Mon, 15 Oct 2018

Package marmap updated to version 1.0.2 with previous version 1.0.1 dated 2018-09-22

Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <http://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <http://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>

Diff between marmap versions 1.0.1 dated 2018-09-22 and 1.0.2 dated 2018-10-15

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Package crminer updated to version 0.2.0 with previous version 0.1.4 dated 2017-08-12

Title: Fetch 'Scholary' Full Text from 'Crossref'
Description: Text mining client for 'Crossref' (<https://crossref.org>). Includes functions for getting getting links to full text of articles, fetching full text articles from those links or Digital Object Identifiers ('DOIs'), and text extraction from 'PDFs'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

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Package cosinor2 updated to version 0.2.1 with previous version 0.2.0 dated 2018-10-01

Title: Extended Tools for Cosinor Analysis of Rhythms
Description: Statistical procedures for calculating population–mean cosinor, non–stationary cosinor, estimation of best–fitting period, tests of population rhythm differences and more. See Cornélissen, G. (2014). <doi:10.1186/1742-4682-11-16>.
Author: Augustin Mutak <mutak94@gmail.com>
Maintainer: Augustin Mutak <mutak94@gmail.com>

Diff between cosinor2 versions 0.2.0 dated 2018-10-01 and 0.2.1 dated 2018-10-15

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Package ungroup updated to version 1.1.1 with previous version 1.1.0 dated 2018-09-30

Title: Penalized Composite Link Model for Efficient Estimation of Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data) assuming that counts are Poisson distributed and that the underlying sequence on a fine grid to be estimated is smooth. The method is based on the composite link model and estimation is achieved by maximizing a penalized likelihood. Smooth detailed sequences of counts and rates are so estimated from the binned counts. Ungrouping binned data can be desirable for many reasons: Bins can be too coarse to allow for accurate analysis; comparisons can be hindered when different grouping approaches are used in different histograms; and the last interval is often wide and open-ended and, thus, covers a lot of information in the tail area. Age-at-death distributions grouped in age classes and abridged life tables are examples of binned data. Because of modest assumptions, the approach is suitable for many demographic and epidemiological applications. For a detailed description of the method and applications see Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Author: Marius D. Pascariu [aut, cre] (<https://orcid.org/0000-0002-2568-6489>), Silvia Rizzi [aut], Jonas Schoeley [aut] (<https://orcid.org/0000-0002-3340-8518>), Maciej J. Danko [aut] (<https://orcid.org/0000-0002-7924-9022>)
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>

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Package hdme updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-19

Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for measurement error problems (aka. errors-in-variables). The package contains a version of the lasso (L1-penalization) which corrects for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>). It also contains an implementation of the Generalized Matrix Uncertainty Selector, which is a version the (Generalized) Dantzig Selector for the case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package define updated to version 0.2.8 with previous version 0.2.7 dated 2018-03-13

Title: Create FDA-Style Data and Program Definitions
Description: Creates a directory of archived files with a descriptive 'PDF' document at the root level (i.e. 'define.pdf') containing tables of definitions of data items and relative-path hyperlinks to the documented files. Converts file extensions to 'txt' per FDA expectations and converts 'CSV' files to 'SAS' Transport format. Relies on data item descriptors stored as per R package 'spec'. See 'package?define'. See also '?define'. Requires a compatible installation of 'pdflatex', e.g. <https://miktex.org/>.
Author: Tim Bergsma [aut, cre], Scott Pivirotto [ctb]
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package decisionSupport updated to version 1.103.8 with previous version 1.103.7 dated 2018-05-15

Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based decision making processes using Monte Carlo simulations. Decision support is given on two levels: (i) The actual decision level is to choose between two alternatives under probabilistic uncertainty. This package calculates the optimal decision based on maximizing expected welfare. (ii) The meta decision level is to allocate resources to reduce the uncertainty in the underlying decision problem, i.e to increase the current information to improve the actual decision making process. This problem is dealt with using the Value of Information Analysis. The Expected Value of Information for arbitrary prospective estimates can be calculated as well as Individual Expected Value of Perfect Information. The probabilistic calculations are done via Monte Carlo simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (ICRAF), Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting), World Agroforesrtry Centre (ICRAF) [cph]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

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Package stormwindmodel updated to version 0.1.1 with previous version 0.1.0 dated 2017-01-09

Title: Model Tropical Cyclone Wind Speeds
Description: Allows users to input tracking data for a hurricane or other tropical storm, along with a data frame of grid points at which to model wind speeds. Functions in this package will then calculate wind speeds at each point based on wind model equations. This modeling framework is currently set up to model winds for North American locations with Atlantic basin storms. This work was supported in part by grants from the National Institute of Environmental Health Sciences (R00ES022631), the National Science Foundation (1331399), and the Department of Energy (DE-FG02-08ER64644).
Author: Brooke Anderson [aut, cre], Andrea Schumacher [aut], Seth Guikema [aut], Steven Quiring [aut], Joshua Ferreri [aut], Andrea Staid [ctb], Michael Guo [ctb], Lei Ming [ctb], Laiyin Zhu [ctb]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>

Diff between stormwindmodel versions 0.1.0 dated 2017-01-09 and 0.1.1 dated 2018-10-15

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 stormwindmodel-0.1.1/stormwindmodel/DESCRIPTION                                                                          |   27 
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 stormwindmodel-0.1.1/stormwindmodel/build/vignette.rds                                                                   |binary
 stormwindmodel-0.1.1/stormwindmodel/inst/doc/Details.R                                                                   |   47 
 stormwindmodel-0.1.1/stormwindmodel/inst/doc/Details.Rmd                                                                 |   50 
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 stormwindmodel-0.1.1/stormwindmodel/inst/doc/Overview.R                                                                  |   65 
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 stormwindmodel-0.1.1/stormwindmodel/man/add_forward_speed.Rd                                                             |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/add_inflow.Rd                                                                    |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/add_storm_track.Rd                                                               |    5 
 stormwindmodel-0.1.1/stormwindmodel/man/add_wind_radii.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_R1.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_and_summarize_grid_wind.Rd                                                  |    8 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_bearing.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_forward_speed.Rd                                                            |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_gradient_speed.Rd                                                           |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_grid_wind.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/check_over_land.Rd                                                               |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/county_points.Rd                                                                 |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/create_full_track.Rd                                                             |    4 
 stormwindmodel-0.1.1/stormwindmodel/man/degrees_to_radians.Rd                                                            |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/figures                                                                          |only
 stormwindmodel-0.1.1/stormwindmodel/man/floyd_tracks.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/get_grid_winds.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/gradient_to_surface.Rd                                                           |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/interp_track.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/katrina_tracks.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/landmask.Rd                                                                      |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/latlon_to_km.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/map_wind.Rd                                                                      |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/radians_to_degrees.Rd                                                            |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/remove_forward_speed.Rd                                                          |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/solve_for_xi.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/summarize_grid_wind.Rd                                                           |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will1.Rd                                                                         |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will10a.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will10b.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will10c.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will1a.Rd                                                                        |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will2.Rd                                                                         |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will3_deriv_func.Rd                                                              |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will3_right.Rd                                                                   |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will7a.Rd                                                                        |    1 
 stormwindmodel-0.1.1/stormwindmodel/vignettes/Details.Rmd                                                                |   50 
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Package dLagM updated to version 1.0.8 with previous version 1.0.7 dated 2018-09-27

Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>

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Sun, 14 Oct 2018

Package paran updated to version 1.5.2 with previous version 1.5.1 dated 2012-09-10

Title: Horn's Test of Principal Components/Factors
Description: An implementation of Horn's technique for numerically and graphically evaluating the components or factors retained in a principle components analysis (PCA) or common factor analysis (FA). Horn's method contrasts eigenvalues produced through a PCA or FA on a number of random data sets of uncorrelated variables with the same number of variables and observations as the experimental or observational data set to produce eigenvalues for components or factors that are adjusted for the sample error-induced inflation. Components with adjusted eigenvalues greater than one are retained. paran may also be used to conduct parallel analysis following Glorfeld's (1995) suggestions to reduce the likelihood of over-retention.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>

Diff between paran versions 1.5.1 dated 2012-09-10 and 1.5.2 dated 2018-10-14

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Package analytics updated to version 3.0 with previous version 2.0 dated 2017-06-14

Title: Regression Outlier Detection, Stationary Bootstrap, Testing Weak Stationarity, NA Imputation, and Other Tools for Data Analysis
Description: Current version includes outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, missing value imputation, column/rows sums/means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.
Author: Albert Dorador
Maintainer: Albert Dorador <albert.dorador.chalar@gmail.com>

Diff between analytics versions 2.0 dated 2017-06-14 and 3.0 dated 2018-10-14

 analytics-2.0/analytics/R/rowmeanV2.R            |only
 analytics-3.0/analytics/DESCRIPTION              |   18 +--
 analytics-3.0/analytics/MD5                      |   22 ++-
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 analytics-3.0/analytics/R/tgsbootV1.R            |   13 +-
 analytics-3.0/analytics/R/weakly.stationaryV1.R  |  136 +++++++++++------------
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 analytics-3.0/analytics/man/offliers.Rd          |    4 
 analytics-3.0/analytics/man/rowmean.Rd           |   35 +++--
 analytics-3.0/analytics/man/weakly.stationary.Rd |    8 +
 16 files changed, 140 insertions(+), 102 deletions(-)

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Package sjPlot updated to version 2.6.1 with previous version 2.6.0 dated 2018-08-23

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Carsten Schwemmer [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjPlot versions 2.6.0 dated 2018-08-23 and 2.6.1 dated 2018-10-14

 sjPlot-2.6.0/sjPlot/R/Deprecated.R                       |only
 sjPlot-2.6.0/sjPlot/man/sjp.glmer.Rd                     |only
 sjPlot-2.6.1/sjPlot/DESCRIPTION                          |   12 
 sjPlot-2.6.1/sjPlot/MD5                                  |  112 +++-----
 sjPlot-2.6.1/sjPlot/NAMESPACE                            |   11 
 sjPlot-2.6.1/sjPlot/NEWS.md                              |   25 +
 sjPlot-2.6.1/sjPlot/R/html_print.R                       |   10 
 sjPlot-2.6.1/sjPlot/R/plot_diag_linear.R                 |   27 +
 sjPlot-2.6.1/sjPlot/R/plot_diag_stan.R                   |   11 
 sjPlot-2.6.1/sjPlot/R/plot_gpt.R                         |    2 
 sjPlot-2.6.1/sjPlot/R/plot_likert.R                      |    2 
 sjPlot-2.6.1/sjPlot/R/plot_model.R                       |   17 -
 sjPlot-2.6.1/sjPlot/R/plot_model_estimates.R             |   83 ++++-
 sjPlot-2.6.1/sjPlot/R/plot_models.R                      |   16 -
 sjPlot-2.6.1/sjPlot/R/plot_point_estimates.R             |   42 ++-
 sjPlot-2.6.1/sjPlot/R/plot_scatter.R                     |    1 
 sjPlot-2.6.1/sjPlot/R/plot_type_eff.R                    |   12 
 sjPlot-2.6.1/sjPlot/R/plot_type_est.R                    |    5 
 sjPlot-2.6.1/sjPlot/R/plot_type_int.R                    |    9 
 sjPlot-2.6.1/sjPlot/R/select_helpers.R                   |   28 --
 sjPlot-2.6.1/sjPlot/R/sjPlotFA.R                         |    1 
 sjPlot-2.6.1/sjPlot/R/sjPlotFrequencies.R                |    2 
 sjPlot-2.6.1/sjPlot/R/sjPlotPCA.R                        |    1 
 sjPlot-2.6.1/sjPlot/R/sjTabCorr.R                        |    2 
 sjPlot-2.6.1/sjPlot/R/sjTabItemAnalysis.R                |    3 
 sjPlot-2.6.1/sjPlot/R/sjTabLinReg.R                      |    9 
 sjPlot-2.6.1/sjPlot/R/sjTabOdds.R                        |    6 
 sjPlot-2.6.1/sjPlot/R/sjTabPropTable.R                   |    1 
 sjPlot-2.6.1/sjPlot/R/sjTabStackFrq.R                    |    1 
 sjPlot-2.6.1/sjPlot/R/tab_model.R                        |   72 ++++-
 sjPlot-2.6.1/sjPlot/R/tidiers.R                          |   45 +--
 sjPlot-2.6.1/sjPlot/R/utils.R                            |   26 +
 sjPlot-2.6.1/sjPlot/build/partial.rdb                    |binary
 sjPlot-2.6.1/sjPlot/build/vignette.rds                   |binary
 sjPlot-2.6.1/sjPlot/inst/doc/blackwhitefigures.html      |    6 
 sjPlot-2.6.1/sjPlot/inst/doc/custplot.html               |   10 
 sjPlot-2.6.1/sjPlot/inst/doc/plot_interactions.html      |    4 
 sjPlot-2.6.1/sjPlot/inst/doc/plot_marginal_effects.R     |   14 -
 sjPlot-2.6.1/sjPlot/inst/doc/plot_marginal_effects.Rmd   |   18 +
 sjPlot-2.6.1/sjPlot/inst/doc/plot_marginal_effects.html  |   10 
 sjPlot-2.6.1/sjPlot/inst/doc/plot_model_estimates.html   |   30 +-
 sjPlot-2.6.1/sjPlot/inst/doc/sjtitemanalysis.html        |    4 
 sjPlot-2.6.1/sjPlot/inst/doc/tab_bayes.Rmd               |    4 
 sjPlot-2.6.1/sjPlot/inst/doc/tab_bayes.html              |  208 +++++++--------
 sjPlot-2.6.1/sjPlot/inst/doc/tab_mixed.html              |   13 
 sjPlot-2.6.1/sjPlot/inst/doc/tab_model_estimates.html    |   84 +++---
 sjPlot-2.6.1/sjPlot/inst/doc/table_css.html              |   28 +-
 sjPlot-2.6.1/sjPlot/man/plot_gpt.Rd                      |    2 
 sjPlot-2.6.1/sjPlot/man/plot_model.Rd                    |   13 
 sjPlot-2.6.1/sjPlot/man/plot_models.Rd                   |   10 
 sjPlot-2.6.1/sjPlot/man/sjp.aov1.Rd                      |    2 
 sjPlot-2.6.1/sjPlot/man/tab_model.Rd                     |   16 +
 sjPlot-2.6.1/sjPlot/tests/testthat.R                     |    4 
 sjPlot-2.6.1/sjPlot/tests/testthat/test-plot_model_std.R |  129 ++++++---
 sjPlot-2.6.1/sjPlot/tests/testthat/test-sjp_grpfrq.R     |  109 ++++---
 sjPlot-2.6.1/sjPlot/tests/testthat/test-tab_model.R      |  127 ++++++---
 sjPlot-2.6.1/sjPlot/vignettes/plot_marginal_effects.Rmd  |   18 +
 sjPlot-2.6.1/sjPlot/vignettes/tab_bayes.Rmd              |    4 
 58 files changed, 864 insertions(+), 597 deletions(-)

