Mon, 21 Aug 2017

Package seplyr updated to version 0.1.4 with previous version 0.1.3 dated 2017-08-01

Title: Standard Evaluation Interfaces for Common 'dplyr' Tasks
Description: The 'seplyr' (standard evaluation data.frame 'dplyr') package supplies standard evaluation adapter methods for important common 'dplyr' methods that currently have a non-standard programming interface. This allows the analyst to use 'dplyr' to perform fundamental data transformation steps such as arranging rows, grouping rows, aggregating selecting columns without having to use learn the details of 'rlang'/'tidyeval' non-standard evaluation and without continuing to rely on now deprecated 'dplyr' "underscore verbs." 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), and 'add_group_indices()' (which adds per-group identifies to a 'data.frame' without depending on row-order).
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package BNSP updated to version 2.0.1 with previous version 2.0.0 dated 2017-08-20

Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for variable selection in mean/variance regression models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>

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Package ProjectionBasedClustering updated to version 1.0.4 with previous version 1.0.2 dated 2017-08-01

Title: Projection Based Clustering
Description: A clustering approach for every projection method based on the generalized U*-matrix visualization of a topographic map is made available here [Thrun/Ultsch,2017] <DOI:10.13140/RG.2.2.13124.53124>. The number of clusters and the cluster structure can be estimated by counting the valleys in a topographic map. If the number of clusters and the clustering method are chosen correctly, then the clusters will be well separated by mountains in the visualization. Most projection methods are wrappers for already available methods in R. However, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.
Author: Michael Thrun [aut, cre], Florian Lerch [aut], Felix Pape [aut], Kristian Nybo [cph], Jarkko Venna [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package BayesBD updated to version 1.2 with previous version 1.1 dated 2016-12-14

Title: Bayesian Inference for Image Boundaries
Description: Provides tools for carrying out a Bayesian analysis of image boundaries. Functions are provided for both binary (Bernoulli) and continuous (Gaussian) images. Examples, along with an interactive shiny function illustrate how to perform simulations, analyze custom data, and plot estimates and credible intervals.
Author: Nicholas Syring, Meng Li
Maintainer: Nicholas Syring <nasyrin@gmail.com>

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Package RJSplot updated to version 2.3 with previous version 2.1 dated 2017-05-19

Title: Interactive Graphs with R
Description: Creates interactive graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package.
Author: Carlos Prieto <cprietos@usal.es>, David Barrios <metal@usal.es>
Maintainer: Carlos Prieto <cprietos@usal.es>

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Package influxdbr updated to version 0.13.0 with previous version 0.12.0 dated 2017-07-13

Title: R Interface to InfluxDB
Description: An R interface to the InfluxDB time series database <https://www.influxdata.com>. This package allows you to fetch and write time series data from/to an InfluxDB server. Additionally, handy wrappers for the Influx Query Language (IQL) to manage and explore a remote database are provided.
Author: Dominik Leutnant [aut, cre]
Maintainer: Dominik Leutnant <leutnant@fh-muenster.de>

Diff between influxdbr versions 0.12.0 dated 2017-07-13 and 0.13.0 dated 2017-08-21

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Package descomponer updated to version 1.4 with previous version 1.3 dated 2017-04-24

Title: Seasonal Adjustment by Frequency Analysis
Description: Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain.
Author: Francisco Parra <parra_fj@cantabria.es>
Maintainer: Francisco Parra <parra_fj@cantabria.es>

Diff between descomponer versions 1.3 dated 2017-04-24 and 1.4 dated 2017-08-21

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Package BeviMed updated to version 5.3 with previous version 5.1 dated 2017-07-03

Title: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Description: A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.
Author: Daniel Greene, Sylvia Richardson and Ernest Turro
Maintainer: Daniel Greene <dg333@cam.ac.uk>

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Package RBesT updated to version 1.2-3 with previous version 1.2-2 dated 2017-07-12

Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases).
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Beat Neuenschwander [ctb], Heinz Schmidli [ctb], Baldur Magnusson [ctb], Yue Li [ctb], Satrajit Roychoudhury [ctb]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

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Package npcp updated to version 0.1-7 with previous version 0.1-6 dated 2015-07-24

Title: Some Nonparametric CUSUM Tests for Change-Point Detection in Possibly Multivariate Observations
Description: Provides nonparametric CUSUM tests for detecting changes in possibly serially dependent univariate or multivariate observations. Tests sensitive to changes in the expectation, the variance, the covariance, the autocovariance, the distribution function, Spearman's rho, Kendall's tau, Gini's mean difference, and the copula are provided, as well as a test for detecting changes in the distribution of independent block maxima (with environmental studies in mind). The latest additions are a test sensitive to changes in the autocopula and a combined test of stationarity sensitive to changes in the distribution function and the autocopula.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>

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Package RVAideMemoire updated to version 0.9-68 with previous version 0.9-66 dated 2017-07-10

Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as much methods from different packages as possible.
Author: Maxime HervÚ
Maintainer: Maxime HervÚ <maxime.herve@univ-rennes1.fr>

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Package revdbayes updated to version 1.2.1 with previous version 1.2.0 dated 2017-07-14

Title: Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis
Description: Provides functions for the Bayesian analysis of extreme value models. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution. The functionality of 'revdbayes' is similar to the 'evdbayes' package <https://cran.r-project.org/package=evdbayes>, which uses Markov Chain Monte Carlo ('MCMC') methods for posterior simulation. See the 'revdbayes' website for more information, documentation and examples.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>

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Package moveVis updated to version 0.9.5 with previous version 0.9.4 dated 2017-06-29

Title: Movement Data Visualization
Description: Tools to visualize movement data of any kind, e. g. by creating path animations from GPS point data.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>

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Package magick updated to version 1.2 with previous version 1.1 dated 2017-08-14

Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package KFAS updated to version 1.2.9 with previous version 1.2.8 dated 2017-06-08

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: State space modelling is an efficient and flexible method for statistical inference of a broad class of time series and other data. KFAS (Helske 2017) <doi:10.18637/jss.v078.i10> includes fast functions for Kalman filtering, smoothing, forecasting, and simulation of multivariate exponential family state space models, with observations from Gaussian, Poisson, binomial, negative binomial, and gamma distributions.
Author: Jouni Helske <jouni.helske@iki.fi>
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package highriskzone updated to version 1.4-1 with previous version 1.3-1 dated 2016-03-11

Title: Determining and Evaluating High-Risk Zones
Description: Functions for determining and evaluating high-risk zones and simulating and thinning point process data, as described in 'Determining high risk zones using point process methodology - Realization by building an R package' Seibold (2012) <http://highriskzone.r-forge.r-project.org/Bachelorarbeit.pdf> and 'Determining high-risk zones for unexploded World War II bombs by using point process methodology', Mahling et al. (2013) <doi:10.1111/j.1467-9876.2012.01055.x>.
Author: Heidi Seibold <Heidi.Seibold@uzh.ch>, Monia Mahling <monia.mahling@stat.uni-muenchen.de>, Sebastian Linne <Sebastian.Linne@campus.lmu.de>, Felix Guenther <felix.guenther@stat.uni-muenchen.de>
Maintainer: Felix Guenther <felix.guenther@stat.uni-muenchen.de>

