.0 dated 2018-06-18

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Package ahnr updated to version 0.3.1 with previous version 0.3.0 dated 2018-06-16

Title: An Implementation of the Artificial Hydrocarbon Networks
Description: Implementation of the Artificial Hydrocarbon Networks for data modeling.
Author: Jose Roberto Ayala Solares [aut, cre]
Maintainer: Jose Roberto Ayala Solares <ichbinjras@gmail.com>

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Package RCzechia updated to version 1.2.5 with previous version 1.2.4 dated 2018-05-11

Title: Spatial Objects of the Czech Republic
Description: Administrative regions, rivers and water bodies of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>

Diff between RCzechia versions 1.2.4 dated 2018-05-11 and 1.2.5 dated 2018-06-18

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Package MetaComp updated to version 1.1.2 with previous version 1.1.1 dated 2018-02-19

Title: EDGE Taxonomy Assignments Visualization
Description: Implements routines for metagenome sample taxonomy assignments collection, aggregation, and visualization. Accepts the EDGE-formatted output from GOTTCHA/GOTTCHA2, BWA, Kraken, MetaPhlAn, DIAMOND, and Pangia. Produces SVG and PDF heatmap-like plots comparing taxa abundances across projects.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <senin@hawaii.edu>

Diff between MetaComp versions 1.1.1 dated 2018-02-19 and 1.1.2 dated 2018-06-18

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Package geoops updated to version 0.2.0 with previous version 0.1.8 dated 2018-03-19

Title: 'GeoJSON' Topology Calculations and Operations
Description: Tools for doing calculations and manipulations on 'GeoJSON', a 'geospatial' data interchange format (<https://tools.ietf.org/html/rfc7946>). 'GeoJSON' is also valid 'JSON'.
Author: Scott Chamberlain [aut, cre], Niels Lohmann [cph]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

Diff between geoops versions 0.1.8 dated 2018-03-19 and 0.2.0 dated 2018-06-18

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Permanent link

Package causalsens updated to version 0.1.2 with previous version 0.1.1 dated 2015-07-01

Title: Selection Bias Approach to Sensitivity Analysis for Causal Effects
Description: The causalsens package provides functions to perform sensitivity analyses and to study how various assumptions about selection bias affects estimates of causal effects.
Author: Matthew Blackwell <mblackwell@gov.harvard.edu.edu>
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>

Diff between causalsens versions 0.1.1 dated 2015-07-01 and 0.1.2 dated 2018-06-18

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Package scrm updated to version 1.7.2-3 with previous version 1.7.2-1 dated 2017-12-07

Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cph, ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab <develop@paulstaab.de>

Diff between scrm versions 1.7.2-1 dated 2017-12-07 and 1.7.2-3 dated 2018-06-18

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Package mgcv updated to version 1.8-24 with previous version 1.8-23 dated 2018-01-14

Title: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Description: Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>

Diff between mgcv versions 1.8-23 dated 2018-01-14 and 1.8-24 dated 2018-06-18

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Package IAPWS95 updated to version 1.1.0 with previous version 1.0.0 dated 2016-09-07

Title: Thermophysical Properties of Water and Steam
Description: Functions for Water and Steam Properties based on the IAPWS Formulation 1995 for the Thermodynamic Properties of Ordinary Water Substance for General and Scientific Use and on the releases for viscosity, conductivity, surface tension and melting pressure.
Author: Benedito Baptista [aut, cre]
Maintainer: Benedito Baptista <bene46@msn.com>

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Package SpaDES.tools updated to version 0.2.0 with previous version 0.1.1 dated 2018-02-01

Title: Additional Tools for Developing Spatially Explicit Discrete Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling tools for developing cellular automata, dynamic raster models, and agent based models in 'SpaDES'. Included are various methods for spatial spreading, spatial agents, GIS operations, random map generation, and others. See '?SpaDES.tools' for an categorized overview of these additional tools.
Author: Alex M Chubaty [aut, cre], Eliot J B McIntire [aut], Yong Luo [ctb], Steve Cumming [ctb], Jean Marchal [ctb], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>