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Package wTO updated to version 1.6.2 with previous version 1.6.1 dated 2018-06-28

Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>

Diff between wTO versions 1.6.1 dated 2018-06-28 and 1.6.2 dated 2018-10-14

 DESCRIPTION               |    8 ++++----
 MD5                       |   12 ++++++++----
 NAMESPACE                 |    1 +
 R/rmcor.R                 |only
 R/wTO.rep_measure.R       |only
 inst/CITATION             |    5 +++--
 inst/doc/wTOvignette.html |    4 ++--
 man/rmcor.Rd              |only
 man/wTO.rep_measure.Rd    |only
 9 files changed, 18 insertions(+), 12 deletions(-)

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Package GetDFPData updated to version 1.2 with previous version 1.0 dated 2018-08-28

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

Diff between GetDFPData versions 1.0 dated 2018-08-28 and 1.2 dated 2018-10-14

 DESCRIPTION                               |    8 ++++----
 MD5                                       |   10 +++++-----
 NEWS.md                                   |    8 ++++++++
 R/gdfpd_read_dfp_zip_file.R               |   16 ++++++++++------
 R/gdfpd_read_fre_zip_file.R               |   15 ++++++++++++++-
 inst/doc/gdfpd-vignette-introduction.html |    4 ++--
 6 files changed, 43 insertions(+), 18 deletions(-)

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New package SAVER with initial version 1.1.1
Package: SAVER
Type: Package
Version: 1.1.1
Title: Single-Cell RNA-Seq Gene Expression Recovery
Description: An implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. See Huang M, et al (2018) <doi:10.1038/s41592-018-0033-z> for more details.
Authors@R: c( person("Mo", "Huang", email = "mohuangx@gmail.com", role = c("aut", "cre")), person("Nancy", "Zhang", email = "nzh@wharton.upenn.edu", role = "aut"), person("Mingyao", "Li", email = "mingyao@pennmedicine.upenn.edu", role = "aut") )
Maintainer: Mo Huang <mohuangx@gmail.com>
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.1)
Imports: glmnet, foreach, methods, iterators, doParallel, Matrix
RoxygenNote: 6.1.0
URL: https://github.com/mohuangx/SAVER
BugReports: https://github.com/mohuangx/SAVER/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-09-27 18:16:18 UTC; mohuang
Author: Mo Huang [aut, cre], Nancy Zhang [aut], Mingyao Li [aut]
Repository: CRAN
Date/Publication: 2018-10-14 17:20:10 UTC

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New package rocsvm.path with initial version 0.1.0
Package: rocsvm.path
Type: Package
Title: The Entire Solution Paths for ROC-SVM
Version: 0.1.0
Authors@R: c(person("Seung Jun", "Shin", email = "sjshin@korea.ac.kr", role = c("aut","cre")),person("Do Hyun", "Kim", email = "09dohkim@gmail.com", role = c("aut")))
Description: We develop the entire solution paths for ROC-SVM presented by Rakotomamonjy. The ROC-SVM solution path algorithm greatly facilitates the tuning procedure for regularization parameter, lambda in ROC-SVM by avoiding grid search algorithm which may be computationally too intensive. For more information on the ROC-SVM, see the report in the ROC Analysis in AI workshop(ROCAI-2004) : Hernàndez-Orallo, José, et al. (2004) <doi:10.1145/1046456.1046489>.
Imports: quadprog, svmpath
Depends: R (>= 3.4.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Maintainer: Seung Jun Shin <sjshin@korea.ac.kr>
Packaged: 2018-10-07 00:50:22 UTC; KimDoHyun
Author: Seung Jun Shin [aut, cre], Do Hyun Kim [aut]
Repository: CRAN
Date/Publication: 2018-10-14 17:30:03 UTC

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New package PDFEstimator with initial version 0.1-0
Package: PDFEstimator
Version: 0.1-0
Date: 2018-09-24
Title: Nonparametric Probability Density Estimator
Author: Jenny Farmer <jfarmer6@uncc.edu> and Donald Jacobs <djacobs1@uncc.ecu>
Maintainer: Jenny Farmer <jfarmer6@uncc.edu>
Description: A nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2018-10-05 15:04:11 UTC; jenny
Repository: CRAN
Date/Publication: 2018-10-14 17:20:15 UTC

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New package nvmix with initial version 0.0-1
Package: nvmix
Version: 0.0-1
Encoding: UTF-8
Title: Multivariate Normal Variance Mixtures (Including Student's t Distribution for Non-Integer Degrees of Freedom)
Description: Functions for working with multivariate normal variance mixture distributions including evaluating their distribution functions, densities and random number generation.
Authors@R: c(person(given = "Marius", family = "Hofert", role = c("aut", "cre"), email = "marius.hofert@uwaterloo.ca"), person(given = "Erik", family = "Hintz", role = "aut", email = "erik.hintz@uwaterloo.ca"), person(given = "Christiane", family = "Lemieux", role = "aut", email = "clemieux@uwaterloo.ca"))
Author: Marius Hofert [aut, cre], Erik Hintz [aut], Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Depends: R (>= 3.2.0)
Imports: stats, methods, qrng
Suggests: knitr, RColorBrewer, lattice
Enhances:
License: GPL (>= 3) | file LICENCE
NeedsCompilation: yes
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2018-10-14 17:20:03 UTC
Packaged: 2018-10-07 15:58:51 UTC; mhofert

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New package nprotreg with initial version 1.0.0
Package: nprotreg
Title: Nonparametric Rotations for Sphere-Sphere Regression
Version: 1.0.0
Authors@R: c( person(c("Charles","C."), "Taylor", email = "charles@maths.leeds.ac.uk", role = c("aut")), person("Giovanni", "Lafratta", email = "giovanni.lafratta@unich.it", role = c("aut", "cre")), person("Stefania", "Fensore", email = "stefania.fensore@unich.it", role = c("aut")))
Description: Fits sphere-sphere regression models by estimating locally weighted rotations. Simulation of sphere-sphere data according to non-rigid rotation models. Provides methods for bias reduction applying iterative procedures within a Newton-Raphson learning scheme. Cross-validation is exploited to select smoothing parameters. See Marco Di Marzio, Agnese Panzera & Charles C. Taylor (2018) <doi:10.1080/01621459.2017.1421542>.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: testthat
Imports: methods, expm, stats
NeedsCompilation: no
Packaged: 2018-10-05 11:52:07 UTC; giova
Author: Charles C. Taylor [aut], Giovanni Lafratta [aut, cre], Stefania Fensore [aut]
Maintainer: Giovanni Lafratta <giovanni.lafratta@unich.it>
Repository: CRAN
Date/Publication: 2018-10-14 17:20:06 UTC

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New package Immigrate with initial version 0.0.1
Package: Immigrate
Title: Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection
Version: 0.0.1
Author: Ruzhang Zhao, Pengyu Hong, Jun S. Liu
Description: Based on large margin principle, this package performs feature selection methods: "IM4E"(Iterative Margin-Maximization under Max-Min Entropy Algorithm); "imIM4E"(imbalance Iterative Margin-Maximization under Max-Min Entropy Algorithm); "Immigrate"(Iterative Max-Min Entropy Margin-Maximization with Interaction Terms Algorithm); "Simba"(Iterative Search Margin Based Algorithm); "LFE"(Local Feature Extraction Algorithm). This package also performs prediction for the above feature selection methods.
Maintainer: Ruzhang Zhao<zrz6787@gmail.com>
Depends: R (>= 3.0.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0.9000
LinkingTo: Rcpp
Imports: Rcpp, pROC
NeedsCompilation: yes
Packaged: 2018-10-06 13:06:38 UTC; zhaoruzhang
Repository: CRAN
Date/Publication: 2018-10-14 17:20:18 UTC

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Package fuzzyreg updated to version 0.4 with previous version 0.3 dated 2018-06-07

Title: Fuzzy Linear Regression
Description: Estimators for fuzzy linear regression. The functions estimate parameters of fuzzy linear regression models with crisp or fuzzy independent variables (triangular fuzzy numbers are supported). Implements multiple methods for parameter estimation and algebraic operations with triangular fuzzy numbers. Includes functions for summarising, printing and plotting the model fit. Calculates predictions from the model and total error of fit. Diamond (1988) <doi:10.1016/0020-0255(88)90047-3>, Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004>, Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98>, Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008>, Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>.
Author: Pavel Skrabanek [aut, cph], Natalia Martinkova [aut, cre, cph]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>

Diff between fuzzyreg versions 0.3 dated 2018-06-07 and 0.4 dated 2018-10-14

 DESCRIPTION                  |   20 ++--
 MD5                          |   66 ++++++++------
 NAMESPACE                    |   48 +++++-----
 NEWS                         |only
 R/TEF.r                      |only
 R/dom.r                      |only
 R/fuzzylm.R                  |   10 +-
 R/plot.fuzzylm.R             |  200 +++++++++++++++++++++----------------------
 R/print.summary.fuzzylm.R    |    6 -
 R/summary.fuzzylm.R          |   64 ++++++-------
 build                        |only
 inst/doc                     |only
 man/TEF.Rd                   |only
 man/diamond.Rd               |   77 +++++++++-------
 man/dom.Rd                   |only
 man/fls.Rd                   |   94 ++++++++++----------
 man/fuzzydat.Rd              |   78 ++++++++--------
 man/fuzzylm.Rd               |  155 ++++++++++++++++-----------------
 man/hung.Rd                  |   92 ++++++++++---------
 man/lee.Rd                   |  103 +++++++++++-----------
 man/moflr.Rd                 |  110 +++++++++++------------
 man/nasrabadi.Rd             |  104 +++++++++++-----------
 man/oplr.Rd                  |  106 +++++++++++-----------
 man/plot.fuzzylm.Rd          |  101 +++++++++++----------
 man/plr.Rd                   |  100 ++++++++++-----------
 man/plrls.Rd                 |  118 ++++++++++++-------------
 man/predict.fuzzylm.Rd       |   60 ++++++------
 man/print.fuzzylm.Rd         |   48 +++++-----
 man/print.summary.fuzzylm.Rd |   50 +++++-----
 man/prodFuzzy.Rd             |   54 +++++------
 man/prodSfuzzy.Rd            |   62 ++++++-------
 man/sumFuzzy.Rd              |   54 +++++------
 man/summary.fuzzylm.Rd       |   56 +++++-------
 man/tanaka.Rd                |   86 +++++++++---------
 tests                        |only
 vignettes                    |only
 36 files changed, 1083 insertions(+), 1039 deletions(-)

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New package classyfireR with initial version 0.1.1
Package: classyfireR
Type: Package
Title: R Interface to the ClassyFire RESTful API
Version: 0.1.1
Date: 2018-10-05
Authors@R: c( person("Tom", "Wilson", , "tpw2@aber.ac.uk", c("aut", "cre")))
Description: Access to the ClassyFire RESTful API <http://classyfire.wishartlab.com>. Retrieve existing entity classifications and submit new entities for classification.
Depends: magrittr
Imports: httr, jsonlite, tibble, crayon, clisymbols
Suggests: testthat, covr, dplyr, purrr, tidyr
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://github.com/wilsontom/classyfireR
BugReports: https://github.com/wilsontom/classyfireR/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-05 10:03:50 UTC; tom
Author: Tom Wilson [aut, cre]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>
Repository: CRAN
Date/Publication: 2018-10-14 17:10:02 UTC

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New package carbonate with initial version 0.1.0
Package: carbonate
Title: Interact with 'carbon.js'
Version: 0.1.0
Authors@R: person(given = "Jonathan", family = "Sidi", email = "yonicd@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4222-1819"))
Description: Create beautiful images of source code using 'carbon.js'<https://carbon.now.sh/about>.
Depends: R (>= 3.2.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: R6, clipr, magick, wdman, RSelenium, utils, httr, rtweet, yaml
Suggests: testthat, covr, knitr, rmarkdown
URL: https://github.com/yonicd/carbonate
BugReports: https://github.com/yonicd/carbonate/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-05 15:43:20 UTC; yonis
Author: Jonathan Sidi [aut, cre] (<https://orcid.org/0000-0002-4222-1819>)
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-14 17:10:05 UTC

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New package ssdtools with initial version 0.0.2
Package: ssdtools
Version: 0.0.2
Date: 2018-10-04
Title: Species Sensitivity Distributions
Description: Fits and plots species sensitivity distributions using maximum likelihood and information-theoretic-based model averaging.
Authors@R: c( person("Joe", "Thorley", email = "joe@poissonconsulting.ca", role = c("aut", "cre", "ctr"), comment = c(ORCID = "0000-0002-7683-4592")), person("Carl", "Schwarz", role = c("aut", "ctr")), person("Ali", "Azizishirazi", email = "Ali.Azizishirazi@gov.bc.ca", role = "ctb"), person("Angeline", "Tillmanns", role = "ctb"), person("Stephanie", "Hazlitt", role = "ctb"), person("Province of British Columbia", role = "cph") )
License: Apache License (== 2.0) | file LICENSE
URL: https://github.com/bcgov/ssdca
BugReports: https://github.com/bcgov/ssdca/issues
Depends: R (>= 3.4.0), graphics, stats, VGAM, ggplot2, fitdistrplus
Imports: actuar, checkr, dplyr, FAdist, grid, magrittr, plyr, pryr, purrr, tibble, scales
Suggests: covr, knitr, rmarkdown, testthat
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-05 02:20:52 UTC; joe
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>), Carl Schwarz [aut, ctr], Ali Azizishirazi [ctb], Angeline Tillmanns [ctb], Stephanie Hazlitt [ctb], Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-10-14 16:50:03 UTC