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Package fastcluster updated to version 1.1.24 with previous version 1.1.23 dated 2017-08-21

Title: Fast Hierarchical Clustering Routines for R and Python
Description: This is a two-in-one package which provides interfaces to both R and Python. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the SciPy package 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the 'flashClust' package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the Python files, see the file INSTALL in the source distribution.
Author: Daniel M├╝llner [aut, cph, cre]
Maintainer: Daniel M├╝llner <daniel@danifold.net>

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Package dartR updated to version 0.93 with previous version 0.91 dated 2017-08-15

Title: Importing and Analysing Snp and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis
Description: Functions are provided that facilitate the import and analysis of snp and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE. Other functions are available for visualization after PCoA, or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip packages etc.
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>

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Package vegdata updated to version 0.9.1 with previous version 0.9 dated 2016-07-15

Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from different sources ( Turboveg <http://www.synbiosys.alterra.nl/turboveg/>; the German national repository <http://www.vegetweb.de> and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", <http://germansl.infinitenature.org>).
Author: Florian Jansen <florian.jansen@uni-rostock.de>
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>

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Package sjstats updated to version 0.11.0 with previous version 0.10.3 dated 2017-07-23

Title: Collection of Convenient Functions for Common Statistical Computations
Description: Collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort (like standard errors or root mean squared errors). Second, these shortcut functions are generic (if appropriate), and can be applied not only to vectors, but also to other objects as well (e.g., the Coefficient of Variation can be computed for vectors, linear models, or linear mixed models; the r2()-function returns the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects). The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models and mixed effects models. However, some of the functions also deal with other statistical measures, like Cronbach's Alpha, Cramer's V, Phi etc.
Author: Daniel L├╝decke <d.luedecke@uke.de>
Maintainer: Daniel L├╝decke <d.luedecke@uke.de>

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Package MANOVA.RM updated to version 0.1.2 with previous version 0.1.1 dated 2017-07-10

Title: Analysis of Multivariate Data and Repeated Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures and general MANOVA designs that do neither assume multivariate normality nor covariance homogeneity, i.e., the procedures are applicable for a wide range of general multivariate factorial designs.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>

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Package DiagrammeR updated to version 0.9.1 with previous version 0.9.0 dated 2017-01-03

Title: Graph/Network Visualization
Description: Graph and network visualization using tabular data.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib, http://github.com/knsv/mermaid/), Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib, http://github.com/cpettitt/dagre-d3), Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib, http://github.com/mdaines/viz.js/), Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>