Diff between SpaDES.tools versions 0.1.1 dated 2018-02-01 and 0.2.0 dated 2018-06-18

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Permanent link

Package mdsr updated to version 0.1.6 with previous version 0.1.5 dated 2017-12-20

Title: Complement to 'Modern Data Science with R'
Description: A complement to *Modern Data Science with R* (ISBN: 978-1498724487, publisher URL: <https://www.crcpress.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9781498724487>). This package contains all of the data and code necessary to complete exercises and reproduce examples from the text. It also facilitates connections to the SQL database server used in the book.
Author: Ben Baumer [aut, cre], Nicholas Horton [aut], Daniel Kaplan [aut]
Maintainer: Ben Baumer <ben.baumer@gmail.com>

Diff between mdsr versions 0.1.5 dated 2017-12-20 and 0.1.6 dated 2018-06-18

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Package designmatch updated to version 0.3.1 with previous version 0.3.0 dated 2017-05-17

Title: Matched Samples that are Balanced and Representative by Design
Description: Includes functions for the construction of matched samples that are balanced and representative by design. Among others, these functions can be used for matching in observational studies with treated and control units, with cases and controls, in related settings with instrumental variables, and in discontinuity designs. Also, they can be used for the design of randomized experiments, for example, for matching before randomization. By default, 'designmatch' uses the 'GLPK' optimization solver, but its performance is greatly enhanced by the 'Gurobi' optimization solver and its associated R interface. For their installation, please follow the instructions at <http://user.gurobi.com/download/gurobi-optimizer> and <http://www.gurobi.com/documentation/7.0/refman/r_api_overview.html>. We have also included directions in the gurobi_installation file in the inst folder.
Author: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>, Cinar Kilcioglu <ckilcioglu16@gsb.columbia.edu>, Juan P. Vielma <jvielma@mit.edu>
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>

Diff between designmatch versions 0.3.0 dated 2017-05-17 and 0.3.1 dated 2018-06-18

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Package VineCopula updated to version 2.1.6 with previous version 2.1.5 dated 2018-05-16

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Thomas Nagler [aut, cre], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthias Killiches [ctb], Harry Joe [ctb], Thibault Vatter [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

Diff between VineCopula versions 2.1.5 dated 2018-05-16 and 2.1.6 dated 2018-06-18

 DESCRIPTION                 |    8 
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 NEWS.md                     |   12 
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More information about VineCopula at CRAN
Permanent link

Package Mega2R updated to version 1.0.4 with previous version 1.0.3 dated 2018-05-22

Title: Accessing and Processing a 'Mega2' Genetic Database
Description: Uses as input genetic data that have been reformatted and stored in a 'SQLite' database; this database is initially created by the standalone 'mega2' C++ program (available freely from <https://watson.hgen.pitt.edu/register/>). Loads and manipulates data frames containing genotype, phenotype, and family information from the input 'SQLite' database, and decompresses needed subsets of the genotype data, on the fly, in a memory efficient manner. We have also created several more functions that illustrate how to use the data frames as well as perform useful tasks: these permit one to run the 'pedgene' package to carry out gene-based association tests on family data using selected marker subsets, to run the 'SKAT' package to carry out gene-based association tests using selected marker subsets, to output the 'Mega2R' data as a VCF file and related files (for phenotype and family data), and to convert the data frames into CoreArray Genomic Data Structure (GDS) format.
Author: Robert V. Baron [aut], Daniel E. Weeks [aut, cre], University of Pittsburgh [cph]
Maintainer: Daniel E. Weeks <weeks@pitt.edu>

Diff between Mega2R versions 1.0.3 dated 2018-05-22 and 1.0.4 dated 2018-06-18

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Package bayeslm updated to version 0.8.0 with previous version 0.7.0 dated 2018-02-21

Title: Efficient Sampling for Gaussian Linear Regression with Arbitrary Priors
Description: Efficient sampling for Gaussian linear regression with arbitrary priors, Hahn, He and Hedibert (2018) <arXiv:1806.05738>.
Author: P. Richard Hahn, Jingyu He, Hedibert Lopes
Maintainer: Jingyu He <jingyu.he@chicagobooth.edu>