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New package scoper with initial version 0.1.0
Package: scoper
Type: Package
Version: 0.1.0
Date: 2018-10-04
Authors@R: c(person("Nima", "Nouri", role=c("aut", "cre"), email="nima.nouri@yale.edu"), person("Jason", "Vander Heiden", role=c("ctb"), email="jason.vanderheiden@yale.edu"), person("Steven", "Kleinstein", role=c("aut", "cph"), email="steven.kleinstein@yale.edu"))
Title: Spectral Clustering-Based Method for Identifying B Cell Clones
Description: Provides a computational framework for unsupervised identification B cell clones from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. This method is based on spectral clustering of the junction sequences of B cell receptors (BCRs, also referred to as Immunoglobulins, (Igs)) that share the same V gene, J gene and junction length.
License: CC BY-SA 4.0
URL: https://scoper.readthedocs.io
BugReports: https://bitbucket.org/kleinstein/scoper/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.1.2), ggplot2 (>= 2.0.0)
Imports: alakazam (>= 0.2.11), shazam (>= 0.1.10), doParallel, foreach, dplyr (>= 0.7.0), stringi, methods, stats, iterators, lazyeval
Suggests: knitr, rmarkdown, testthat
RoxygenNote: 6.1.0
Collate: 'Data.R' 'Scoper.R' 'Functions.R'
NeedsCompilation: no
Packaged: 2018-10-04 20:58:03 UTC; nima
Author: Nima Nouri [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer: Nima Nouri <nima.nouri@yale.edu>
Repository: CRAN
Date/Publication: 2018-10-14 17:00:03 UTC

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New package pubchunks with initial version 0.1.0
Package: pubchunks
Title: Fetch Sections of XML Scholarly Articles
Description: Get chunks of XML scholarly articles without having to know how to work with XML. Custom mappers for each publisher and for each article section pull out the information you want. Works with outputs from package 'fulltext', 'xml2' package documents, and file paths to XML documents.
Version: 0.1.0
License: MIT + file LICENSE
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "sckott@protonmail.com", comment = c(ORCID = "0000-0003-1444-9135")) )
URL: https://github.com/ropensci/pubchunks
BugReports: https://github.com/ropensci/pubchunks/issues
Encoding: UTF-8
Language: en-US
Imports: xml2 (>= 1.1.1), data.table
Suggests: fulltext (>= 1.0.1), testthat
RoxygenNote: 6.1.0
X-schema.org-applicationCategory: Literature
X-schema.org-keywords: text-ming, literature, pdf, xml, publications, citations, full-text, TDM
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2018-10-04 20:07:53 UTC; sckott
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Repository: CRAN
Date/Publication: 2018-10-14 16:50:07 UTC

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New package Omisc with initial version 0.1.0
Package: Omisc
Type: Package
Title: Univariate Bootstrapping and Other Things
Version: 0.1.0
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>
Description: Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi.org/10.1037/1082-989X.12.4.414>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: MASS, base, stats, psych
Suggests: lavaan
NeedsCompilation: no
Packaged: 2018-10-04 14:37:12 UTC; Patrick
Repository: CRAN
Date/Publication: 2018-10-14 16:50:12 UTC

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New package nasapower with initial version 1.0.1
Package: nasapower
Type: Package
Title: 'NASA' 'POWER' 'API' Client
Version: 1.0.1
Authors@R: c( person("Adam H.", "Sparks", role = c("aut", "cre"), email = "adamhsparks@gmail.com", comment = c(ORCID = "0000-0002-0061-8359")), person("Scott", "Chamberlain", role = "rev", email = "myrmecocystus@gmail.com", comment = c(ORCID = "0000-0003-1444-9135")), person("Hazel", "Kavili", role = "rev"), person("Alison", "Boyer", role = "rev"))
URL: https://github.com/ropensci/nasapower
BugReports: https://github.com/ropensci/nasapower/issues
Description: Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 0.5 by 0.5 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves and a web-based data viewer and access, please see <https://power.larc.nasa.gov/>.
Depends: R (>= 3.2.0)
License: MIT + file LICENSE
Imports: APSIM, crul, curl, dplyr, lubridate, jsonlite, readr, tibble, utils
RoxygenNote: 6.1.0
Encoding: UTF-8
NeedsCompilation: no
Repository: CRAN
LazyData: TRUE
ByteCompile: TRUE
Suggests: covr, ggplot2, knitr, raster, rmarkdown, testthat, vcr
VignetteBuilder: knitr
X-schema.org-applicationCategory: Tools
X-schema.org-keywords: NASA, meteorological-data, weather, global, weather, weather-data, meteorology, NASA-POWER, agroclimatology, earth-science, data-access
X-schema.org-isPartOf: https://ropensci.org
Packaged: 2018-10-04 08:49:44 UTC; adamsparks
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>), Hazel Kavili [rev], Alison Boyer [rev]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Date/Publication: 2018-10-14 16:10:03 UTC

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New package jsonify with initial version 0.1.1
Package: jsonify
Type: Package
Title: Converts 'R' Objects to Javascript Object Notation (JSON)
Version: 0.1.1
Date: 2018-10-04
Authors@R: c( person("David", "Cooley", ,"dcooley@symbolix.com.au", role = c("aut", "cre")) )
Description: Converts 'R' objects into Javascript Object Notation (JSON) using the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.18), rapidjsonr
LinkingTo: Rcpp, rapidjsonr
RoxygenNote: 6.1.0
Suggests: microbenchmark, jsonlite, testthat, covr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2018-10-10 08:04:35 UTC; dave
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Repository: CRAN
Date/Publication: 2018-10-14 16:20:03 UTC

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New package jjb with initial version 0.1.0
Package: jjb
Type: Package
Title: Balamuta Miscellaneous
Version: 0.1.0
Authors@R: c( person("James", "Balamuta", email = "balamut2@illinois.edu", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-2826-8458")) )
License: GPL (>= 2)
Description: Set of common functions used for manipulating colors, detecting and interacting with 'RStudio', modeling, formatting, determining users' operating system, feature scaling, and more!
RoxygenNote: 6.1.0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-10-04 04:07:45 UTC; ronin
Author: James Balamuta [aut, cre, cph] (<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Balamuta <balamut2@illinois.edu>
Repository: CRAN
Date/Publication: 2018-10-14 16:30:02 UTC

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New package imputeR with initial version 2.1
Package: imputeR
Title: A General Multivariate Imputation Framework
Version: 2.1
Date: 2018-10-05
Authors@R: c( person("Steffen", "Moritz", email="steffen.moritz10@gmail.com", role=c("aut", "cre"), comment = c(ORCID = "0000-0002-0085-1804")),person("Lingbing", "Feng", role=c("aut")),person("Gen", "Nowak", role=c("ctb")),person("Alan. H.", "Welsh", role=c("ctb")),person("Terry. J.", "O'Neill", role=c("ctb")) )
Author: Steffen Moritz [aut, cre] (<https://orcid.org/0000-0002-0085-1804>), Lingbing Feng [aut], Gen Nowak [ctb], Alan. H. Welsh [ctb], Terry. J. O'Neill [ctb]
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Description: Multivariate Expectation-Maximization (EM) based imputation framework that offers several different algorithms. These include regularisation methods like Lasso and Ridge regression, tree-based models and dimensionality reduction methods like PCA and PLS.
LazyData: yes
Type: Package
ByteCompile: TRUE
BugReports: https://github.com/SteffenMoritz/imputeR/issues
URL: http://github.com/SteffenMoritz/imputeR
Repository: CRAN
Depends: R (>= 3.1.0),
Imports: stats, utils, graphics, reshape2
Suggests: testthat, rda, caret, glmnet, pls, Cubist, ridge, gbm, mboost, rpart, earth
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-10-05 02:53:04 UTC; Steve
Date/Publication: 2018-10-14 16:40:02 UTC

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New package EZtune with initial version 1.0.0
Package: EZtune
Type: Package
Title: Tunes AdaBoost, Support Vector Machines, and Gradient Boosting Machines
Version: 1.0.0
Authors@R: person("Jill", "Lundell", email = "jflundell@gmail.com", role = c("aut", "cre"))
Maintainer: Jill Lundell <jflundell@gmail.com>
Description: Contains two functions that are intended to make tuning supervised learning methods easy. The eztune function uses a genetic algorithm or quasi-Newton-Raphson optimizer to find the best set of tuning parameters. The user can choose the optimizer, the learning method, and if optimization will be based on accuracy obtained through resubstitution or cross-validation. The function eztune.cv will compute a cross-validated error rate. The purpose of eztune.cv is to provide a cross-validated accuracy when resubstitution is used for optimization because resubstitution typically produces an accuracy that is too high.
Depends: R (>= 3.1.0)
Imports: ada, e1071, GA, gbm, mlbench, parallel, doParallel
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-05 07:03:07 UTC; jflun
Author: Jill Lundell [aut, cre]
Repository: CRAN
Date/Publication: 2018-10-14 16:50:17 UTC

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Package vimp updated to version 1.1.4 with previous version 1.1.3 dated 2018-10-02

Title: Nonparametric Variable Importance
Description: Calculate point estimates of and valid confidence intervals for nonparametric variable importance measures in high and low dimensions, using flexible estimators of the underlying regression functions. For more information about the methods, please see Williamson et al. (2017) <https://biostats.bepress.com/uwbiostat/paper422/>.
Author: Brian D. Williamson [aut, cre], Noah Simon [aut], Marco Carone [aut]
Maintainer: Brian D. Williamson <brianw26@uw.edu>

Diff between vimp versions 1.1.3 dated 2018-10-02 and 1.1.4 dated 2018-10-14

 DESCRIPTION                        |    6 +++---
 MD5                                |   14 +++++++-------
 R/average_vim.R                    |    1 +
 R/cv_vim.R                         |    4 +++-
 R/cv_vim_nodonsker.R               |    4 +++-
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New package trelliscopejs with initial version 0.1.14
Package: trelliscopejs
Title: Create Interactive Trelliscope Displays
Version: 0.1.14
Authors@R: c( person("Ryan", "Hafen", email = "rhafen@gmail.com", role = c("aut", "cre")), person("Barret", "Schloerke", email = "schloerke@gmail.com", role = "aut") )
Description: Trelliscope is a scalable, flexible, interactive approach to visualizing data (Hafen, 2013 <doi:10.1109/LDAV.2013.6675164>). This package provides methods that make it easy to create a Trelliscope display specification for TrelliscopeJS. High-level functions are provided for creating displays from within 'dplyr' or 'ggplot2' workflows. Low-level functions are also provided for creating new interfaces.
Depends: R (>= 3.4.0)
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, purrr, tidyr, grid, htmltools, DistributionUtils, grDevices, gtable, digest, jsonlite, ggplot2 (> 2.1.0), base64enc, htmlwidgets, graphics, progress, utils, knitr, webshot, autocogs, rlang
Suggests: rbokeh, plotly, Cairo, testthat, covr, gapminder, housingData, packagedocs
RoxygenNote: 6.1.0
URL: https://github.com/hafen/trelliscopejs
BugReports: https://github.com/hafen/trelliscopejs/issues
VignetteBuilder: packagedocs
NeedsCompilation: no
Packaged: 2018-10-02 21:06:14 UTC; hafen
Author: Ryan Hafen [aut, cre], Barret Schloerke [aut]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-14 15:30:03 UTC

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New package ppgmmga with initial version 1.0
Package: ppgmmga
Version: 1.0
Date: 2018-10-02
Title: Projection Pursuit Based on Gaussian Mixtures and Evolutionary Algorithms
Description: Projection Pursuit (PP) algorithm for dimension reduction based on Gaussian Mixture Models (GMMs) for density estimation using Genetic Algorithms (GAs) to maximise an approximated negentropy index.
Authors@R: c(person("Alessio", "Serafini", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8579-5695"), email = "srf.alessio@gmail.com"), person("Luca", "Scrucca", role = c("aut"), comment = c(ORCID = "0000-0003-3826-0484"), email = "luca.scrucca@unipg.it"))
Depends: R (>= 3.4)
Imports: Rcpp (>= 0.12.5), mclust (>= 5.0), GA (>= 3.1), ggplot2 (>= 2.2.1), ggthemes (>= 3.4.0), cli, crayon
LinkingTo: Rcpp, RcppArmadillo (>= 0.7)
Suggests: knitr (>= 1.8)
License: GPL (>= 2)
URL: https://github.com/luca-scr/ppgmmga
BugReports: https://github.com/luca-scr/ppgmmga/issues
VignetteBuilder: knitr
ByteCompile: true
Repository: CRAN
NeedsCompilation: yes
LazyLoad: yes
Encoding: UTF-8
Packaged: 2018-10-02 11:15:28 UTC; alessioserafini
Author: Alessio Serafini [aut, cre] (<https://orcid.org/0000-0002-8579-5695>), Luca Scrucca [aut] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Alessio Serafini <srf.alessio@gmail.com>
Date/Publication: 2018-10-14 15:30:08 UTC

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New package MLGL with initial version 0.5
Package: MLGL
Type: Package
Title: Multi-Layer Group-Lasso
Version: 0.5
Date: 2018-09-24
Authors@R: c(person("Quentin", "Grimonprez", role = c("aut", "cre"), email = "quentin.grimonprez@inria.fr"), person("Samuel", "Blanck", role = "ctb"), person("Alain", "Celisse", role = "ths"), person("Guillemette", "Marot", role = "ths"), person("Yi","Yang", role = "ctb"), person("Hui","Zou", role = "ctb"))
Copyright: Inria
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
License: GPL (>= 2)
Imports: gglasso, MASS, Matrix, fastcluster, FactoMineR
RoxygenNote: 6.1.0
Encoding: UTF-8
Author: Quentin Grimonprez [aut, cre], Samuel Blanck [ctb], Alain Celisse [ths], Guillemette Marot [ths], Yi Yang [ctb], Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Repository: CRAN
Repository/R-Forge/Project: hcgglasso
Repository/R-Forge/Revision: 33
Repository/R-Forge/DateTimeStamp: 2018-10-03 07:11:50
Date/Publication: 2018-10-14 15:50:04 UTC
NeedsCompilation: no
Packaged: 2018-10-03 07:30:09 UTC; rforge

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New package MachineShop with initial version 0.1-1
Package: MachineShop
Type: Package
Title: Machine Learning Models and Tools
Version: 0.1-1
Date: 2018-10-02
Authors@R: person("Brian J", "Smith", email = "brian-j-smith@uiowa.edu", role = c("aut", "cre"))
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Imports: abind, foreach, ggplot2, Hmisc, irr, kernlab, magrittr, methods, MLmetrics, ModelMetrics, party, recipes, rsample, survival, survivalROC, utils
Suggests: C50, doParallel, gbm, glmnet, kableExtra, knitr, MASS, nnet, pls, randomForest, rmarkdown, rms, testthat
License: GPL-3
URL: https://github.com/brian-j-smith/MachineShop
BugReports: https://github.com/brian-j-smith/MachineShop/issues
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-02 19:09:28 UTC; bjsmith
Repository: CRAN
Date/Publication: 2018-10-14 15:30:19 UTC