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 DiagrammeR-0.9.1/DiagrammeR/man/add_node.Rd                                           |   20 
 DiagrammeR-0.9.1/DiagrammeR/man/add_node_df.Rd                                        |    7 
 DiagrammeR-0.9.1/DiagrammeR/man/add_nodes_from_df_cols.Rd                             |   53 
 DiagrammeR-0.9.1/DiagrammeR/man/add_nodes_from_table.Rd                               |   31 
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 DiagrammeR-0.9.1/DiagrammeR/man/add_to_series.Rd                                      |    9 
 DiagrammeR-0.9.1/DiagrammeR/man/cache_edge_attrs.Rd                                   |   50 
 DiagrammeR-0.9.1/DiagrammeR/man/cache_edge_attrs_ws.Rd                                |   70 
 DiagrammeR-0.9.1/DiagrammeR/man/cache_edge_count_ws.Rd                                |   34 
 DiagrammeR-0.9.1/DiagrammeR/man/cache_node_attrs.Rd                                   |   27 
 DiagrammeR-0.9.1/DiagrammeR/man/cache_node_attrs_ws.Rd                                |   40 
 DiagrammeR-0.9.1/DiagrammeR/man/cache_node_count_ws.Rd                                |   16 
 DiagrammeR-0.9.1/DiagrammeR/man/clear_global_graph_attrs.Rd                           |    8 
 DiagrammeR-0.9.1/DiagrammeR/man/clear_selection.Rd                                    |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/colorize_edge_attrs.Rd                                |   35 
 DiagrammeR-0.9.1/DiagrammeR/man/colorize_node_attrs.Rd                                |   54 
 DiagrammeR-0.9.1/DiagrammeR/man/combine_edfs.Rd                                       |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/combine_graphs.Rd                                     |   10 
 DiagrammeR-0.9.1/DiagrammeR/man/combine_ndfs.Rd                                       |    5 
 DiagrammeR-0.9.1/DiagrammeR/man/copy_edge_attrs.Rd                                    |   44 
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 DiagrammeR-0.9.1/DiagrammeR/man/create_graph.Rd                                       |    9 
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 DiagrammeR-0.9.1/DiagrammeR/man/create_random_graph.Rd                                |   11 
 DiagrammeR-0.9.1/DiagrammeR/man/create_series.Rd                                      |   18 
 DiagrammeR-0.9.1/DiagrammeR/man/create_subgraph_ws.Rd                                 |   16 
 DiagrammeR-0.9.1/DiagrammeR/man/delete_edge.Rd                                        |   65 
 DiagrammeR-0.9.1/DiagrammeR/man/delete_edges_ws.Rd                                    |    7 
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 DiagrammeR-0.9.1/DiagrammeR/man/do_dfs.Rd                                             |   27 
 DiagrammeR-0.9.1/DiagrammeR/man/drop_edge_attrs.Rd                                    |   15 
 DiagrammeR-0.9.1/DiagrammeR/man/drop_node_attrs.Rd                                    |   19 
 DiagrammeR-0.9.1/DiagrammeR/man/edge_count.Rd                                         |    3 
 DiagrammeR-0.9.1/DiagrammeR/man/edge_info.Rd                                          |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/edge_present.Rd                                       |   10 
 DiagrammeR-0.9.1/DiagrammeR/man/edge_rel.Rd                                           |   38 
 DiagrammeR-0.9.1/DiagrammeR/man/export_csv.Rd                                         |    4 
 DiagrammeR-0.9.1/DiagrammeR/man/export_graph.Rd                                       |   18 
 DiagrammeR-0.9.1/DiagrammeR/man/from_adj_matrix.Rd                                    |    6 
 DiagrammeR-0.9.1/DiagrammeR/man/from_igraph.Rd                                        |   14 
 DiagrammeR-0.9.1/DiagrammeR/man/generate_dot.Rd                                       |    1 
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 DiagrammeR-0.9.1/DiagrammeR/man/get_betweenness.Rd                                    |   40 
 DiagrammeR-0.9.1/DiagrammeR/man/get_bridging.Rd                                       |   41 
 DiagrammeR-0.9.1/DiagrammeR/man/get_cache.Rd                                          |   27 
 DiagrammeR-0.9.1/DiagrammeR/man/get_closeness.Rd                                      |   41 
 DiagrammeR-0.9.1/DiagrammeR/man/get_closeness_vitality.Rd                             |only
 DiagrammeR-0.9.1/DiagrammeR/man/get_cmty_edge_btwns.Rd                                |   33 
 DiagrammeR-0.9.1/DiagrammeR/man/get_cmty_fast_greedy.Rd                               |   31 
 DiagrammeR-0.9.1/DiagrammeR/man/get_cmty_l_eigenvec.Rd                                |   43 
 DiagrammeR-0.9.1/DiagrammeR/man/get_cmty_louvain.Rd                                   |   32 
 DiagrammeR-0.9.1/DiagrammeR/man/get_cmty_walktrap.Rd                                  |   41 
 DiagrammeR-0.9.1/DiagrammeR/man/get_common_nbrs.Rd                                    |   18 
 DiagrammeR-0.9.1/DiagrammeR/man/get_constraint.Rd                                     |   55 
 DiagrammeR-0.9.1/DiagrammeR/man/get_coreness.Rd                                       |only
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 DiagrammeR-0.9.1/DiagrammeR/man/get_eccentricity.Rd                                   |   51 
 DiagrammeR-0.9.1/DiagrammeR/man/get_edge_attrs.Rd                                     |   67 
 DiagrammeR-0.9.1/DiagrammeR/man/get_edge_attrs_ws.Rd                                  |only
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 DiagrammeR-0.9.1/DiagrammeR/man/get_edge_ids.Rd                                       |   10 
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 DiagrammeR-0.9.1/DiagrammeR/man/get_graph_log.Rd                                      |only
 DiagrammeR-0.9.1/DiagrammeR/man/get_graph_name.Rd                                     |    6 
 DiagrammeR-0.9.1/DiagrammeR/man/get_graph_time.Rd                                     |    4 
 DiagrammeR-0.9.1/DiagrammeR/man/get_jaccard_similarity.Rd                             |   16 
 DiagrammeR-0.9.1/DiagrammeR/man/get_last_edges_created.Rd                             |only
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 DiagrammeR-0.9.1/DiagrammeR/man/get_min_eccentricity.Rd                               |only
 DiagrammeR-0.9.1/DiagrammeR/man/get_min_spanning_tree.Rd                              |   35 
 DiagrammeR-0.9.1/DiagrammeR/man/get_multiedge_count.Rd                                |only
 DiagrammeR-0.9.1/DiagrammeR/man/get_nbrs.Rd                                           |   24 
 DiagrammeR-0.9.1/DiagrammeR/man/get_node_attrs.Rd                                     |   36 
 DiagrammeR-0.9.1/DiagrammeR/man/get_node_attrs_ws.Rd                                  |only
 DiagrammeR-0.9.1/DiagrammeR/man/get_node_df.Rd                                        |   29 
 DiagrammeR-0.9.1/DiagrammeR/man/get_node_ids.Rd                                       |   10 
 DiagrammeR-0.9.1/DiagrammeR/man/get_non_nbrs.Rd                                       |    6 
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 DiagrammeR-0.9.1/DiagrammeR/man/get_selection.Rd                                      |   28 
 DiagrammeR-0.9.1/DiagrammeR/man/get_similar_nbrs.Rd                                   |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/get_successors.Rd                                     |    7 
 DiagrammeR-0.9.1/DiagrammeR/man/get_w_connected_cmpts.Rd                              |   11 
 DiagrammeR-0.9.1/DiagrammeR/man/grViz.Rd                                              |    3 
 DiagrammeR-0.9.1/DiagrammeR/man/grVizOutput.Rd                                        |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/graph_count.Rd                                        |   13 
 DiagrammeR-0.9.1/DiagrammeR/man/graph_info.Rd                                         |    5 
 DiagrammeR-0.9.1/DiagrammeR/man/image_icon.Rd                                         |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/import_graph.Rd                                       |   75 
 DiagrammeR-0.9.1/DiagrammeR/man/invert_selection.Rd                                   |    1 
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 DiagrammeR-0.9.1/DiagrammeR/man/join_node_attrs.Rd                                    |   38 
 DiagrammeR-0.9.1/DiagrammeR/man/layout_nodes_w_string.Rd                              |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/mermaid.Rd                                            |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/mutate_edge_attrs.Rd                                  |  107 
 DiagrammeR-0.9.1/DiagrammeR/man/mutate_node_attrs.Rd                                  |  140 
 DiagrammeR-0.9.1/DiagrammeR/man/node_count.Rd                                         |    9 
 DiagrammeR-0.9.1/DiagrammeR/man/node_info.Rd                                          |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/node_present.Rd                                       |    6 
 DiagrammeR-0.9.1/DiagrammeR/man/node_type.Rd                                          |   24 
 DiagrammeR-0.9.1/DiagrammeR/man/nudge_node_positions_ws.Rd                            |   20 
 DiagrammeR-0.9.1/DiagrammeR/man/open_graph.Rd                                         |only
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 DiagrammeR-0.9.1/DiagrammeR/man/print.dgr_graph.Rd                                    |only
 DiagrammeR-0.9.1/DiagrammeR/man/recode_edge_attrs.Rd                                  |   14 
 DiagrammeR-0.9.1/DiagrammeR/man/recode_node_attrs.Rd                                  |   54 
 DiagrammeR-0.9.1/DiagrammeR/man/remove_from_series.Rd                                 |   13 
 DiagrammeR-0.9.1/DiagrammeR/man/rename_edge_attrs.Rd                                  |   25 
 DiagrammeR-0.9.1/DiagrammeR/man/rename_node_attrs.Rd                                  |   45 
 DiagrammeR-0.9.1/DiagrammeR/man/renderDiagrammeR.Rd                                   |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/renderGrViz.Rd                                        |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/render_graph.Rd                                       |   90 
 DiagrammeR-0.9.1/DiagrammeR/man/render_graph_from_series.Rd                           |   13 
 DiagrammeR-0.9.1/DiagrammeR/man/reorder_graph_actions.Rd                              |only
 DiagrammeR-0.9.1/DiagrammeR/man/replace_in_spec.Rd                                    |    1 
 DiagrammeR-0.9.1/DiagrammeR/man/rescale_edge_attrs.Rd                                 |   55 
 DiagrammeR-0.9.1/DiagrammeR/man/rescale_node_attrs.Rd                                 |   81 
 DiagrammeR-0.9.1/DiagrammeR/man/rev_edge_dir.Rd                                       |   14 
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 DiagrammeR-0.9.1/DiagrammeR/man/select_edges.Rd                                       |   10 
 DiagrammeR-0.9.1/DiagrammeR/man/select_edges_by_edge_id.Rd                            |   27 
 DiagrammeR-0.9.1/DiagrammeR/man/select_edges_by_node_id.Rd                            |   15 
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 DiagrammeR-0.9.1/DiagrammeR/man/select_nodes.Rd                                       |    7 
 DiagrammeR-0.9.1/DiagrammeR/man/select_nodes_by_degree.Rd                             |   40 
 DiagrammeR-0.9.1/DiagrammeR/man/select_nodes_by_id.Rd                                 |    5 
 DiagrammeR-0.9.1/DiagrammeR/man/select_nodes_in_neighborhood.Rd                       |   29 
 DiagrammeR-0.9.1/DiagrammeR/man/series_info.Rd                                        |   29 
 DiagrammeR-0.9.1/DiagrammeR/man/set_cache.Rd                                          |   38 
 DiagrammeR-0.9.1/DiagrammeR/man/set_df_as_edge_attr.Rd                                |only
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 DiagrammeR-0.9.1/DiagrammeR/man/set_edge_attrs.Rd                                     |   36 
 DiagrammeR-0.9.1/DiagrammeR/man/set_edge_attrs_ws.Rd                                  |   22 
 DiagrammeR-0.9.1/DiagrammeR/man/set_global_graph_attrs.Rd                             |    8 
 DiagrammeR-0.9.1/DiagrammeR/man/set_graph_name.Rd                                     |    5 
 DiagrammeR-0.9.1/DiagrammeR/man/set_graph_time.Rd                                     |    5 
 DiagrammeR-0.9.1/DiagrammeR/man/set_graph_undirected.Rd                               |   11 
 DiagrammeR-0.9.1/DiagrammeR/man/set_node_attr_to_display.Rd                           |   14 
 DiagrammeR-0.9.1/DiagrammeR/man/set_node_attr_w_fcn.Rd                                |only
 DiagrammeR-0.9.1/DiagrammeR/man/set_node_attrs.Rd                                     |    7 
 DiagrammeR-0.9.1/DiagrammeR/man/set_node_attrs_ws.Rd                                  |   12 
 DiagrammeR-0.9.1/DiagrammeR/man/set_node_position.Rd                                  |   25 
 DiagrammeR-0.9.1/DiagrammeR/man/subset_series.Rd                                      |   15 
 DiagrammeR-0.9.1/DiagrammeR/man/to_igraph.Rd                                          |    6 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_both.Rd                                          |   68 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_both_edge.Rd                                     |   78 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_in.Rd                                            |   74 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_in_edge.Rd                                       |  190 -
 DiagrammeR-0.9.1/DiagrammeR/man/trav_in_node.Rd                                       |   95 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_out.Rd                                           |   97 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_out_edge.Rd                                      |  114 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_out_node.Rd                                      |   94 
 DiagrammeR-0.9.1/DiagrammeR/man/trav_reverse_edge.Rd                                  |only
 DiagrammeR-0.9.1/DiagrammeR/man/trigger_graph_actions.Rd                              |only
 DiagrammeR-0.9.1/DiagrammeR/man/visnetwork.Rd                                         |    9 
 DiagrammeR-0.9.1/DiagrammeR/man/x11_hex.Rd                                            |    1 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-add_forward_reverse_edges.R           |only
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-add_graphs.R                          |  667 +++-
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-add_node_edge.R                       |  615 +++
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-add_node_edge_df.R                    |   80 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-add_nodes_edges_from_table.R          |  223 -
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-cache_attrs.R                         |  380 +-
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-colorize_nodes_edges.R                |  139 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-combine_graphs.R                      |   46 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-copy_drop_mutate_recode_attrs.R       |  765 ++--
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-create_combine_edges.R                |   58 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-create_combine_nodes.R                |   37 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-create_graph.R                        |  136 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-create_random_graph.R                 |   53 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-create_subgraph.R                     |   23 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-datatable_compatability.R             |   49 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-degree_total_in_out.R                 |only
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-delete_node_edge.R                    |  278 +
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-dfs_bfs.R                             |  105 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-edge_present.R                        |    2 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-edge_relationship.R                   |   75 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_aggregate_degree.R                |only
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_cmty.R                            |   61 
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_graph_metrics.R                   |  562 ++-
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_graph_properties.R                |only
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_node_calculations.R               |  703 ++++
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_nodes_edges.R                     |  236 +
 DiagrammeR-0.9.1/DiagrammeR/tests/testthat/test-get_paths.R                           |  105 
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Package d3r updated to version 0.6.9 with previous version 0.6.8 dated 2017-08-13

Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kent Russell [aut, cre] (R interface), Gregor Aisch [aut, cph] (d3-jetpack creator, https://github.com/gka/d3-jetpack), Adam Pearce [aut] (core contributor to d3-jetpack), Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between d3r versions 0.6.8 dated 2017-08-13 and 0.6.9 dated 2017-08-21

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Package KappaGUI updated to version 2.0.1 with previous version 2.0.0 dated 2017-07-08

Title: GUI for Cohen's and Fleiss' Kappa
Description: A Shiny front-end for the package 'irr' to compute Cohen's and Fleiss' Kappa.
Author: Frederic Santos
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>

Diff between KappaGUI versions 2.0.0 dated 2017-07-08 and 2.0.1 dated 2017-08-21

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Package fastcluster updated to version 1.1.23 with previous version 1.1.22 dated 2016-12-09

Title: Fast Hierarchical Clustering Routines for R and Python
Description: This is a two-in-one package which provides interfaces to both R and Python. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the SciPy package 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the 'flashClust' package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the Python files, see the file INSTALL in the source distribution.
Author: Daniel M├╝llner [aut, cph, cre]
Maintainer: Daniel M├╝llner <daniel@danifold.net>

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Package dynr updated to version 0.1.11-8 with previous version 0.1.11-2 dated 2017-06-16

Title: Dynamic Modeling in R
Description: Intensive longitudinal data have become increasingly prevalent in various scientific disciplines. Many such data sets are noisy, multivariate, and multi-subject in nature. The change functions may also be continuous, or continuous but interspersed with periods of discontinuities (i.e., showing regime switches). The package 'dynr' (Dynamic Modeling in R) is an R package that implements a set of computationally efficient algorithms for handling a broad class of linear and nonlinear discrete- and continuous-time models with regime-switching properties under the constraint of linear Gaussian measurement functions. The discrete-time models can generally take on the form of a state- space or difference equation model. The continuous-time models are generally expressed as a set of ordinary or stochastic differential equations. All estimation and computations are performed in C, but users are provided with the option to specify the model of interest via a set of simple and easy-to-learn model specification functions in R. Model fitting can be performed using single- subject time series data or multiple-subject longitudinal data.
Author: Lu Ou [aut], Michael D. Hunter [aut, cre], Sy-Miin Chow [aut]
Maintainer: Michael D. Hunter <mhunter.ou@gmail.com>

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Package ChemometricsWithR updated to version 0.1.10 with previous version 0.1.9 dated 2015-09-04

Title: Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences
Description: Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
Author: Ron Wehrens
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>

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Package vardpoor updated to version 0.9.8 with previous version 0.9.6 dated 2017-07-08

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

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Package InfoTrad updated to version 1.2 with previous version 1.1 dated 2017-02-11

Title: Calculates the Probability of Informed Trading (PIN)
Description: Estimates the probability of informed trading (PIN) initially introduced by Easley et. al. (1996) <doi:10.1111/j.1540-6261.1996.tb04074.x> . Contribution of the package is that it uses likelihood factorizations of Easley et. al. (2010) <doi:10.1017/S0022109010000074> (EHO factorization) and Lin and Ke (2011) <doi:10.1016/j.finmar.2011.03.001> (LK factorization). Moreover, the package uses different estimation algorithms. Specifically, the grid-search algorithm proposed by Yan and Zhang (2012) <doi:10.1016/j.jbankfin.2011.08.003> , hierarchical agglomerative clustering approach proposed by Gan et. al. (2015) <doi:10.1080/14697688.2015.1023336> and later extended by Ersan and Alici (2016) <doi:10.1016/j.intfin.2016.04.001> .
Author: Duygu Celik and Murat Tinic
Maintainer: Murat Tinic <tinic@bilkent.edu.tr>