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Package rdryad updated to version 0.4.0 with previous version 0.3.0 dated 2017-11-06

Title: Access for Dryad Web Services
Description: Interface to the Dryad "Solr" API, their "OAI-PMH" service, and fetch datasets. Dryad (<http://datadryad.org/>) is a curated host of data underlying scientific publications.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Carl Boettiger [aut] (<https://orcid.org/0000-0002-1642-628X>), Karthik Ram [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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More information about rdryad at CRAN
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Package geeM updated to version 0.10.1 with previous version 0.10.0 dated 2016-12-05

Title: Solve Generalized Estimating Equations
Description: GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The 'M' in the name 'geeM' is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.
Author: Lee McDaniel [aut, cre], Nick Henderson [aut], Melanie Prague [ctb] (Suggested code to fix weighting)
Maintainer: Lee McDaniel <lmcda4@lsuhsc.edu>

Diff between geeM versions 0.10.0 dated 2016-12-05 and 0.10.1 dated 2018-06-18

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Package GPrank updated to version 0.1.3 with previous version 0.1.2 dated 2016-12-21

Title: Gaussian Process Ranking of Multiple Time Series
Description: Implements a Gaussian process (GP)-based ranking method which can be used to rank multiple time series according to their temporal activity levels. An example is the case when expression levels of all genes are measured over a time course and the main concern is to identify the most active genes, i.e. genes which show significant non-random variation in their expression levels. This is achieved by computing Bayes factors for each time series by comparing the marginal likelihoods under time-dependent and time-independent GP models. Additional variance information from pre-processing of the observations is incorporated into the GP models, which makes the ranking more robust against model overfitting. The package supports exporting the results to 'tigreBrowser' for visualisation, filtering or ranking.
Author: Hande Topa [aut, cre], Antti Honkela [aut]
Maintainer: Hande Topa <hande.topa@helsinki.fi>

Diff between GPrank versions 0.1.2 dated 2016-12-21 and 0.1.3 dated 2018-06-18

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Package RLumShiny updated to version 0.2.1 with previous version 0.2.0 dated 2017-06-26

Title: 'Shiny' Applications for the R Package 'Luminescence'
Description: A collection of 'shiny' applications for the R package 'Luminescence'. These mainly, but not exclusively, include applications for plotting chronometric data from e.g. luminescence or radiocarbon dating. It further provides access to bootstraps tooltip and popover functionality and contains the 'jscolor.js' library with a custom 'shiny' output binding.
Author: Christoph Burow [aut, cre], Urs Tilmann Wolpert [aut], Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>), R Luminescence Package Team [ctb], Jan Odvarko [cph] (jscolor.js in www/jscolor), AnalytixWare [cph] (ShinySky package), RStudio [cph] (chooser_inputBinding.js in www/ and chooser.R in R/)
Maintainer: Christoph Burow <christoph.burow@uni-koeln.de>

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Package rlfsm updated to version 0.2.0 with previous version 0.1.0 dated 2018-03-15

Title: Simulations and Statistical Inference for Linear Fractional Stable Motions
Description: Contains functions for simulating linear fractional stable motions, according to techniques developed by Stoev and Taqqu (2004) <doi:10.1142/S0218348X04002379>, as well as functions for computing important statistics used with these processes introduced by Mazur, Otryakhin and Podolskij (2018) <arXiv:1802.06373>, and also different quantities related to those statistics.
Author: Dmitry Otryakhin [aut, cre], Stepan Mazur [aut]
Maintainer: Dmitry Otryakhin <d.otryakhin.acad@protonmail.ch>

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Package kofdata updated to version 0.1.3.1 with previous version 0.1.3 dated 2018-02-05

Title: Get Data from the 'KOF Datenservice' API
Description: Read Swiss time series data from the 'KOF Datenservice' API, <https://datenservice.kof.ethz.ch>. The API provides macroeconomic survey data, business cycle and further macro economic time series about Switzerland. The package itself is a set of wrappers around the 'KOF Datenservice' API. The 'kofdata' package is able to consume public information as well as data that requires an API token.
Author: Matthias Bannert [aut, cre], Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>