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New package galgo with initial version 1.4
Package: galgo
Version: 1.4
Date: 2018-09-18
Title: Genetic Algorithms for Multivariate Statistical Models from Large-Scale Functional Genomics Data
Authors@R: c(person("Victor", "Trevino", role=c("aut","cre"), email="vtrevino@itesm.mx"), person("Francesco", "Falciani", role=c("aut"), email="F.Falciani@liverpool.ac.uk"), person("Copyright (C) The R Core Team", role=c("cph","ctb")), person("Copyright (C) The R Foundation", role=c("cph","ctb")))
Author: Victor Trevino [aut, cre], Francesco Falciani [aut], Copyright (C) The R Core Team [cph, ctb], Copyright (C) The R Foundation [cph, ctb]
Maintainer: Victor Trevino <vtrevino@itesm.mx>
Description: Build multivariate predictive models from large datasets having far larger number of features than samples such as in functional genomics datasets. Trevino and Falciani (2006) <doi:10.1093/bioinformatics/btl074>.
License: GPL (>= 2)
LazyLoad: no
Depends: R (>= 3.0.0), R.oo
Imports: e1071, rpart, nnet, randomForest, MASS
URL: https://github.com/vtrevino/GALGO
NeedsCompilation: yes
Packaged: 2018-10-02 21:16:04 UTC; victortrevino
Repository: CRAN
Date/Publication: 2018-10-14 15:30:11 UTC

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Package RcppCCTZ updated to version 0.2.5 with previous version 0.2.4 dated 2018-10-06

Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppCCTZ versions 0.2.4 dated 2018-10-06 and 0.2.5 dated 2018-10-14

 ChangeLog                     |   34 ++++++++++++++++
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Package pricesensitivitymeter updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-12

Title: Van Westendorp Price Sensitivity Meter Analysis
Description: An implementation of the van Westendorp Price Sensitivity Meter in R, which is a survey-based approach to analyze consumer price preferences and sensitivity (van Westendorp 1976, isbn:9789283100386).
Author: Max Alletsee [aut, cre]
Maintainer: Max Alletsee <max.alletsee@gmail.com>

Diff between pricesensitivitymeter versions 0.3.2 dated 2018-05-12 and 0.3.3 dated 2018-10-14

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 7 files changed, 27 insertions(+), 22 deletions(-)

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Package touch updated to version 0.1-4 with previous version 0.1-3 dated 2016-12-17

Title: Tools of Utilization and Cost in Healthcare
Description: R implementation of the software tools developed in the H-CUP (Healthcare Cost and Utilization Project) <https://www.hcup-us.ahrq.gov> and AHRQ (Agency for Healthcare Research and Quality) <https://www.ahrq.gov>. It currently contains functions for mapping ICD-9 codes to the AHRQ comorbidity measures and translating ICD-9 (resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General Equivalence Mappings) from CMS (Centers for Medicare and Medicaid Services).
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>), Yan Li [aut], Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

Diff between touch versions 0.1-3 dated 2016-12-17 and 0.1-4 dated 2018-10-14

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Sat, 13 Oct 2018

Package treemapify updated to version 2.5.2 with previous version 2.5.1 dated 2018-10-06

Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins <david@wilkox.org>
Maintainer: David Wilkins <david@wilkox.org>

Diff between treemapify versions 2.5.1 dated 2018-10-06 and 2.5.2 dated 2018-10-13

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 7 files changed, 26 insertions(+), 14 deletions(-)

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Package scBio updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-07

Title: Single Cell Genomics for Enhancing Cell Composition Inference from Bulk Genomics Data
Description: Cellular population mapping (CPM) a deconvolution algorithm in which single-cell genomics is required in only one or a few samples, where in other samples of the same tissue, only bulk genomics is measured and the underlying fine resolution cellular heterogeneity is inferred.
Author: Amit Frishberg [aut, cre], Naama Peshes-Yaloz [aut], Irit Gat-Viks [aut]
Maintainer: Amit Frishberg <amfrishberg@gmail.com>

Diff between scBio versions 0.1.0 dated 2018-08-07 and 0.1.1 dated 2018-10-13

 DESCRIPTION |    6 ++--
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Package Rnightlights updated to version 0.2.3 with previous version 0.2.2 dated 2018-07-24

Title: Satellite Nightlight Data Extraction
Description: Extracts raster and zonal statistics from satellite nightlight rasters downloaded from the United States National Oceanic and Atmospheric Administration (<http://www.noaa.gov>) free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly nightlight raster data are supported. Satellite nightlight raster tiles are downloaded and cropped to the country boundaries using shapefiles from the GADM database of Global Administrative Areas (<http://gadm.org>). Zonal statistics are then calculated at the lowest administrative boundary for the selected country and cached locally for future retrieval. Finally, a simple data explorer/browser is included that allows one to visualize the cached data e.g. graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph]
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>

Diff between Rnightlights versions 0.2.2 dated 2018-07-24 and 0.2.3 dated 2018-10-13

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Package MRPC updated to version 2.0.0 with previous version 1.0.0 dated 2018-08-14

Title: Mendelian Randomization (MR) Based PC Algorithm
Description: Infer causal graphs using the principle of Mendelian randomization-based PC (MRPC) algorithm. See Badsha and Fu (2018) <doi:10.1101/171348>,Badsha et al. (2018) <arXiv:1806.01899>.
Author: Md Bahadur Badsha [aut,cre],Evan A Martin [ctb] and Audrey Qiuyan Fu [aut]
Maintainer: Md Bahadur Badsha <mdbadsha@uidaho.edu>

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Package MetFns updated to version 3.2.2 with previous version 3.2.1 dated 2018-08-23

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 tm1r updated to version 1.0.2 with previous version 1.0.1 dated 2018-08-09

Title: The Integration Between 'IBM COGNOS TM1' and R
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>

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Package scriptexec updated to version 0.2.3 with previous version 0.2.2 dated 2018-10-01

Title: Execute Native Scripts
Description: Run complex native scripts with a single command, similar to system commands.
Author: Sagie Gur-Ari [aut, cre]
Maintainer: Sagie Gur-Ari <sagiegurari@gmail.com>

Diff between scriptexec versions 0.2.2 dated 2018-10-01 and 0.2.3 dated 2018-10-13

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Package GSED updated to version 1.10 with previous version 1.9 dated 2018-09-26

Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

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Package xSub updated to version 2.0.1 with previous version 0.0.1 dated 2017-10-11

Title: Cross-National Data on Sub-National Violence
Description: Tools to download and merge data files on sub-national conflict, violence and protests from <http://www.x-sub.org>.
Author: Yuri Zhukov [cre], Christian Davenport [aut], Nadiya Kostyuk [aut]
Maintainer: Yuri Zhukov <zhukov@umich.edu>

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Package refuge updated to version 0.2.0 with previous version 0.1.1 dated 2018-04-20

Title: Locate Trans and Intersex-Friendly Toilets
Description: Access the 'Refuge' API, a web-application for locating trans and intersex-friendly restrooms, including unisex and accessible restrooms. Includes data on the location of restrooms, along with directions, comments, user ratings and amenities. Coverage is global, but data is most comprehensive in the United States. See <https://www.refugerestrooms.org/api/docs/> for full API documentation.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>)
Maintainer: Evan Odell <evanodell91@gmail.com>

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Package REAT updated to version 2.0.3 with previous version 2.0.2 dated 2018-10-04

Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>

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Package UCSCXenaTools updated to version 0.2.5 with previous version 0.2.4 dated 2018-09-12

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded. This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package testthat updated to version 2.0.1 with previous version 2.0.0 dated 2017-12-13

Title: Unit Testing for R
Description: Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy learn and use, and integrates with your existing 'workflow'.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd], R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between testthat versions 2.0.0 dated 2017-12-13 and 2.0.1 dated 2018-10-13

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Package SCINA updated to version 1.0.1 with previous version 1.0.0 dated 2018-10-08

Title: A Semi-Supervised Category Identification and Assignment Tool
Description: An automatic cell type detection and assignment algorithm for single cell RNA-Seq and Cytof/FACS data. 'SCINA' is capable of assigning cell type identities to a pool of cells profiled by scRNA-Seq or Cytof/FACS data with prior knowledge of markers, such as genes and protein symbols that are highly or lowly expressed in each category.
Author: Ze Zhang
Maintainer: Ze Zhang <Ze.Zhang@utsouthwestern.edu>

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Package psychmeta updated to version 2.2.1 with previous version 2.2.0 dated 2018-09-18

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

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Package crfsuite (with last version 0.1.1) was removed from CRAN

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

2018-10-02 0.1.1
2018-09-28 0.1

Permanent link
Package hoardr updated to version 0.5.0 with previous version 0.2.0 dated 2017-05-09

Title: Manage Cached Files
Description: Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between hoardr versions 0.2.0 dated 2017-05-09 and 0.5.0 dated 2018-10-13

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Fri, 12 Oct 2018

Package mase updated to version 0.1.2 with previous version 0.1.1 dated 2018-06-14

Title: Model-Assisted Survey Estimators
Description: A set of model-assisted survey estimators and corresponding variance estimators for single stage, unequal probability, without replacement sampling designs. All of the estimators can be written as a generalized regression estimator with the Horvitz-Thompson, ratio, post-stratified, and regression estimators summarized by Sarndal et al. (1992, ISBN:978-0-387-40620-6). Two of the estimators employ a statistical learning model as the assisting model: the elastic net regression estimator, which is an extension of the lasso regression estimator given by McConville et al. (2017) <doi:10.1093/jssam/smw041>, and the regression tree estimator described in McConville and Toth (2017) <arXiv:1712.05708>. The variance estimators which approximate the joint inclusion probabilities can be found in Berger and Tille (2009) <doi:10.1016/S0169-7161(08)00002-3> and the bootstrap variance estimator is presented in Mashreghi et al. (2016) <doi:10.1214/16-SS113>.
Author: Kelly McConville [aut, cre, cph], Becky Tang [aut], George Zhu [aut], Sida Li [ctb], Shirley Chueng [ctb], Daniell Toth [ctb, cph] (Author and copyright holder of treeDesignMatrix helper function)
Maintainer: Kelly McConville <mcconville@reed.edu>

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Package BOIN updated to version 2.6.4 with previous version 2.6.3 dated 2018-04-10

Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials. The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>

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Package nlts updated to version 1.0-2 with previous version 0.2-2 dated 2017-08-28

Title: Nonlinear Time Series Analysis
Description: R functions for (non)linear time series analysis with an emphasis on nonparametric autoregression and order estimation, and tests for linearity / additivity.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Package icr updated to version 0.5.7 with previous version 0.5.6 dated 2018-07-24

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

Diff between icr versions 0.5.6 dated 2018-07-24 and 0.5.7 dated 2018-10-12

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Package comperes updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-11

Title: Manage Competition Results
Description: Tools for storing and managing competition results. Competition is understood as a set of games in which players gain some abstract scores. There are two ways for storing results: in long (one row per game-player) and wide (one row per game with fixed amount of players) formats. This package provides functions for creation and conversion between them. Also there are functions for computing their summary and Head-to-Head values for players. They leverage grammar of data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package bayesPop updated to version 7.0-0 with previous version 6.2-4 dated 2018-03-16

Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy.
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package rococo updated to version 1.1.7 with previous version 1.1.5 dated 2017-07-08

Title: Robust Rank Correlation Coefficient and Test
Description: Provides the robust gamma rank correlation coefficient as introduced by Bodenhofer, Krone, and Klawonn (2013) <DOI:10.1016/j.ins.2012.11.026> along with a permutation-based rank correlation test. The rank correlation coefficient and the test are explicitly designed for dealing with noisy numerical data.
Author: Martin Krone, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

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Package Phase123 updated to version 1.7 with previous version 1.5 dated 2018-03-28

Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>

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Package egoTERGM updated to version 2.0.1 with previous version 1.0.0 dated 2018-04-25

Title: Estimation of Ego-Temporal Exponential Random Graph Models via Expectation Maximization (EM)
Description: Estimation of ego-temporal exponential random graph models with two-stage estimation including initialization through k-means clustering on temporal exponential random graph model parameters and EM as per Campbell (2018) <doi:10.7910/DVN/TWHEZ9>.
Author: Benjamin W. Campbell [aut, cre], Michael Salter-Townshend [ctb], Thomas Brendan Murphy [ctb]
Maintainer: Benjamin W. Campbell <campbell.1721@osu.edu>

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New package ChemoSpecUtils with initial version 0.1.62
Package: ChemoSpecUtils
Type: Package
Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Version: 0.1.62
Date: 2018-10-12
Authors@R: c( person("Bryan A.", "Hanson", role = c("aut", "cre"), email = "hanson@depauw.edu", comment = "ORCID 0000-0003-3536-8246"))
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
License: GPL-3
Depends: R (>= 3.1)
Suggests: ChemoSpec (>= 5.0), ChemoSpec2D
Imports: plyr, robustbase, RColorBrewer
URL: https://github.com/bryanhanson/ChemoSpecUtils
ByteCompile: TRUE
BugReports: https://github.com/bryanhanson/ChemoSpecUtils/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-12 13:45:37 UTC; bryanhanson
Author: Bryan A. Hanson [aut, cre] (ORCID 0000-0003-3536-8246)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Repository: CRAN
Date/Publication: 2018-10-12 16:50:21 UTC

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Package crqa updated to version 1.0.9 with previous version 1.0.8 dated 2018-08-19

Title: Cross-Recurrence Quantification Analysis for Categorical and Continuous Time-Series
Description: Cross-recurrence quantification analysis of two time-series, of either categorical or continuous values. It provides different methods for profiling cross-recurrence, i.e., only looking at the diagonal recurrent points, as well as more in-depth measures of the whole cross-recurrence plot, e.g., recurrence rate. Please refer to by Coco and Dale (2014) <doi:10.3389/fpsyg.2014.00510> for further details about the method.
Author: Moreno I. Coco and Rick Dale with contributions of James D. Dixon and John Nash
Maintainer: Moreno I. Coco <moreno.cocoi@gmail.com>