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Sun, 20 Aug 2017

Package corpus updated to version 0.9.1 with previous version 0.9.0 dated 2017-08-19

Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, for searching for term occurrences, and for computing term occurrence frequencies (including n-grams).
Author: Patrick O. Perry [aut, cre], Martin Porter and Richard Boulton [ctb, cph] (Snowball), Carlo Strapparava and Alessandro Valitutti [ctb, cph] (WordNet-Affect), Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

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Package MOEADr updated to version 1.0.0 with previous version 0.2.1 dated 2017-03-20

Title: Component-Wise MOEA/D Implementation
Description: Modular implementation of Multiobjective Evolutionary Algorithms based on Decomposition (MOEA/D) [Zhang and Li (2007), <DOI:10.1109/TEVC.2007.892759>] for quick assembling and testing of new algorithmic components, as well as easy replication of published MOEA/D proposals.
Author: Felipe Campelo [aut, cre], Lucas Batista [com], Claus Aranha [aut]
Maintainer: Felipe Campelo <fcampelo@ufmg.br>

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Package RcppArmadillo updated to version 0.7.960.1.1 with previous version 0.7.960.1.0 dated 2017-08-17

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package zonator updated to version 0.5.8 with previous version 0.5.7 dated 2017-07-09

Title: Utilities for Zonation Spatial Conservation Prioritization Software
Description: Create new analysis setups and deal with results of Zonation conservation prioritization software <https://github.com/cbig/zonation-core>. This package uses data available in the 'zdat' (7.7 MB) package for building the vignettes.
Author: Joona Lehtomaki [aut, cre]
Maintainer: Joona Lehtomaki <joona.lehtomaki@gmail.com>

Diff between zonator versions 0.5.7 dated 2017-07-09 and 0.5.8 dated 2017-08-20

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Package stpm updated to version 1.6.8 with previous version 1.6.6 dated 2017-04-07

Title: Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided. For more information, see: (i)"Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al. (2007), Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>; (ii) "Health decline, aging and mortality: how are they related?" by Yashin A. et al. (2007), Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, Liang He, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>

Diff between stpm versions 1.6.6 dated 2017-04-07 and 1.6.8 dated 2017-08-20

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Package edgarWebR updated to version 0.1.1 with previous version 0.1.0 dated 2017-08-15

Title: SEC Filings Access
Description: A set of methods to access and parse live filing information from the U.S. Securities and Exchange Commission (SEC - <https://sec.gov>) including company and fund filings along with all associated metadata.
Author: Micah J Waldstein [aut, cre]
Maintainer: Micah J Waldstein <micah@waldste.in>

Diff between edgarWebR versions 0.1.0 dated 2017-08-15 and 0.1.1 dated 2017-08-20

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Package sjmisc updated to version 2.6.1 with previous version 2.6.0 dated 2017-08-05

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 L├╝decke <d.luedecke@uke.de>
Maintainer: Daniel L├╝decke <d.luedecke@uke.de>

Diff between sjmisc versions 2.6.0 dated 2017-08-05 and 2.6.1 dated 2017-08-20

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Package SpatialExtremes updated to version 2.0-3 with previous version 2.0-2 dated 2015-06-11

Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (althought not completely in agreement with the extreme value theory) are avaible such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Author: Mathieu Ribatet [aut, cre], Richard Singleton [ctb], R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@umontpellier.fr>

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Package latentnet updated to version 2.8.0 with previous version 2.7.1 dated 2015-06-19

Title: Latent Position and Cluster Models for Statistical Networks
Description: Fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre], Mark S. Handcock [aut], Susan M. Shortreed [ctb], Jeremy Tantrum [ctb], Peter D. Hoff [ctb], Li Wang [ctb], Kirk Li [ctb], Jake Fisher [ctb], Jordan T. Bates [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>

Diff between latentnet versions 2.7.1 dated 2015-06-19 and 2.8.0 dated 2017-08-20

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Package httr updated to version 1.3.1 with previous version 1.3.0 dated 2017-08-16

Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package HSAUR2 updated to version 1.1-17 with previous version 1.1-16 dated 2017-06-21

Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Description: Functions, data sets, analyses and examples from the second edition of the book ''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2008). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, the package contains Sweave code for producing slides for selected chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package geojsonio updated to version 0.4.0 with previous version 0.3.8 dated 2017-07-24

Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes, including vectors, lists, data frames, shape files, and spatial classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but rather aims to be a high level client to simplify conversions of data from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre], Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package GeneralizedUmatrix updated to version 0.9.5 with previous version 0.9.4 dated 2017-05-18

Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections from a high-dimensional data space onto a two-dimensional plane are used to detect structures, such as clusters, in multivariate data. The generalized Umatrix is able to visualize errors of these two-dimensional scatter plots by using a 3D topographic map.
Author: Michael Thrun, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>

Diff between GeneralizedUmatrix versions 0.9.4 dated 2017-05-18 and 0.9.5 dated 2017-08-20

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Package ergm updated to version 3.8.0 with previous version 3.7.1 dated 2017-03-21

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis.
Author: Mark S. Handcock [aut], David R. Hunter [aut], Carter T. Butts [aut], Steven M. Goodreau [aut], Pavel N. Krivitsky [aut, cre], Martina Morris [aut], Li Wang [ctb], Kirk Li [ctb], Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>

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Package bookdown updated to version 0.5 with previous version 0.4 dated 2017-05-20

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre], JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Christophe Dervieux [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Peter Hickey [ctb], Sahir Bhatnagar [ctb], Steve Simpson [ctb], Vincent Fulco [ctb], Yixuan Qiu [ctb], Zhuoer Dong [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

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Package mdmb updated to version 0.4-15 with previous version 0.3-11 dated 2017-07-12

Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation. The regression model can be nonlinear (e.g., including interaction or quadratic effects). Multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package easycsv updated to version 1.0.5 with previous version 1.0.2 dated 2017-08-09

Title: Load Multiple 'csv' and 'txt' Tables
Description: Allows users to easily read multiple comma separated tables and create a data frame under the same name. Is able to read multiple comma separated tables from a local directory, a zip file or a zip file on a remote directory.
Author: Dror Bogin [aut, cre]
Maintainer: Dror Bogin <dror.bogin@gmail.com>

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Package BNSP updated to version 2.0.0 with previous version 1.1.1 dated 2017-02-27

Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>

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Sat, 19 Aug 2017

Package rsMove updated to version 0.2.1 with previous version 0.1 dated 2017-07-15

Title: Remote Sensing for Movement Ecology
Description: Tools to analyze animal tracking data with remote sensing.
Author: Ruben Remelgado [aut, cre]
Maintainer: Ruben Remelgado <ruben.remelgado@uni-wuerzburg.de>

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Package NetworkChange updated to version 0.3 with previous version 0.2 dated 2017-05-30

Title: Bayesian Package for Network Changepoint Analysis
Description: Network changepoint analysis for undirected network data. The package implements a hidden Markov multilinear tensor regression model (Park and Sohn, 2017, <http://jhp.snu.ac.kr/NetworkChange.pdf>). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.
Author: Jong Hee Park [aut,cre], Yunkyu Sohn [aut]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>