Diff between kofdata versions 0.1.3 dated 2018-02-05 and 0.1.3.1 dated 2018-06-18

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Package lfe updated to version 2.7-2383 with previous version 2.6-2291 dated 2018-02-16

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>

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Package nomisr updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-19

Title: Access 'Nomis' UK Labour Market Data
Description: Access UK official statistics from the 'Nomis' database. 'Nomis' includes data from the Census, the Labour Force Survey, DWP benefit statistics and other economic and demographic data from the Office for National Statistics, based around statistical geographies. See <https://www.nomisweb.co.uk/api/v01/help> for full API documentation.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>), Paul Egeler [rev, ctb], Christophe Dervieux [rev] (<https://orcid.org/0000-0003-4474-2498>)
Maintainer: Evan Odell <evanodell91@gmail.com>

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Package tsbox updated to version 0.0.3 with previous version 0.0.2 dated 2018-05-14

Title: Class-Agnostic Time Series
Description: Time series toolkit with identical behavior for all time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo', 'timeSeries', 'tsibble'. Also converts reliably between these classes.
Author: Christoph Sax [aut, cre]
Maintainer: Christoph Sax <christoph.sax@gmail.com>

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Package CircularDDM updated to version 0.1.0 with previous version 0.0.9 dated 2017-04-04

Title: Circular Drift-Diffusion Model
Description: Circular drift-diffusion model for continuous reports.
Author: Yi-Shin Lin [aut, cre], Andrew Heathcote [aut], Peter Kvam [aut]
Maintainer: Yi-Shin Lin <yishin.lin@utas.edu.au>

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Sun, 17 Jun 2018

Package refinr updated to version 0.3.1 with previous version 0.3.0 dated 2018-05-06

Title: Cluster and Merge Similar Values Within a Character Vector
Description: These functions take a character vector as input, identify and cluster similar values, and then merge clusters together so their values become identical. The functions are an implementation of the key collision and ngram fingerprint algorithms from the open source tool Open Refine <http://openrefine.org/>. More info on key collision and ngram fingerprint can be found here <https://github.com/OpenRefine/OpenRefine/wiki/Clustering-In-Depth>.
Author: Chris Muir [aut, cre]
Maintainer: Chris Muir <chrismuirRVA@gmail.com>

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Package rgdax updated to version 0.6.0 with previous version 0.5.0 dated 2018-04-08

Title: Wrapper for 'GDAX' Cryptocurrency Exchange
Description: Allow access to both public and private end points to 'GDAX' cryptocurrency exchange. For authenticated flow, users must have valid api, secret and passphrase to be able to connect. Read more details on getting access to 'GDAX' API at: <https://support.gdax.com/customer/en/portal/articles/2425383-how-can-i-create-an-api-key-for-gdax->.
Author: person("Dheeraj", "Agarwal", email = "dheeeraj.agarwal@gmail.com", role = c("aut", "cre"))
Maintainer: Dheeraj Agarwal <dheeeraj.agarwal@gmail.com>

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Package optparse updated to version 1.6.0 with previous version 1.4.4 dated 2017-07-18

Title: Command Line Option Parser
Description: A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
Author: Trevor L Davis [aut, cre], Allen Day [ctb] (Some documentation and examples ported from the getopt package.), Python Software Foundation [ctb] (Some documentation from the optparse Python module.), Steve Lianoglou [ctb], Jim Nikelski [ctb], Kirill Müller [ctb], Peter Humburg [ctb], Rich FitzJohn [ctb], Gyu Jin Choi [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>

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Package iplots updated to version 1.1-7.1 with previous version 1.1-7 dated 2013-12-03

Title: iPlots - interactive graphics for R
Description: Interactive plots for R.
Author: Simon Urbanek <simon.urbanek@r-project.org>, Tobias Wichtrey <tobias@tarphos.de>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>

Diff between iplots versions 1.1-7 dated 2013-12-03 and 1.1-7.1 dated 2018-06-17

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Package hypervolume updated to version 2.0.10 with previous version 2.0.9 dated 2018-05-28