Diff between crqa versions 1.0.8 dated 2018-08-19 and 1.0.9 dated 2018-10-12

 DESCRIPTION    |    8 ++++----
 MD5            |    4 ++--
 R/drpdfromts.R |   23 ++---------------------
 3 files changed, 8 insertions(+), 27 deletions(-)

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New package VFS with initial version 1.0.2
Package: VFS
Title: Vegetated Filter Strip and Erosion Model
Version: 1.0.2
Date: 2018-10-01
Authors@R: c(person("Sarah", "Goslee", role = c("aut", "cre"), email = "Sarah.Goslee@ars.usda.gov"), person("Heather", "Gall", role = "aut"), person("Tamie", "Veith", role = "aut"))
Depends: R (>= 3.4.0)
Imports: stats, graphics, e1071, nleqslv (>= 3.3.0)
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Description: Empirical models for runoff, erosion, and phosphorus loss across a vegetated filter strip, given slope, soils, climate, and vegetation (Gall et al., 2018) <doi:10.1007/s00477-017-1505-x>. It also includes functions for deriving climate parameters from measured daily weather data, and for simulating rainfall. Models implemented include MUSLE (Williams, 1975) and APLE (Vadas et al., 2009 <doi:10.2134/jeq2008.0337>).
License: GPL-3
BugReports: https://github.com/sgoslee/VFS/issues
LazyData: true
NeedsCompilation: no
Packaged: 2018-10-01 16:20:35 UTC; sarahg
Author: Sarah Goslee [aut, cre], Heather Gall [aut], Tamie Veith [aut]
Maintainer: Sarah Goslee <Sarah.Goslee@ars.usda.gov>
Repository: CRAN
Date/Publication: 2018-10-12 13:20:10 UTC

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New package varbin with initial version 0.2.1
Package: varbin
Type: Package
Title: Optimal Binning of Continuous and Categorical Variables
Version: 0.2.1
Date: 2018-09-21
Author: Daniel Safai
Maintainer: Daniel Safai <danielsafai@gmail.com>
Description: Tool for easy and efficient discretization of continuous and categorical data. The package calculates the most optimal binning of a given explanatory variable with respect to a user-specified target variable. The purpose is to assign a unique Weight-of-Evidence value to each of the calculated binpoints in order to recode the original variable. The package allows users to impose certain restrictions on the functional form on the resulting binning while maximizing the overall information value in the original data. The package is well suited for logistic scoring models where input variables may be subject to restrictions such as linearity by e.g. regulatory authorities. An excellent source describing in detail the development of scorecards, and the role of Weight-of-Evidence coding in credit scoring is (Siddiqi 2006, ISBN: 978–0-471–75451–0). The package utilizes the discrete nature of decision trees and Isotonic Regression to accommodate the trade-off between flexible functional forms and maximum information value.
License: GPL (>= 2)
Imports: rpart
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-02 12:56:54 UTC; danielsafai
Repository: CRAN
Date/Publication: 2018-10-12 13:50:03 UTC

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Package TBFmultinomial updated to version 0.1.3 with previous version 0.1.2 dated 2018-08-23

Title: TBF Methodology Extension for Multinomial Outcomes
Description: Extends the test-based Bayes factor (TBF) methodology to multinomial regression models and discrete time-to-event models with competing risks. The TBF methodology has been well developed and implemented for the generalised linear model [Held et al. (2015) <doi:10.1214/14-STS510>] and for the Cox model [Held et al. (2016) <doi:10.1002/sim.7089>].
Author: Rachel Heyard [aut, cre]
Maintainer: Rachel Heyard <rachel.heyard@uzh.ch>

Diff between TBFmultinomial versions 0.1.2 dated 2018-08-23 and 0.1.3 dated 2018-10-12

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 8 files changed, 98 insertions(+), 80 deletions(-)

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New package slouch with initial version 2.1.0
Package: slouch
Type: Package
Title: Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses
Version: 2.1.0
Date: 2018-10-02
Authors@R: c(person("Bj\u00F8rn Tore", "Kopperud", role =c("aut", "cre"), email = "b.t.kopperud@nhm.uio.no"), person("Jason", "Pienaar", role = c("aut")), person("Kjetil Lysne", "Voje", role = c("aut")), person("Steven Hecht", "Orzack", role = c("aut")), person("Thomas F.", "Hansen", role = c("aut")), person("Mark", "Grabowski", role = c("ctb")))
Description: An implementation of a phylogenetic comparative method. It can fit univariate among-species Ornstein-Uhlenbeck models of phenotypic trait evolution, where the trait evolves towards a primary optimum. The optimum can be modelled as a single parameter, as multiple discrete regimes on the phylogenetic tree, and/or with continuous covariates.
License: GPL-2
LazyData: FALSE
ByteCompile: FALSE
RoxygenNote: 6.1.0
Depends: R (>= 3.0.0), base, stats
Imports: parallel, ape, memoise
Suggests: knitr, rmarkdown, bookdown, testthat
URL: http://github.com/kopperud/slouch
BugReports: http://github.com/kopperud/slouch/issues
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-10-02 15:50:37 UTC; bjorntko
Author: Bjørn Tore Kopperud [aut, cre], Jason Pienaar [aut], Kjetil Lysne Voje [aut], Steven Hecht Orzack [aut], Thomas F. Hansen [aut], Mark Grabowski [ctb]
Maintainer: Bjørn Tore Kopperud <b.t.kopperud@nhm.uio.no>
Repository: CRAN
Date/Publication: 2018-10-12 13:50:06 UTC

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New package RcppNLoptExample with initial version 0.0.1
Package: RcppNLoptExample
Type: Package
Title: 'Rcpp' Package Illustrating Header-Only Access to 'NLopt'
Version: 0.0.1
Date: 2018-10-01
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Description: An example package which shows use of 'NLopt' functionality from C++ via 'Rcpp' without requiring linking, and relying just on 'nloptr' thanks to the exporting API added there by Jelmer Ypma. This package is a fully functioning, updated, and expanded version of the initial example by Julien Chiquet at <https://github.com/jchiquet/RcppArmadilloNLoptExample> also containing a large earlier pull request of mine.
License: GPL (>= 2)
Encoding: UTF-8
LinkingTo: Rcpp, nloptr (>= 1.2.0)
Imports: Rcpp, nloptr (>= 1.2.0)
Depends: R (>= 3.0.2)
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-10-02 02:32:59 UTC; edd
Repository: CRAN
Date/Publication: 2018-10-12 13:40:02 UTC

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New package pmpp with initial version 0.1.0
Package: pmpp
Type: Package
Title: Posterior Mean Panel Predictor
Version: 0.1.0
Date: 2018-09-23
Authors@R: person("Michal", "Oleszak", email = "oleszak.michal@gmail.com", role = c("aut", "cre"))
Description: Dynamic panel modelling framework based on an empirical-Bayes approach. Contains tools for computing point forecasts and bootstrapping prediction intervals. Reference: Liu et al. (2016) <doi:10.2139/ssrn.2889000>.
URL: https://github.com/veneficusnl/pmpp
BugReports: https://github.com/veneficusnl/pmpp/issues
License: GPL (>= 2)
Depends: R (>= 3.4.0)
Imports: plm, pracma, MASS, Matrix, minqa, dplyr, data.table, moments, magrittr, ggplot2, stats, utils, graphics
Suggests: testthat, lintr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-01 21:09:02 UTC; Asus
Author: Michal Oleszak [aut, cre]
Maintainer: Michal Oleszak <oleszak.michal@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-12 13:50:09 UTC

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New package learnPopGen with initial version 0.9.8
Package: learnPopGen
Version: 0.9.8
Date: 2018-10-1
Title: Population Genetic Simulations & Numerical Analysis
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Depends: R (>= 2.6)
Imports: grDevices, graphics, gtools, methods, phytools, stats
Suggests:
ZipData: no
Description: Conducts various numerical analyses and simulations in population genetics and evolutionary theory, primarily for the purpose of teaching (and learning about) key concepts in population & quantitative genetics, and evolutionary theory.
License: GPL (>= 2)
URL: http://github.com/liamrevell/PopGen
Packaged: 2018-10-01 19:51:28 UTC; liamj
Repository: CRAN
Date/Publication: 2018-10-12 13:20:03 UTC
NeedsCompilation: no

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New package ioanalysis with initial version 0.1
Package: ioanalysis
Title: Input Output Analysis
Version: 0.1
Authors@R: c( person("John", "Wade", email = "jjpwade2@illinois.edu", role = c("aut", "cre")), person("Ignacio", "Sarmiento-Barbieri", email = "srmntbr2@illinois.edu", role = c("aut")))
Author: John Wade [aut, cre], Ignacio Sarmiento-Barbieri [aut]
Maintainer: John Wade <jjpwade2@illinois.edu>
Description: Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>, Ghosh, A. (1958) <doi:10.2307/2550694>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
Depends: R (>= 3.4.0)
License: GPL (>= 2)
URL: http://www.real.illinois.edu
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-10-01 19:14:16 UTC; JJPWade
Repository: CRAN
Date/Publication: 2018-10-12 13:20:06 UTC

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New package HARModel with initial version 0.1
Package: HARModel
Type: Package
Title: Heterogeneous Autoregressive Models
Version: 0.1
Date: 2018-09-26
Author: Emil Sjoerup
Maintainer: Emil Sjoerup <emilsjoerup@live.dk>
Description: Estimation, simulation, and forecasting using the HAR model from Corsi(2009) <DOI:10.1093/jjfinec/nbp001>.
License: GPL-3
Imports: Rcpp (>= 0.12.17) , xts, zoo, sandwich,
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Depends: R (>= 2.10), methods
Packaged: 2018-10-02 06:00:33 UTC; emils
Repository: CRAN
Date/Publication: 2018-10-12 14:00:02 UTC

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New package descstatsr with initial version 0.1.0
Package: descstatsr
Type: Package
Title: Descriptive Univariate Statistics
Version: 0.1.0
Author: Harish Kumar
Maintainer: Harish Kumar <kadamatiharish@gmail.com>
Description: It generates summary statistics on the input dataset using different descriptive univariate statistical measures on entire data or at a group level. Though there are other packages which does similar job but each of these are deficient in one form or other, in the measures generated, in treating numeric, character and date variables alike, no functionality to view these measures on a group level or the way the output is represented. Given the foremost role of the descriptive statistics in any of the exploratory data analysis or solution development, there is a need for a more constructive, structured and refined version over these packages. This is the idea behind the package and it brings together all the required descriptive measures to give an initial understanding of the data quality, distribution in a faster,easier and elaborative way.The function brings an additional capability to be able to generate these statistical measures on the entire dataset or at a group level. It calculates measures of central tendency (mean, median), distribution (count, proportion), dispersion (min, max, quantile, standard deviation, variance) and shape (skewness, kurtosis). Addition to these measures, it provides information on the data type, count on no. of rows, unique entries and percentage of missing entries. More importantly the measures are generated based on the data types as required by them,rather than applying numerical measures on character and data variables and vice versa. Output as a dataframe object gives a very neat representation, which often is useful when working with a large number of columns. It can easily be exported as csv and analyzed further or presented as a summary report for the data.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: datasets,zoo,moments
Suggests: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-01 18:05:07 UTC; sudo
Repository: CRAN
Date/Publication: 2018-10-12 13:10:03 UTC

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New package balance with initial version 0.1.6
Package: balance
Title: Visualize Balances of Compositional Data
Version: 0.1.6
URL: http://github.com/tpq/balance
BugReports: http://github.com/tpq/balance/issues
Authors@R: c( person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")) )
Description: Balances have become a cornerstone of compositional data analysis. However, conceptualizing balances is difficult, especially for high-dimensional data. Most often, investigators visualize balances with "balance dendrograms". However, this visualization tool does not scale well for large data. This package provides an alternative scheme for visualizing balances, described in [Quinn (2018) <DOI:10.12688/f1000research.15858.1>]. This package also provides a method for principal balance analysis.
License: GPL-2
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Encoding: UTF-8
Imports: methods, ggplot2, grid
Depends: R (>= 3.2.2)
Suggests: ape, ggthemes, knitr, philr, propr, reshape2, rmarkdown, robCompositions, testthat
NeedsCompilation: no
Packaged: 2018-10-02 08:28:52 UTC; thom
Author: Thomas Quinn [aut, cre]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-12 13:30:03 UTC

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New package AlphaSimR with initial version 0.8.1
Package: AlphaSimR
Type: Package
Title: Breeding Program Simulations
Version: 0.8.1
Date: 2018-10-01
Authors@R: c(person("Chris", "Gaynor", email = "gaynor.robert@hotmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0558-6656")), person("Gregor", "Gorjanc", role = "ctb", comment = c(ORCID = "0000-0001-8008-2787")), person("David", "Wilson", role = "ctb"), person("Daniel", "Money", role = "ctb"), person("John", "Hickey", role = "ctb", comment = c(ORCID = "0000-0001-5675-3974")))
Description: The successor to the 'AlphaSim' software for breeding program simulation (Faux et al., 2016, <doi:10.3835/plantgenome2016.02.0013>). Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history (Chen et al., 2009, <doi:10.1101/gr.083634.108>).
License: MIT + file LICENSE
URL: https://alphagenes.roslin.ed.ac.uk/wp/software/alphasimr/, https://bitbucket.org/hickeyjohnteam/alphasimr
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0), methods, R6
Imports: Rcpp (>= 0.12.7)
LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-10-01 17:43:20 UTC; rgaynor
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>), Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>), David Wilson [ctb], Daniel Money [ctb], John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>)
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Repository: CRAN
Date/Publication: 2018-10-12 13:10:06 UTC

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Package PxWebApiData updated to version 0.2.0 with previous version 0.1.0 dated 2018-06-06

Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Øyvind Langsrud and Jan Bruusgaard
Maintainer: Øyvind Langsrud <oyl@ssb.no>

Diff between PxWebApiData versions 0.1.0 dated 2018-06-06 and 0.2.0 dated 2018-10-12

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Package binb updated to version 0.0.3 with previous version 0.0.2 dated 2018-09-27

Title: 'binb' is not 'Beamer'
Description: A collection of 'LaTeX' styles using 'Beamer' customization for pdf-based presentation slides in 'RMarkdown'. At present it contains 'RMarkdown' adaptations of the LaTeX themes 'Metropolis' (formerly 'mtheme') theme by Matthias Vogelgesang and others (now included in 'TeXLive'), the 'IQSS' by Ista Zahn (which is included here), and the 'Monash' theme by Rob J Hyndman. Additional (free) fonts may be needed: 'Metropolis' prefers 'Fira', and 'IQSS' requires 'Libertinus'.
Author: Dirk Eddelbuettel, Ista Zahn and Rob Hyndman
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between binb versions 0.0.2 dated 2018-09-27 and 0.0.3 dated 2018-10-12