Diff between NetworkChange versions 0.2 dated 2017-05-30 and 0.3 dated 2017-08-19

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More information about NetworkChange at CRAN
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Package corpus updated to version 0.9.0 with previous version 0.8.0 dated 2017-07-19

Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, for searching for term occurrences, and for computing term occurrence frequencies (including n-grams).
Author: Patrick O. Perry [aut, cre], Martin Porter and Richard Boulton [ctb, cph] (Snowball), Carlo Strapparava and Alessandro Valitutti [ctb, cph] (WordNet-Affect), Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

Diff between corpus versions 0.8.0 dated 2017-07-19 and 0.9.0 dated 2017-08-19

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Package ccRemover updated to version 1.0.4 with previous version 1.0.3 dated 2017-08-12

Title: Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data
Description: Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.
Author: Jun Li [aut, cre], Martin Barron [aut]
Maintainer: Jun Li <jun.li@nd.edu>

Diff between ccRemover versions 1.0.3 dated 2017-08-12 and 1.0.4 dated 2017-08-19

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 MD5                              |    6 +++---
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 inst/doc/ccRemover_tutorial.html |    4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

More information about ccRemover at CRAN
Permanent link

Package blscrapeR updated to version 3.0.0 with previous version 2.1.5 dated 2017-06-19

Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from <https://www.bls.gov/>. The U.S. Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>

Diff between blscrapeR versions 2.1.5 dated 2017-06-19 and 3.0.0 dated 2017-08-19

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Package alleHap updated to version 0.9.9 with previous version 0.9.7 dated 2016-07-17

Title: Allele Imputation and Haplotype Reconstruction from Pedigree Databases
Description: Tools to simulate alphanumeric alleles, impute genetic missing data and reconstruct non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used with simulated datasets or real databases (previously loaded in .ped format). Haplotype reconstruction can be carried out even with missing data, since the program firstly imputes each family genotype (without a reference panel), to later reconstruct the corresponding haplotypes for each family member. All this considering that each individual (due to meiosis) should unequivocally have two alleles per marker (one inherited from each parent) and thus imputation and reconstruction results can be deterministically calculated.
Author: Nathan Medina-Rodriguez and Angelo Santana
Maintainer: Nathan Medina-Rodriguez <nathan.medina@ulpgc.es>

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Package ECharts2Shiny updated to version 0.2.12 with previous version 0.2.11 dated 2017-05-09

Title: Embedding Interactive Charts Generated with ECharts Library into Shiny Applications
Description: Embed interactive charts to their Shiny applications. These charts will be generated by ECharts library developed by Baidu (<http://echarts.baidu.com/>). Current version supports line chart, bar chart, pie chart, scatter plot, gauge, word cloud, radar chart, tree map, and heat map.
Author: Xiaodong Deng [aut, cre], Hao Zhu [ctr], Yiheng Li [ctr], Janet Wagner [ctr]
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>

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Package ordinalNet updated to version 2.1 with previous version 2.0 dated 2017-05-08

Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty. Supported model families include cumulative probability, stopping ratio, continuation ratio, and adjacent category. These families are a subset of vector glm's which belong to a model class we call the elementwise link multinomial-ordinal (ELMO) class. Each family in this class links a vector of covariates to a vector of class probabilities. Each of these families has a parallel form, which is appropriate for ordinal response data, as well as a nonparallel form that is appropriate for an unordered categorical response, or as a more flexible model for ordinal data. The parallel model has a single set of coefficients, whereas the nonparallel model has a set of coefficients for each response category except the baseline category. It is also possible to fit a model with both parallel and nonparallel terms, which we call the semi-parallel model. The semi-parallel model has the flexibility of the nonparallel model, but the elastic net penalty shrinks it toward the parallel model.
Author: Michael Wurm [aut, cre], Paul Rathouz [aut], Bret Hanlon [aut]
Maintainer: Michael Wurm <wurm@wisc.edu>

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Fri, 18 Aug 2017

Package getCRUCLdata updated to version 0.1.9 with previous version 0.1.8 dated 2017-07-08

Title: Use and Explore CRU CL v. 2.0 Climatology Elements in R
Description: Provides functions that automate downloading and importing University of East Anglia Climate Research Unit (CRU) CL v. 2.0 climatology data into R, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a tidy data frame as a tibble or a list of raster stack objects for use in an R session. CRU CL v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arcminutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (http://orcid.org/0000-0002-0061-8359)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package GSODR updated to version 1.0.5 with previous version 1.0.4 dated 2017-07-23

Title: Global Summary Daily Weather Data in R
Description: Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day (GSOD) weather data from the from the USA National Centers for Environmental Information (NCEI) for use in R. Units are converted from from United States Customary System (USCS) units to International System of Units (SI). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure (es), actual vapour pressure (ea) and relative humidity are calculated from the original data and included in the final data set. The resulting data include station identification information, state, country, latitude, longitude, elevation, weather observations and associated flags. Data may be automatically saved to disk. File output may be returned as a comma-separated values (CSV) or GeoPackage (GPKG) file. Additional data are included with this R package: a list of elevation values for stations between -60 and 60 degrees latitude derived from the Shuttle Radar Topography Measuring Mission (SRTM). For information on the GSOD data from NCEI, please see the GSOD readme.txt file available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (http://orcid.org/0000-0002-0061-8359), Tomislav Hengl [aut] (http://orcid.org/0000-0002-9921-5129), Andrew Nelson [aut] (http://orcid.org/0000-0002-7249-3778)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package MetFns updated to version 3.0.0 with previous version 2.2.0 dated 2017-02-01

Title: Analysis of Visual Meteor Data
Description: Functions for selection of visual meteor data, calculations of Zenithal Hourly Rate (ZHR) and population index, graphics of population index, ZHR and magnitude distribution.
Author: Kristina Veljkovic
Maintainer: Kristina Veljkovic <mackikac@gmail.com>

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Package rWind updated to version 0.3.0 with previous version 0.2.0 dated 2017-06-12

Title: Download, Edit and Transform Wind Data from GFS
Description: Tools for downloading, editing and transforming wind data from Global Forecast System (GFS, see <https://www.ncdc.noaa.gov/data-access/model-data/model-datasets/global-forcast-system-gfs>) of the USA's National Weather Service (NWS, see <http://www.weather.gov/>).
Author: Javier Fernández-López [aut, cre], Klaus Schliep [aut]
Maintainer: Javier Fernández-López <jflopez@rjb.csic.es>

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Package HSAUR3 updated to version 1.0-8 with previous version 1.0-7 dated 2017-06-21

Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Description: Functions, data sets, analyses and examples from the third edition of the book ''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides). The publishers web page is '<http://www.crcpress.com/product/isbn/9781482204582>'.
Author: Torsten Hothorn and Brian S. Everitt
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package HSAUR updated to version 1.3-9 with previous version 1.3-8 dated 2017-06-21

Title: A Handbook of Statistical Analyses Using R (1st Edition)
Description: Functions, data sets, analyses and examples from the book ''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2006). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available.
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package wppExplorer updated to version 2.1-1 with previous version 2.1-0 dated 2017-06-29