Title: High Dimensional Geometry and Set Operations Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Author: Benjamin Blonder, with contributions from David J. Harris
Maintainer: Benjamin Blonder <bblonder@gmail.com>

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Package spData updated to version 0.2.9.0 with previous version 0.2.8.3 dated 2018-03-25

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

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Package reproducible updated to version 0.2.0 with previous version 0.1.4 dated 2018-01-25

Title: A Set of Tools that Enhance Reproducibility Beyond Package Management
Description: Collection of high-level, robust, machine- and OS-independent tools for making deeply reproducible and reusable content in R. This includes light weight package management (similar to 'packrat' and 'checkpoint', but more flexible, lightweight and simpler than both), tools for caching, downloading and verifying or writing checksums, post-processing of common spatial datasets, and accessing GitHub repositories. Some features are still under active development.
Author: Eliot J B McIntire [aut, cre], Alex M Chubaty [aut], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

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Package MetaLandSim updated to version 1.0.4 with previous version 1.0.3 dated 2018-03-16

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

Diff between MetaLandSim versions 1.0.3 dated 2018-03-16 and 1.0.4 dated 2018-06-17

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Package belg updated to version 0.2.3 with previous version 0.2.1 dated 2018-03-24

Title: Boltzmann Entropy of a Landscape Gradient
Description: Calculates the Boltzmann entropy of a landscape gradient. This package uses the analytical method created by Gao, P., Zhang, H. and Li, Z., 2018 (<doi:10.1111/tgis.12315>). It also extend the original idea by allowing calculations on data with missing values.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>), Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package h2o updated to version 3.20.0.2 with previous version 3.18.0.11 dated 2018-05-24

Title: R Interface for 'H2O'
Description: R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as generalized linear models, gradient boosting machines (including xgboost), random forests, deep neural networks (deep learning), stacked ensembles, naive bayes, cox proportional hazards, k-means, PCA, word2vec, as well as a fully automatic machine learning algorithm (AutoML).
Author: Erin LeDell [aut, cre], Navdeep Gill [aut], Spencer Aiello [aut], Anqi Fu [aut], Arno Candel [aut], Cliff Click [aut], Tom Kraljevic [aut], Tomas Nykodym [aut], Patrick Aboyoun [aut], Michal Kurka [aut], Michal Malohlava [aut], Ludi Rehak [ctb], Eric Eckstrand [ctb], Brandon Hill [ctb], Sebastian Vidrio [ctb], Surekha Jadhawani [ctb], Amy Wang [ctb], Raymond Peck [ctb], Wendy Wong [ctb], Jan Gorecki [ctb], Matt Dowle [ctb], Yuan Tang [ctb], Lauren DiPerna [ctb], H2O.ai [cph, fnd]
Maintainer: Erin LeDell <erin@h2o.ai>

Diff between h2o versions 3.18.0.11 dated 2018-05-24 and 3.20.0.2 dated 2018-06-17

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Package PMCMRplus updated to version 1.1.0 with previous version 1.0.1 dated 2018-04-26

Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended
Description: For one-way layout experiments the one-way ANOVA can be performed as an omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test, Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally distributed residuals and equal within variance are available. Furthermore, all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for normally distributed residuals and heterogeneous variances are provided. Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one tests is provided for non-normally distributed residuals and homogeneous variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and all-pairs tests (Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test, Dunn test, U-test) are given for the analysis of variance by ranks. Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra test, Spearman test) are included. In addition, a Friedman-test for one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack test for unbalanced CRBD is provided with consequent all-pairs tests (Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and many-to-one tests (Nemenyi test, Demsar test, Exact test). A trend can be tested with Pages's test. Durbin's test for a two-way balanced incomplete block design (BIBD) is given in this package as well as Gore's test for CRBD with multiple observations per cell is given. Outlier tests, Mandel's k- and h statistic as well as functions for Type I error and Power analysis as well as generic summary, print and plot methods are provided.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

Diff between PMCMRplus versions 1.0.1 dated 2018-04-26 and 1.1.0 dated 2018-06-17

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