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Package mMPA updated to version 1.2.0 with previous version 0.1.0 dated 2017-03-22

Title: Implementation of Marker-Assisted Mini-Pooling with Algorithm
Description: To determine the number of quantitative assays needed for a sample of data using pooled testing methods, which include mini-pooling (MP), MP with algorithm (MPA), and marker-assisted MPA (mMPA). To estimate the number of assays needed, the package also provides a tool to conduct Monte Carlo (MC) to simulate different orders in which the sample would be collected to form pools. Using MC avoids the dependence of the estimated number of assays on any specific ordering of the samples to form pools.
Author: "Tao Liu, PhD <tliu@stat.brown.edu> [aut, cre]" "Yizhen Xu, ScM <yizhen_xu@brown.edu> [aut]"
Maintainer: "Tao Liu, PhD" <tliu@stat.brown.edu>

Diff between mMPA versions 0.1.0 dated 2017-03-22 and 1.2.0 dated 2018-10-12

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Package mrfDepth updated to version 1.0.10 with previous version 1.0.9 dated 2018-09-26

Title: Depth Measures in Multivariate, Regression and Functional Settings
Description: Tools to compute depth measures and implementations of related tasks such as outlier detection, data exploration and classification of multivariate, regression and functional data.
Author: Pieter Segaert [aut], Mia Hubert [aut], Peter Rousseeuw [aut], Jakob Raymaekers [aut, cre], Kaveh Vakili [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>

Diff between mrfDepth versions 1.0.9 dated 2018-09-26 and 1.0.10 dated 2018-10-12

 DESCRIPTION         |    8 ++++----
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 man/dprojdepth.Rd   |    2 +-
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Package komaletter updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-13

Title: Simple yet Flexible Letters via the 'KOMA-Script LaTeX Bundle'
Description: An R Markdown template for writing beautiful yet versatile letters, using the 'KOMA-Script' letter class 'scrlttr2' and an adaptation of the 'pandoc-letter' template. 'scrlttr2' provides layouts for many different window envelope types and the possibility to define your own.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>), Dirk Eddelbuettel [aut], Aaron Wolen [aut]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>

Diff between komaletter versions 0.2.0 dated 2018-04-13 and 0.3.0 dated 2018-10-12

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Package ExPanDaR updated to version 0.3.0 with previous version 0.2.0 dated 2018-05-11

Title: Explore Panel Data Interactively
Description: Provides a shiny-based front end (the 'ExPanD' app) and a set of functions for exploratory panel data analysis. Run as a web-based app, 'ExPanD' enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can also use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use 'ExPanD' and/or the functions of this package.
Author: Joachim Gassen [aut, cre] (<https://orcid.org/0000-0003-4364-2911>)
Maintainer: Joachim Gassen <gassen@wiwi.hu-berlin.de>

Diff between ExPanDaR versions 0.2.0 dated 2018-05-11 and 0.3.0 dated 2018-10-12

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Package trackeR updated to version 1.2.0 with previous version 1.1 dated 2018-09-24

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

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Package bamlss updated to version 1.0-1 with previous version 1.0-0 dated 2018-04-13

Title: Bayesian Additive Models for Location Scale and Shape (and Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2017) <doi:10.1080/10618600.2017.1407325>.
Author: Nikolaus Umlauf [aut, cre], Nadja Klein [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Meike Koehler [aut], Thorsten Simon [ctb], Stanislaus Stadlmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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Package ddsPLS updated to version 1.0.1 with previous version 1.0.0 dated 2018-09-19

Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>

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Package survey updated to version 3.34 with previous version 3.33-2 dated 2018-03-12

Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>

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Package SQRL updated to version 0.5.0 with previous version 0.4.0 dated 2018-06-03

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

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Package bayesTFR updated to version 6.2-0 with previous version 6.1-2 dated 2018-01-19

Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu), Bailey Fosdick (bfosdick@uw.edu), Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Thu, 11 Oct 2018

Package globals updated to version 0.12.4 with previous version 0.12.3 dated 2018-09-17

Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package ttScreening updated to version 1.6 with previous version 1.5 dated 2014-11-14

Title: Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples
Description: A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.
Author: Meredith Ray, Xin Tong, Hongmei Zhang
Maintainer: Meredith Ray <maray@memphis.edu>

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Package ITNr updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-26

Title: Analysis of the International Trade Network
Description: Functions to clean and process international trade data into an international trade network (ITN) are provided. It then provides a set a functions to undertake analysis and plots of the ITN (extract the backbone, centrality, blockmodels, clustering). Examining the key players in the ITN and regional trade patterns.
Author: Matthew Smith
Maintainer: Matthew Smith <matt_smith.90@hotmail.co.uk>

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Package remotes updated to version 2.0.0 with previous version 1.1.1 dated 2017-12-20

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package is a lightweight replacement of the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre], Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], RStudio [cph], Martin Morgan [aut], Dan Tenenbaum [aut], Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package pkgload updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-07

Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Jim Hester <james.hester@rstudio.com>

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Package dslabs updated to version 0.5.0 with previous version 0.4.0 dated 2018-08-02

Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops.
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>

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Package VBLPCM updated to version 2.4.5 with previous version 2.4.4 dated 2015-12-18

Title: Variational Bayes Latent Position Cluster Model for Networks
Description: Fit and simulate latent position and cluster models for network data, using a fast Variational Bayes approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend <mike.saltertownshend@gmail.com>

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Package sysfonts updated to version 0.8 with previous version 0.7.2 dated 2018-01-16

Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts <https://fonts.google.com/> into R, in order to support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package Rlabkey updated to version 2.2.3 with previous version 2.2.2 dated 2018-07-12

Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, <http://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

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Package GetLattesData updated to version 1.2 with previous version 1.1 dated 2018-08-19

Title: Reading Bibliometric Data from Lattes Platform
Description: A simple API for downloading and reading xml data directly from Lattes <http://lattes.cnpq.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetLattesData versions 1.1 dated 2018-08-19 and 1.2 dated 2018-10-11

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Package tidyLPA updated to version 0.2.2 with previous version 0.2.1 dated 2018-10-11

Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Daniel Anderson [ctb], Caspar van Lissa [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

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Package Rodam updated to version 0.1.4 with previous version 0.1.3 dated 2018-06-01

Title: Wrapper Functions for 'ODAM' (Open Data for Access and Mining) Web Services
Description: 'ODAM' (Open Data for Access and Mining) is a framework that implements a simple way to make research data broadly accessible and fully available for reuse, including by a script language such as R. The main purpose is to make a data set accessible online with a minimal effort from the data provider, and to allow any scientists or bioinformaticians to be able to explore the data set and then extract a subpart or the totality of the data according to their needs. The Rodam package has only one class, 'odamws', that provides methods to allow you to retrieve online data using 'ODAM' Web Services. This obviously requires that data are implemented according the 'ODAM' approach , namely that the data subsets were deposited in the suitable data repository in the form of TSV files associated with their metadata also described in TSV files. See <http://www.slideshare.net/danieljacob771282/odam-open-data-access-and-mining>.
Author: Daniel Jacob [cre, aut] (<https://orcid.org/0000-0002-6687-7169>)
Maintainer: Daniel Jacob <daniel.jacob@inra.fr>

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Package GSODR updated to version 1.2.3 with previous version 1.2.2 dated 2018-08-17

Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
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. 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] (<https://orcid.org/0000-0002-0061-8359>), Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>), Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>), Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>), Bob Rudis [cph, ctb] (<https://orcid.org/0000-0001-5670-2640>), Gwenael Giboire [ctb] (Several bug reports in early versions and testing feedback), Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation), Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package FLightR updated to version 0.4.7 with previous version 0.4.6 dated 2017-03-14

Title: A Package for Reconstructing Animal Paths from Solar Geolocation Loggers
Description: Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology (Rakhimberdiev et al., 2015)<doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution (Rakhimberdiev et al., 2017)<doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology (Rakhimberdiev et al. 2016)<doi:10.1111/jav.00891>.
Author: Eldar Rakhimberdiev [aut, cre], Anatoly Saveliev [aut], Julia Karagicheva [aut], Simeon Lisovski [ctb]
Maintainer: Eldar Rakhimberdiev <eldar@nioz.nl>

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Package stacomiR updated to version 0.5.4.0 with previous version 0.5.3.1 dated 2018-01-04

Title: Fish Migration Monitoring
Description: Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Agency for Biodiversity (AFB) institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Author: Cedric Briand [aut, cre], Marion Legrand [aut], Timothee Besse [aut]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>

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Package polyCub updated to version 0.7.0 with previous version 0.6.1 dated 2017-10-02

Title: Cubature over Polygonal Domains
Description: Numerical integration of continuously differentiable functions f(x,y) over simple closed polygonal domains. The following cubature methods are implemented: product Gauss cubature (Sommariva and Vianello, 2007, <doi:10.1007/s10543-007-0131-2>), the simple two-dimensional midpoint rule (wrapping 'spatstat' functions), adaptive cubature for radially symmetric functions via line integrate() along the polygon boundary (Meyer and Held, 2014, <doi:10.1214/14-AOAS743>, Supplement B), and integration of the bivariate Gaussian density based on a triangulation of the polygonal domain. For simple integration along the axes, the packages 'cubature' and 'R2Cuba' are more appropriate.
Author: Sebastian Meyer [aut, cre, trl] (<https://orcid.org/0000-0002-1791-9449>), Leonhard Held [ths], Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>

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Package partialCI updated to version 1.2.0 with previous version 1.1.1 dated 2018-03-06

Title: Partial Cointegration
Description: A collection of time series is partially cointegrated if a linear combination of these time series can be found so that the residual spread is partially autoregressive - meaning that it can be represented as a sum of an autoregressive series and a random walk. This concept is useful in modeling certain sets of financial time series and beyond, as it allows for the spread to contain transient and permanent components alike. Partial cointegration has been introduced by Clegg and Krauss (2017) <doi:10.1080/14697688.2017.1370122>, along with a large-scale empirical application to financial market data. The partialCI package comprises estimation, testing, and simulation routines for partial cointegration models in state space. Clegg et al. (2017) <https://hdl.handle.net/10419/150014> provide an in in-depth discussion of the package functionality as well as illustrating examples in the fields of finance and macroeconomics.
Author: Matthew Clegg [aut], Christopher Krauss [aut], Jonas Rende [cre, aut]
Maintainer: Jonas Rende <jonas.rende@fau.de>

Diff between partialCI versions 1.1.1 dated 2018-03-06 and 1.2.0 dated 2018-10-11

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Permanent link

Package drfit updated to version 0.7.2 with previous version 0.7.1 dated 2017-07-19

Title: Dose-Response Data Evaluation
Description: A somewhat outdated package of basic and easy-to-use functions for fitting dose-response curves to continuous dose-response data, calculating some toxicological parameters and plotting the results. Please consider using the more powerful and actively developed 'drc' package. Functions that are fitted are the cumulative density function of the log-normal distribution ('probit' fit), of the logistic distribution ('logit' fit), of the Weibull distribution ('weibull' fit) and a linear-logistic model ('linlogit' fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving dose-response data retrieved from a database accessed via 'odbc' are included. As an alternative to the original fitting methods, the algorithms from the 'drc' package can be used.
Author: Johannes Ranke [aut, cre] (<https://orcid.org/0000-0003-4371-6538>)
Maintainer: Johannes Ranke <jranke@uni-bremen.de>

Diff between drfit versions 0.7.1 dated 2017-07-19 and 0.7.2 dated 2018-10-11

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Package antaresViz updated to version 0.15.0 with previous version 0.14.0 dated 2018-06-12

Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations. You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>.
Author: Jalal-Edine ZAWAM [aut, cre], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], Baptiste SEGUINOT [ctb], RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>

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Package tidyLPA updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-13

Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Daniel Anderson [ctb], Caspar van Lissa [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

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Package RMCriteria updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-13

Title: Multicriteria Package
Description: Provides a methodology to solve most of multicriteria ranking problems using partial and total pre-order from Promethee methods. Albuquerque & Montenegro (2015) <doi:10.1080/03610926.2014.942432>.
Author: Pedro Albuquerque and Gustavo Monteiro
Maintainer: Pedro Albuquerque <pedroa@unb.br>

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Package itunesr updated to version 0.1.3 with previous version 0.1.2 dated 2018-09-14

Title: Access iTunes App Store Ratings and Reviews using R
Description: To enable 'iOS' App Developers to access iTunes App Store Ratings and Reviews using R to extract Basic App Information and Reviews submitted by their App users, Since Apple Store does not provide this straightforward.
Author: AbdulMajedRaja RS [aut, cre]
Maintainer: AbdulMajedRaja RS <amrrs.data@gmail.com>

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Package BatchGetSymbols updated to version 2.2 with previous version 2.1 dated 2018-05-08

Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo or Google Finance.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package wevid updated to version 0.5.1 with previous version 0.4.2 dated 2018-06-15

Title: Quantifying Performance of a Binary Classifier Through Weight of Evidence
Description: The distributions of the weight of evidence (log Bayes factor) favouring case over noncase status in a test dataset (or test folds generated by cross-validation) can be used to quantify the performance of a diagnostic test (McKeigue (2018), <doi:10.1177/0962280218776989>). The package can be used with any test dataset on which you have observed case-control status and have computed prior and posterior probabilities of case status using a model learned on a training dataset. To quantify how the predictor will behave as a risk stratifier, the quantiles of the distributions of weight of evidence in cases and controls can be calculated and plotted.
Author: Paul McKeigue [aut] (<https://orcid.org/0000-0002-5217-1034>), Marco Colombo [ctb, cre] (<https://orcid.org/0000-0001-6672-0623>)
Maintainer: Marco Colombo <m.colombo@ed.ac.uk>

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Package tidyselect updated to version 0.2.5 with previous version 0.2.4 dated 2018-02-26

Title: Select from a Set of Strings
Description: A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package bayesmeta updated to version 2.3 with previous version 2.2 dated 2018-04-12

Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, posterior predictive p-values, etc.
Author: Christian Roever [aut, cre] (<https://orcid.org/0000-0002-6911-698X>), Tim Friede [ctb] (<https://orcid.org/0000-0001-5347-7441>)
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>

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Package GROAN updated to version 1.2.0 with previous version 1.1.0 dated 2017-10-07