Title: Explorer of World Population Prospects
Description: Explore data in the 'wpp2017' (or 2015, 2012, 2010) package using a 'shiny' interface.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package mpath updated to version 0.3-3 with previous version 0.2-4 dated 2016-08-30

Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>

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Package ivmodel updated to version 1.7 with previous version 1.6 dated 2017-05-04

Title: Statistical Inference and Sensitivity Analysis for Instrumental Variables Model
Description: Contains functions for carrying out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics.
Author: Yang Jiang, Hyunseung Kang, Dylan Small, and Qingyuan Zhao
Maintainer: Hyunseung Kang <hyunseung@stat.wisc.edu>

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Package Surrogate updated to version 0.4 with previous version 0.2 dated 2017-06-05

Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

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Package FedData updated to version 2.4.6 with previous version 2.4.5 dated 2017-03-01

Title: Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from six datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 3, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>

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Package dataone updated to version 2.1.0 with previous version 2.0.1 dated 2016-08-29

Title: R Interface to the DataONE REST API
Description: Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Rob Nahf [aut], Carl Boettiger [aut], Chris Jones [aut], Jordan Read [aut], Lauren Walker [aut], Edmund Hart [aut], Scott Chamberlain [aut], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>

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More information about dataone at CRAN
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Package ahnr updated to version 0.2.0 with previous version 0.1.0 dated 2017-07-08

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>

Diff between ahnr versions 0.1.0 dated 2017-07-08 and 0.2.0 dated 2017-08-18

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Package rrecsys updated to version 0.9.7.1 with previous version 0.9.5.4 dated 2016-06-27

Title: Environment for Evaluating Recommender Systems
Description: Processes standard recommendation datasets (e.g., a user-item rating matrix) as input and generates rating predictions and lists of recommended items. Standard algorithm implementations which are included in this package are the following: Global/Item/User-Average baselines, Weighted Slope One, Item-Based KNN, User-Based KNN, FunkSVD, BPR and weighted ALS. They can be assessed according to the standard offline evaluation methodology (Shani, et al. (2011) <doi:10.1007/978-0-387-85820-3_8>) for recommender systems using measures such as MAE, RMSE, Precision, Recall, F1, AUC, NDCG, RankScore and coverage measures. The package (Coba, et al.(2017) <doi: 10.1007/978-3-319-60042-0_36>) is intended for rapid prototyping of recommendation algorithms and education purposes.
Author: Ludovik Çoba [aut, cre, cph], Markus Zanker [ctb], Panagiotis Symeonidis [ctb]
Maintainer: Ludovik Çoba <Ludovik.Coba@inf.unibz.it>

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Package RInno updated to version 0.1.0 with previous version 0.0.3 dated 2017-03-31

Title: An Installation Framework for Shiny Apps
Description: Installs shiny apps using Inno Setup, an open source software that builds installers for Windows programs <http://www.jrsoftware.org/ishelp/>.
Author: Jon Hill [aut, cre, cph], W. Lee Pang [aut, cph] (DesktopDeployR project at https://github.com/wleepang/DesktopDeployR), Hanjo Odendaal [ctb]
Maintainer: Jon Hill <jon.mark.hill@gmail.com>

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Package batchtools updated to version 0.9.5 with previous version 0.9.4 dated 2017-08-07

Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<http://www-03.ibm.com/systems/spectrum-computing/products/lsf/>), 'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>), 'TORQUE/PBS' (<http://www.adaptivecomputing.com/products/open-source/torque/>), or 'Docker Swarm' (<https://docs.docker.com/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut], Bernd Bischl [aut], Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

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Package tsBSS updated to version 0.3.1 with previous version 0.3 dated 2017-07-03

Title: Tools for Blind Source Separation and Supervised Dimension Reduction for Time Series
Description: Different estimates are provided to solve the blind source separation problem for multivariate time series with stochastic volatility and supervised dimension reduction problem for multivariate time series.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Markus Matilainen <markus.matilainen@utu.fi>

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Package CIAAWconsensus updated to version 1.2 with previous version 1.1 dated 2016-12-31

Title: Isotope Ratio Meta-Analysis
Description: Calculation of consensus values for atomic weights, isotope amount ratios, and isotopic abundances with the associated uncertainties using multivariate meta-regression approach for consensus building.
Author: Juris Meija and Antonio Possolo
Maintainer: Juris Meija <juris.meija@nrc-cnrc.gc.ca>

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Package ImputeRobust updated to version 1.2 with previous version 1.1-2 dated 2017-04-20

Title: Robust Multiple Imputation with Generalized Additive Models for Location Scale and Shape
Description: Provides new imputation methods for the 'mice' package based on generalized additive models for location, scale, and shape (GAMLSS) as described in de Jong, van Buuren and Spiess <doi:10.1080/03610918.2014.911894>.
Author: Daniel Salfran [aut, cre], Martin Spiess [aut, ths]
Maintainer: Daniel Salfran <daniel.salfran@uni-hamburg.de>

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Package timetools updated to version 1.12.0 with previous version 1.11.4 dated 2017-04-10

Title: Seasonal/Sequential (Instants/Durations, Even or not) Time Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>

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Package document updated to version 2.1.0 with previous version 2.0.0 dated 2017-08-04

Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation comments for one of your functions that was not part of one of your packages (yet)? This is exactly what this package is about: running 'roxygen2' on (chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>

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Package dataPreparation updated to version 0.2 with previous version 0.1 dated 2017-07-08

Title: Automated Data Preparation
Description: Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of data.table efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Author: Emmanuel-Lin Toulemonde [aut, cre]
Maintainer: Emmanuel-Lin Toulemonde <el.toulemonde@protonmail.com>

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Package mHG updated to version 1.1 with previous version 1.0 dated 2015-07-26

Title: Minimum-Hypergeometric Test
Description: Runs a minimum-hypergeometric (mHG) test as described in: Eden, E. (2007). Discovering Motifs in Ranked Lists of DNA Sequences. Haifa.
Author: Kobi Perl
Maintainer: Kobi Perl <kobipe3@gmail.com>

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Thu, 17 Aug 2017

Package RefManageR updated to version 0.14.20 with previous version 0.14.12 dated 2017-07-04

Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>

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Package metacom updated to version 1.4.7 with previous version 1.4.6 dated 2017-03-29

Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas <tdallas@ucdavis.edu>

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Package inlmisc updated to version 0.3.2 with previous version 0.3.1 dated 2017-08-14

Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics, performing raster-based analysis, processing MODFLOW-based models, etc. Used to support packages and scripts written by researchers at the United States Geological Survey (USGS) Idaho National Laboratory (INL) Project Office.
Author: Jason C. Fisher [aut, cre]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>

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Package gamCopula updated to version 0.0-4 with previous version 0.0-3 dated 2017-08-14

Title: Generalized Additive Models for Bivariate Conditional Dependence Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to apply generalized additive models to bivariate dependence structures and non-simplified vine copulas.
Author: Thomas Nagler [aut], Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>

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Package compareGroups updated to version 3.3 with previous version 3.2.4 dated 2017-03-14

Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as?publication-ready univariate or bivariate tables?in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures?to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics?(mean, median, frequencies, incidences, etc.). Perform the appropriate tests?(t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data?(Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, H\'ector Sanz, Gavin Lucas, Judith Pe\~nafiel and David Gim\'enez
Maintainer: Isaac Subirana <isubirana@imim.es>

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Package SiMRiv updated to version 1.0.1 with previous version 1.0.0 dated 2017-07-27

Title: Individual-Based, Spatially-Explicit Simulation and Analysis of Multi-State Movements in River Networks, Homogeneous, and Heterogeneous Landscapes
Description: Provides functions to generate and analyze individual-based spatially-explicit simulations of multi-state movements in heterogeneous landscapes, based on "resistance" rasters. Although originally conceived and designed to simulate spatially-explicit trajectories of species constrained to linear habitats or dendritic ecological networks (e.g., river networks), the simulation algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently on the landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as mechanistic null models to test e.g. for species site fidelity and other 'Movement Ecology' hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), or for other predictive purposes. The package should thus be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface of animal behaviour, landscape, spatial and movement ecology, disease and invasive species spread, and population dynamics.
Author: Lorenzo Quaglietta [aut], Miguel Porto [aut, cre], Erida Gjini [ctb]
Maintainer: Miguel Porto <mpbertolo@gmail.com>

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Package polysat updated to version 1.7-2 with previous version 1.7-1 dated 2017-07-23

Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi', 'POPDIST', 'STRand', and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics and Polymorphic Information Content are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise or global differentiation statistics based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci. polysat is described by Clark and Jasieniuk (2011) <doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2016) <doi:10.1111/1755-0998.12639>.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>

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Package FuzzyLP updated to version 0.1-5 with previous version 0.1-4 dated 2017-06-25

Title: Fuzzy Linear Programming
Description: Provides methods to solve Fuzzy Linear Programming Problems with fuzzy constraints (following different approaches proposed by Verdegay, Zimmermann, Werners and Tanaka), fuzzy costs, and fuzzy technological matrix.
Author: Carlos A. Rabelo [aut, cre], Pablo J. Villacorta [ctb]
Maintainer: Carlos A. Rabelo <carabelo@gmail.com>

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Package bayesDP updated to version 1.2.2 with previous version 1.2.1 dated 2017-08-01

Title: Tools for the Bayesian Discount Prior Function
Description: Functions for data augmentation using the Bayesian discount prior function for 1 arm and 2 arm clinical trials.
Author: Shawn Balcome [cre], Donnie Musgrove [aut], Tarek Haddad [aut], Christopher Jackson [ctb] (For the ppexp R code that was ported to C++.)
Maintainer: Shawn Balcome <sbalcome@mdic.org>

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Package zipfR updated to version 0.6-10 with previous version 0.6-6 dated 2012-04-03

Title: Statistical Models for Word Frequency Distributions
Description: Statistical models and utilities for the analysis of word frequency distributions. The utilities include functions for loading, manipulating and visualizing word frequency data and vocabulary growth curves. The package also implements several statistical models for the distribution of word frequencies in a population. (The name of this package derives from the most famous word frequency distribution, Zipf's law.)
Author: Stefan Evert <stefan.evert@fau.de>, Marco Baroni <marco.baroni@unitn.it>
Maintainer: Stefan Evert <stefan.evert@fau.de>

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Package servr updated to version 0.7 with previous version 0.6 dated 2017-05-12

Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.
Author: Yihui Xie [aut, cre], Carson Sievert [ctb], Jesse Anderson [ctb], Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package PowerTOST updated to version 1.4-6 with previous version 1.4-5 dated 2017-05-20

Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability and/or uncertain theta0. ----- Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval). ----- Contains further functions for power and sample size calculations based on non-inferiority t-test. This is not a TOST procedure but eventually useful if the question of 'non-superiority' must be evaluated. The power and sample size calculations based on non-inferiority test may also performed via 'expected' power in case of uncertain (estimated) variability and/or uncertain theta0. ----- Contains functions power.scABEL() and sampleN.scABEL() to calculate power and sample size for the BE decision via scaled (widened) BE acceptance limits (EMA recommended) based on simulations. Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively adjust alpha in order to maintain the overall consumer risk in ABEL studies and adapt the sample size for the loss in power. Contains further functions power.RSABE() and sampleN.RSABE() to calculate power and sample size for the BE decision via reference scaled ABE criterion according to the FDA procedure based on simulations. Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate power and sample size for the BE decision via the FDA procedure for NTID's based on simulations. Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate power and sample size for the BE decision via the FDA procedure for highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances) ----- Contains functions for power analysis of a sample size plan for ABE (pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA()) analysing power if deviating from assumptions of the plan. ----- Contains further functions for power calculations / sample size estimation for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre], Helmut Schuetz [aut], Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>

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Package opencpu updated to version 2.0.4 with previous version 2.0.3 dated 2017-06-25

Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package mixOmics updated to version 6.2.0 with previous version 6.1.3 dated 2017-05-11

Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <kimanh.lecao@unimelb.edu.au>

Diff between mixOmics versions 6.1.3 dated 2017-05-11 and 6.2.0 dated 2017-08-17

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Package leaflet.minicharts updated to version 0.5.1 with previous version 0.5.0 dated 2017-07-10

Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with package 'leaflet'. These charts can be used to represent at same time multiple variables on a single map.
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between leaflet.minicharts versions 0.5.0 dated 2017-07-10 and 0.5.1 dated 2017-08-17

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Package ecoengine updated to version 1.11.0 with previous version 1.10.0 dated 2016-05-24

Title: Programmatic Interface to the Web Service Methods Provided by UC Berkeley's Natural History Data
Description: The ecoengine ('ecoengine'; <https://ecoengine.berkeley.edu/>). provides access to more than 5 million georeferenced specimen records from the University of California, Berkeley's Natural History Museums.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>

Diff between ecoengine versions 1.10.0 dated 2016-05-24 and 1.11.0 dated 2017-08-17

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Package multigraph updated to version 0.71 with previous version 0.60 dated 2017-05-04

Title: Plot and Manipulate Multigraphs
Description: Functions to plot and manipulate multigraphs, signed, weighted multigraphs, and bipartite graphs with different layout options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>

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Package wpp2017 updated to version 1.1-0 with previous version 1.0-1 dated 2017-06-29

Title: World Population Prospects 2017
Description: Provides data from the United Nation's World Population Prospects 2017.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package RcppArmadillo updated to version 0.7.960.1.0 with previous version 0.7.900.2.0 dated 2017-06-04

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package wru updated to version 0.1-6 with previous version 0.1-5 dated 2017-06-08

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

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Package textmineR updated to version 2.0.6 with previous version 2.0.5 dated 2017-04-07

Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that should be familiar to experienced R users. Provides a wrapper for several topic models that take similarly-formatted input and give similarly-formatted output. Has additional functionality for analyzing and diagnostics for topic models.
Author: Thomas Jones [aut, cre], William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>

Diff between textmineR versions 2.0.5 dated 2017-04-07 and 2.0.6 dated 2017-08-17

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Package outbreaker updated to version 1.1-8 with previous version 1.1-7 dated 2015-12-07

Title: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.
Author: Thibaut Jombart <thibautjombart@gmail.com>, Anne Cori, Joel Hellewell
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

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