Title: Genomic Regression Workbench
Description: Workbench for testing genomic regression accuracy on (optionally noisy) phenotypes.
Author: Nelson Nazzicari & Filippo Biscarini
Maintainer: Nelson Nazzicari <nelson.nazzicari@gmail.com>

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Package FisherEM updated to version 1.5.1 with previous version 1.5 dated 2018-10-09

Title: The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data
Description: The FisherEM algorithm, proposed by Bouveyron & Brunet (201) <doi:10.1007/s11222-011-9249-9>, is an efficient method for the clustering of high-dimensional data. FisherEM models and clusters the data in a discriminative and low-dimensional latent subspace. It also provides a low-dimensional representation of the clustered data. A sparse version of Fisher-EM algorithm is also provided.
Author: Charles Bouveyron and Camille Brunet
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

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Package eplusr updated to version 0.9.3 with previous version 0.9.2 dated 2018-09-30

Title: A Toolkit for Using Whole Building Simulation Program 'EnergyPlus'
Description: A rich toolkit of using the whole building simulation program 'EnergyPlus'(<https://energyplus.net>), which enables programmatic navigation, modification of 'EnergyPlus' models and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuanjia@cqu.edu.cn>

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Package docopt updated to version 0.6.1 with previous version 0.6 dated 2018-08-03

Title: Command-Line Interface Specification Language
Description: Define a command-line interface by just giving it a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

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Package ggeffects updated to version 0.6.0 with previous version 0.5.0 dated 2018-08-11

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are ggpredict() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package ncf updated to version 1.2-6 with previous version 1.2-5 dated 2018-05-24

Title: Spatial Covariance Functions
Description: R functions for analyzing spatial (cross-)covariance: the nonparametric (cross-)covariance function, the spline correlogram, the nonparametric phase coherence function, local indicators of spatial association (LISA), (Mantel) correlogram, (Partial) Mantel test.
Author: Ottar N. Bjornstad [aut, cre], Jun Cai [ctb]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Package EcoVirtual updated to version 1.1 with previous version 1.0 dated 2016-06-29

Title: Simulation of Ecological Models
Description: Computer simulations of classical ecological models as a learning resource.
Author: Alexandre Adalardo de Oliveira and Paulo Inacio Prado <ecovirtualpackage@gmail.com>
Maintainer: Alexandre Adalardo de Oliveira <ecovirtualpackage@gmail.com>

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Package CAST updated to version 0.3.0 with previous version 0.2.1 dated 2018-07-12

Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. This package includes functions to improve spatial-temporal modelling tasks using 'caret'. It prepares data for Leave-Location-Out and Leave-Time-Out cross-validation which are target-oriented validation strategies for spatial-temporal models. To decrease overfitting and improve model performances, the package implements a forward feature selection that selects suitable predictor variables in view to their contribution to the target-oriented performance.
Author: Hanna Meyer [cre, aut], Chris Reudenbach [ctb], Marvin Ludwig [ctb], Thomas Nauss [ctb]
Maintainer: Hanna Meyer <hanna.meyer@geo.uni-marburg.de>

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Wed, 10 Oct 2018

Package RSDA updated to version 2.0.8 with previous version 2.0.7 dated 2018-10-05

Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>

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Package clhs updated to version 0.7-0 with previous version 0.6-0 dated 2018-04-12

Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728-46>).
Author: Pierre Roudier [aut, cre], Colby Brugnard [ctb], Dylan Beaudette [ctb], Benjamin Louis [ctb]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>

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Package BiocManager updated to version 1.30.3 with previous version 1.30.2 dated 2018-08-24

Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>

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Package GetHFData updated to version 1.6 with previous version 1.5 dated 2017-11-28

Title: Download and Aggregate High Frequency Trading Data from Bovespa
Description: Downloads and aggregates high frequency trading data for Brazilian instruments directly from Bovespa ftp site <ftp://ftp.bmf.com.br/MarketData/>.
Author: Marcelo Perlin [aut, cre], Henrique Ramos [ctb]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package ca updated to version 0.71 with previous version 0.70 dated 2016-12-14

Title: Simple, Multiple and Joint Correspondence Analysis
Description: Computation and visualization of simple, multiple and joint correspondence analysis.
Author: Michael Greenacre [aut], Oleg Nenadic [aut, cre], Michael Friendly [ctb]
Maintainer: Oleg Nenadic <onenadi@uni-goettingen.de>

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Package rcheology updated to version 3.5.1.1 with previous version 3.5.1.0 dated 2018-07-20

Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package emdi updated to version 1.1.4 with previous version 1.1.3 dated 2018-07-24

Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation and the model-based approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel.
Author: Ann-Kristin Kreutzmann [aut], Soeren Pannier [aut, cre], Natalia Rojas-Perilla [aut], Timo Schmid [aut], Matthias Templ [aut], Nikos Tzavidis [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>

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Package breathteststan updated to version 0.4.4 with previous version 0.4.3 dated 2018-07-30

Title: Stan-Based Fit to Gastric Emptying Curves
Description: Stan-based curve-fitting function for use with package 'breathtestcore' by the same author. Stan functions are refactored here for easier testing.
Author: Dieter Menne [aut, cre], Menne Biomed Consulting Tuebingen [cph], Benjamin Misselwitz [fnd], Mark Fox [fnd], University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>

Diff between breathteststan versions 0.4.3 dated 2018-07-30 and 0.4.4 dated 2018-10-10

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New package saemix with initial version 2.2
Package: saemix
Type: Package
Title: Stochastic Approximation Expectation Maximization (SAEM) Algorithm
Version: 2.2
Date: 2018-10-05
Author: Emmanuelle Comets, Audrey Lavenu, Marc Lavielle (2017) <doi:10.18637/jss.v080.i03>
Maintainer: Emmanuelle Comets <emmanuelle.comets@inserm.fr>
Description: The SAEMIX package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. The SAEM algorithm: - computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, - provides standard errors for the maximum likelihood estimator - estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm. Several applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group (<http://group.monolix.org/>).
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Suggests: testthat (>= 0.3)
Imports: graphics, stats, methods
Collate: 'aaa_generics.R' 'SaemixData.R' 'SaemixModel.R' 'SaemixRes.R' 'SaemixObject.R' 'compute_LL.R' 'func_FIM.R' 'func_aux.R' 'func_distcond.R' 'func_plots.R' 'func_simulations.R' 'main.R' 'main_estep.R' 'main_initialiseMainAlgo.R' 'main_mstep.R' 'zzz.R'
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-10 13:09:15 UTC; eco
Repository: CRAN
Date/Publication: 2018-10-10 16:00:03 UTC

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New package revealedPrefs with initial version 0.4
Package: revealedPrefs
Type: Package
Title: Revealed Preferences and Microeconomic Rationality
Version: 0.4
Date: 2018-10-10
Author: Julien Boelaert <jubo.stats@gmail.com>
Maintainer: Julien Boelaert <jubo.stats@gmail.com>
Description: Computation of (direct and indirect) revealed preferences, fast non-parametric tests of rationality axioms (WARP, SARP, GARP), simulation of axiom-consistent data, and detection of axiom-consistent subpopulations. Rationality tests follow Varian (1982) <doi:10.2307/1912771>, axiom-consistent subpopulations follow Crawford and Pendakur (2012) <doi:10.1111/j.1468-0297.2012.02545.x>.
License: GPL (>= 3)
Imports: pso
Depends: Rcpp
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2018-10-10 15:01:42 UTC; bart
Repository: CRAN
Date/Publication: 2018-10-10 16:00:20 UTC

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Package digest updated to version 0.6.18 with previous version 0.6.17 dated 2018-09-12

Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, Michel Lang, Viliam Simko, Kurt Hornik and Radford Neal.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between digest versions 0.6.17 dated 2018-09-12 and 0.6.18 dated 2018-10-10

 ChangeLog                  |   27 
 DESCRIPTION                |    8 
 MD5                        |   22 
 README.md                  |    2 
 inst/doc/sha1.html         |    4 
 src/digest.c               |   84 +-
 src/pmurhash.c             |    2 
 src/sha2.c                 |   27 
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 12 files changed, 1131 insertions(+), 818 deletions(-)

More information about digest at CRAN
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Package rhierbaps updated to version 1.1.0 with previous version 1.0.0 dated 2018-07-20

Title: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Description: Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
Author: Gerry Tonkin-Hill [cre, aut]
Maintainer: Gerry Tonkin-Hill <g.tonkinhill@gmail.com>

Diff between rhierbaps versions 1.0.0 dated 2018-07-20 and 1.1.0 dated 2018-10-10

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More information about rhierbaps at CRAN
Permanent link

Package MTS updated to version 1.0 with previous version 0.33 dated 2015-02-12

Title: All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models
Description: Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index, transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.
Author: Ruey S. Tsay and David Wood
Maintainer: Ruey S. Tsay <ruey.tsay@chicagobooth.edu>

Diff between MTS versions 0.33 dated 2015-02-12 and 1.0 dated 2018-10-10

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More information about MTS at CRAN
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New package uwIntroStats with initial version 0.0.7
Package: uwIntroStats
Type: Package
Title: Descriptive Statistics, Inference, Regression, and Plotting in an Introductory Statistics Course
Version: 0.0.7
Date: 2018-10-9
Maintainer: Travis Y. Hee Wai <theewai@uw.edu>
Authors@R: c(person(given = "Scott S.", family = "Emerson", role = "aut"), person(given = "Andrew J.", family = "Spieker", role = "aut"), person(given = "Brian D.", family = "Williamson", role= "aut"), person(given = "Travis Y.", family = "Hee Wai", role = c("aut","cre"),email="theewai@uw.edu"), person(given = "Solomon", family = "Lim", role = "aut"), person("R Core Team", role = "ctb"), person(given = "Terry M", family = "Therneu", role = "ctb"), person("Thomas", "Lumley", role = "ctb"))
Description: A set of tools designed to facilitate easy adoption of R for students in introductory classes with little programming experience. Compiles output from existing routines together in an intuitive format, and adds functionality to existing functions. For instance, the regression function can perform linear models, generalized linear models, Cox models, or generalized estimating equations. The user can also specify multiple-partial F-tests to print out with the model coefficients. We also give many routines for descriptive statistics and plotting.
Imports: Exact, geepack, plyr, survival, sandwich
License: GPL-2
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-10 02:27:52 UTC; theewai
Author: Scott S. Emerson [aut], Andrew J. Spieker [aut], Brian D. Williamson [aut], Travis Y. Hee Wai [aut, cre], Solomon Lim [aut], R Core Team [ctb], Terry M Therneu [ctb], Thomas Lumley [ctb]
Repository: CRAN
Date/Publication: 2018-10-10 11:50:02 UTC

More information about uwIntroStats at CRAN
Permanent link

Package tsibble updated to version 0.5.3 with previous version 0.5.2 dated 2018-09-11

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

Diff between tsibble versions 0.5.2 dated 2018-09-11 and 0.5.3 dated 2018-10-10

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More information about tsibble at CRAN
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Package smcfcs updated to version 1.3.1 with previous version 1.3.0 dated 2017-06-03

Title: Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.
Author: Jonathan Bartlett [aut, cre], Ruth Keogh [aut]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>

Diff between smcfcs versions 1.3.0 dated 2017-06-03 and 1.3.1 dated 2018-10-10

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More information about smcfcs at CRAN
Permanent link

Package CutpointsOEHR updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-06

Title: Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model
Description: Use optimal equal-HR method to determine two optimal cutpoints of a continuous predictor that has a U-shaped relationship with survival outcomes based on Cox regression model. The optimal equal-HR method estimates two optimal cut-points that have approximately the same log hazard value based on Cox regression model and divides individuals into different groups according to their HR values.
Author: Yimin Chen, Zhang Jinxin
Maintainer: Yimin Chen <chenyimin0226@126.com>

Diff between CutpointsOEHR versions 0.1.1 dated 2018-10-06 and 0.1.2 dated 2018-10-10

 DESCRIPTION       |    6 +++---
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 3 files changed, 6 insertions(+), 5 deletions(-)

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Package hNMF updated to version 0.8 with previous version 0.6 dated 2018-06-01

Title: Hierarchical Non-Negative Matrix Factorization
Description: Hierarchical and single-level non-negative matrix factorization. Several NMF algorithms are available.
Author: Nicolas Sauwen
Maintainer: Nicolas Sauwen <nicolas.sauwen@openanalytics.eu>

Diff between hNMF versions 0.6 dated 2018-06-01 and 0.8 dated 2018-10-10

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More information about hNMF at CRAN
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Package airGR updated to version 1.0.15.2 with previous version 1.0.14.1 dated 2018-09-28

Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Description: Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>), Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>), Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>), Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>), Claude Michel [aut, ths], Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>), François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>, 'Parameter estimation' vignettes), Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>), Nicolas Le Moine [ctb], Thibaut Mathevet [ctb], Safouane Mouelhi [ctb], Ludovic Oudin [ctb], Raji Pushpalatha [ctb], Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>

Diff between airGR versions 1.0.14.1 dated 2018-09-28 and 1.0.15.2 dated 2018-10-10

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Package Surrogate updated to version 1.0 with previous version 0.9 dated 2018-06-09

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, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

Diff between Surrogate versions 0.9 dated 2018-06-09 and 1.0 dated 2018-10-10

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Package spotGUI updated to version 0.2.1 with previous version 0.2.0 dated 2018-06-01

Title: Graphical User Interface for the Package 'SPOT'
Description: A graphical user interface for the Sequential Parameter Optimization Toolbox (package 'SPOT'). It includes a quick, graphical setup for spot, interactive 3D plots, export possibilities and more.
Author: Frederik Rehbach [aut, cre], Martin Zaefferer [aut], Thomas Bartz-Beielstein [ctb], Andreas Fischbach [ctb], Lorenzo Gentile [ctb]
Maintainer: Frederik Rehbach <frederik.rehbach@th-koeln.de>

Diff between spotGUI versions 0.2.0 dated 2018-06-01 and 0.2.1 dated 2018-10-10

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Package fiftystater (with last version 1.0.1) was removed from CRAN

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

2016-11-14 1.0.1

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Package DEploid (with last version 0.5.0) was removed from CRAN

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

2018-05-17 0.5.0
2017-08-31 0.4.4
2017-08-09 0.4.2
2017-08-09 0.4.3
2017-07-24 0.4.1
2016-11-25 0.3.2

Permanent link
Package wooldridge updated to version 1.3.1 with previous version 1.3.0 dated 2018-04-09

Title: 111 Data Sets from "Introductory Econometrics: A Modern Approach, 6e" by Jeffrey M. Wooldridge
Description: Students learning both econometrics and R may find the introduction to both challenging. However, if the text is "Introductory Econometrics: A Modern Approach" by Jeffrey M. Wooldridge, they are in luck! The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have all been compressed to a fraction of their original size and are well documented. Documentation files contain the page numbers of the text where each set is used, the original source, time of publication, and notes suggesting ideas for further exploratory data analysis and research. If one need's to brush-up on model syntax, a vignette contains R solutions to examples from each chapter of the text. Data sets are from the 6th edition (Wooldridge 2016, ISBN-13: 978-1-305-27010-7), and are backwards compatible with all versions of the text.
Author: Justin M. Shea [aut, cre], Kennth H. Brown [ctb]
Maintainer: Justin M. Shea <jshea@roosevelt.edu>

Diff between wooldridge versions 1.3.0 dated 2018-04-09 and 1.3.1 dated 2018-10-10

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 NAMESPACE                                        |    4 
 NEWS.md                                          |  168 
 R/admnrev.R                                      |   50 
 R/affairs.R                                      |   78 
 R/airfare.R                                      |   68 
 R/alcohol.R                                      |  106 
 R/apple.R                                        |   74 
 R/approval.R                                     |   72 
 R/athlet1.R                                      |   86 
 R/athlet2.R                                      |   60 
 R/attend.R                                       |   62 
 R/audit.R                                        |   46 
 R/barium.R                                       |  102 
 R/beauty.R                                       |   74 
 R/benefits.R                                     |   76 
 R/beveridge.R                                    |   56 
 R/big9salary.R                                   |  100 
 R/bwght.R                                        |   68 
 R/bwght2.R                                       |   86 
 R/campus.R                                       |   54 
 R/card.R                                         |  108 
 R/catholic.R                                     |   66 
 R/cement.R                                       |  100 
 R/census2000.R                                   |   52 
 R/ceosal1.R                                      |   64 
 R/ceosal2.R                                      |   70 
 R/charity.R                                      |   56 
 R/consump.R                                      |   88 
 R/corn.R                                         |   50 
 R/countymurders.R                                |   80 
 R/cps78_85.R                                     |   70 
 R/cps91.R                                        |   88 
 R/crime1.R                                       |   72 
 R/crime2.R                                       |  108 
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 R/crime4.R                                       |  158 
 R/discrim.R                                      |  114 
 R/driving.R                                      |  152 
 R/earns.R                                        |   68 
 R/econmath.R                                     |   74 
 R/elem94_95.R                                    |   68 
 R/engin.R                                        |   74 
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 R/k401ksubs.R                                    |   62 
 R/kielmc.R                                       |   90 
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 R/lowbrth.R                                      |  112 
 R/mathpnl.R                                      |  144 
 R/meap00_01.R                                    |   58 
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 R/mlb1.R                                         |  134 
 R/mroz.R                                         |   84 
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 R/vote1.R                                        |   60 
 R/vote2.R                                        |   92 
 R/voucher.R                                      |   78 
 R/wage1.R                                        |   88 
 R/wage2.R                                        |   74 
 R/wagepan.R                                      |  128 
 R/wageprc.R                                      |   80 
 R/wine.R                                         |   50 
 README.md                                        |  103 
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 man/happiness.Rd                                 |  118 
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 man/wagepan.Rd                                   |  140 
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 man/wine.Rd                                      |   66 
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 vignettes/Introductory-Econometrics-Examples.Rmd | 1981 +++--
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More information about wooldridge at CRAN
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Package NetworkChange updated to version 0.4 with previous version 0.3 dated 2017-08-19

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>

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Tue, 09 Oct 2018

Package StereoMorph updated to version 1.6.2 with previous version 1.6.1 dated 2017-03-14

Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between StereoMorph versions 1.6.1 dated 2017-03-14 and 1.6.2 dated 2018-10-09

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Package msigdbr updated to version 6.2.1 with previous version 6.1.1 dated 2018-04-12

Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets typically used with the 'Gene Set Enrichment Analysis' (GSEA) software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>) in a standard R data frame with key-value pairs. Included are the original human gene symbols and Entrez IDs as well as the equivalents for various frequently studied model organisms such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>

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Package microbenchmark updated to version 1.4-5 with previous version 1.4-4 dated 2018-01-24

Title: Accurate Timing Functions
Description: Provides infrastructure to accurately measure and compare the execution time of R expressions.
Author: Olaf Mersmann [aut], Claudia Beleites [ctb], Rainer Hurling [ctb], Ari Friedman [ctb], Joshua M. Ulrich [cre]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>

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Package BayesGOF updated to version 5.2 with previous version 5.1 dated 2018-10-05

Title: Bayesian Modeling via Frequentist Goodness-of-Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>

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Package RndTexExams updated to version 1.5 with previous version 1.4.1 dated 2018-01-13

Title: Build and Grade Multiple Choice Exams with Randomized Content
Description: Using as input a 'LaTeX' file with a multiple choice exam, this package will produce several versions with randomized contents of the same exam. Functions for grading are also available.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package evaluate updated to version 0.12 with previous version 0.11 dated 2018-07-17

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

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Package rticles updated to version 0.6 with previous version 0.5 dated 2018-07-06

Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), R Foundation [aut, cph], Hadley Wickham [aut], Journal of Statistical Software [aut, cph], RStudio [cph], Ramnath Vaidyanathan [aut, cph], Association for Computing Machinery [aut, cph], Carl Boettiger [aut, cph], Elsevier [aut, cph], Karl Broman [aut, cph], Kirill Mueller [aut, cph], Bastiaan Quast [aut, cph], Randall Pruim [aut, cph], Ben Marwick [aut, cph], Charlotte Wickham [aut, cph], Oliver Keyes [aut, cph], Miao Yu [aut, cph], Daniel Emaasit [aut, cph], Thierry Onkelinx [aut, cph], Alessandro Gasparini [aut, cph], Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph], MDPI [aut, cph], Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package tsBSS updated to version 0.5.2 with previous version 0.5.1 dated 2018-06-25

Title: 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 (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Joni Virta
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>

Diff between tsBSS versions 0.5.1 dated 2018-06-25 and 0.5.2 dated 2018-10-09

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Package EFAutilities updated to version 1.2.3 with previous version 1.2.2 dated 2018-05-21

Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis are included in this package. In particular, it computes standard errors for parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>

Diff between EFAutilities versions 1.2.2 dated 2018-05-21 and 1.2.3 dated 2018-10-09

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Package intsvy updated to version 2.3 with previous version 2.2 dated 2018-09-20

Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA, ICILS, and PIAAC).
Author: Daniel Caro <dcarov@gmail.com>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <dcarov@gmail.com>

Diff between intsvy versions 2.2 dated 2018-09-20 and 2.3 dated 2018-10-09

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New package RGoogleAnalytics with initial version 0.1.6
Package: RGoogleAnalytics
Version: 0.1.6
Date: 2018-10-01
Title: R Wrapper for the Google Analytics API
Author: Michael Pearmain. Contributions from Nick Mihailowski, Vignesh Prajapati, Kushan Shah, Nicolas Remy and Manuel de Francisco Vera person("Manuel", "de Francisco", email = "mdefraver@hotelspecials.nl", role = c("ctb"))
Description: Provides functions for accessing and retrieving data from the Google Analytics API.
Maintainer: Manuel de Francisco Vera <manueldefrancisco@gmail.com>
BugReports: https://github.com/ManuelDeFrancisco/RGoogleAnalytics/issues
Depends: R(>= 3.0.2), lubridate, httr, digest (>= 0.6.8)
Suggests: testthat
License: Apache License 2.0
NeedsCompilation: no
Repository: CRAN
RoxygenNote: 6.0.1
Packaged: 2018-10-09 13:33:54 UTC; mdefraver
Date/Publication: 2018-10-09 15:30:02 UTC

More information about RGoogleAnalytics at CRAN
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New package FisherEM with initial version 1.5
Package: FisherEM
Type: Package
Title: The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data
Version: 1.5
Date: 2018-10-1
Author: Charles Bouveyron and Camille Brunet
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>
Depends: MASS, elasticnet, parallel
Description: FisherEM is an efficient algorithm for the unsupervised classification of high-dimensional data. FisherEM models and clusters the data in a discriminative and low-dimensional latent subspace. It also provides a low-dimensional representation of the clustered data. A sparse version of Fisher-EM algorithm is also provided.
License: GPL-2
LazyLoad: yes
NeedsCompilation: no
Packaged: 2018-10-09 13:34:33 UTC; bouveyro
Repository: CRAN
Date/Publication: 2018-10-09 15:20:06 UTC

More information about FisherEM at CRAN
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Package bayou updated to version 2.1.1 with previous version 2.1 dated 2018-06-07

Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>

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Package dynamichazard updated to version 0.6.0 with previous version 0.5.3 dated 2018-07-01

Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using state space models. The first implemented model is described in Fahrmeir (1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994) <doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the Extended Kalman filter is replaced by an unscented Kalman filter and other options including particle filters. The implemented particle filters support more general state space models.
Author: Benjamin Christoffersen [cre, aut], Alan Miller [cph], Anthony Williams [cph], Boost developers [cph], R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>

Diff between dynamichazard versions 0.5.3 dated 2018-07-01 and 0.6.0 dated 2018-10-09

 DESCRIPTION                                                                    |    9 
 MD5                                                                            |  263 +-
 NAMESPACE                                                                      |    6 
 NEWS.md                                                                        |   11 
 R/PF.R                                                                         | 1014 ++++++++--
 R/RcppExports.R                                                                |   24 
 R/boot_est.R                                                                   |    5 
 R/ddhazard.R                                                                   |  540 +++--
 R/get_design_matrix.R                                                          |  119 +
 R/hatvalues.R                                                                  |    3 
 R/loglike.R                                                                    |    3 
 R/plot.R                                                                       |   26 
 R/predict.R                                                                    |    3 
 R/residuals.R                                                                  |    2 
 R/static_glm.R                                                                 |   59 
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 inst/doc/Diagnostics.Rmd                                                       |   20 
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 inst/doc/ddhazard.pdf                                                          |binary
 inst/shiny/app.R                                                               |   11 
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 man/PF_control.Rd                                                              |    9 
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 man/ddFixed.Rd                                                                 |    7 
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 man/hatvalues.ddhazard.Rd                                                      |    2 
 man/logLik.ddhazard.Rd                                                         |    2 
 man/plot.PF_clouds.Rd                                                          |    5 
 man/plot.ddhazard.Rd                                                           |    2 
 man/predict.ddhazard.Rd                                                        |    2 
 man/residuals.ddhazard.Rd                                                      |    2 
 man/static_glm.Rd                                                              |    2 
 src/BLAS_LAPACK/arma_BLAS_LAPACK.cpp                                           |    2 
 src/Makevars                                                                   |    4 
 src/Makevars.win                                                               |    6 
 src/PF.cpp                                                                     |  229 +-
 src/PF/PF_data.h                                                               |  221 +-
 src/PF/PF_utils.cpp                                                            |only
 src/PF/PF_utils.h                                                              |  406 ----
 src/PF/PFs.h                                                                   |  211 --
 src/PF/densities.h                                                             |  166 -
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 src/PF/est_params_RW.cpp                                                       |   73 
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 src/PF/get_work_blocks.h                                                       |only
 src/PF/importance_samplers.h                                                   |  257 +-
 src/PF/resamplers.h                                                            |   94 
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 src/PF_fixed_effects.cpp                                                       |  188 +
 src/RcppExports.cpp                                                            |   97 
 src/arma_BLAS_LAPACK.h                                                         |    4 
 src/bigglm_wrapper.cpp                                                         |   70 
 src/bigglm_wrapper.h                                                           |   14 
 src/ddhazard.h                                                                 |   48 
 src/ddhazard/EKF_solver.cpp                                                    |   61 
 src/ddhazard/GMA_solver.cpp                                                    |   15 
 src/ddhazard/SMA_solver.cpp                                                    |   32 
 src/ddhazard/UKF_solver.cpp                                                    |   42 
 src/ddhazard_fit.cpp                                                           |   88 
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 src/family.cpp                                                                 |   20 
 src/family.h                                                                   |  171 +
 src/for_tests.cpp                                                              |   54 
 src/lin_maps.cpp                                                               |   78 
 src/lin_maps.h                                                                 |   33 
 src/loglike.cpp                                                                |   45 
 src/parallel_glm.cpp                                                           |    2 
 src/parallel_qr.cpp                                                            |    3 
 src/parallel_qr.h                                                              |    1 
 src/problem_data.h                                                             |   35 
 src/utils.cpp                                                                  |    8 
 tests/testthat.R                                                               |    2 
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 tests/testthat/helper.R                                                        |    3 
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 tests/testthat/test_GMA.R                                                      |   91 
 tests/testthat/test_PF.R                                                       |  536 ++++-
 tests/testthat/test_SMA.R                                                      |   98 
 tests/testthat/test_UKF.R                                                      |   89 
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 tests/testthat/test_boot_est.R                                                 |   21 
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 tests/testthat/test_hatvalues.R                                                |    6 
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 tests/testthat/test_loglike.R                                                  |   58 
 tests/testthat/test_plot.R                                                     |   22 
 tests/testthat/test_predict.R                                                  |   13 
 tests/testthat/test_print.R                                                    |   20 
 tests/testthat/test_residuals.R                                                |   49 
 tests/testthat/test_static_glm.R                                               |    2 
 tests/testthat/test_summary.R                                                  |    8 
 tests/testthat/test_test_utils.R                                               |    4 
 tests/testthat/test_weights.R                                                  |   13 
 vignettes/Comparing_methods_for_logistic_models.Rmd                            |   63 
 vignettes/Diagnostics.Rmd                                                      |   20 
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Package cffdrs updated to version 1.8.1 with previous version 1.7.6 dated 2017-04-06

Title: Canadian Forest Fire Danger Rating System
Description: This project provides a group of new functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System. Some functions have two versions, table and raster based.
Author: Xianli Wang, Alan Cantin, Marc-André Parisien, Mike Wotton, Kerry Anderson, Brett Moore, Tom Schiks, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>

Diff between cffdrs versions 1.7.6 dated 2017-04-06 and 1.8.1 dated 2018-10-09

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Package rjags updated to version 4-7 with previous version 4-6 dated 2016-02-19

Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>

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Package bibliometrix updated to version 2.0.1 with previous version 2.0.0 dated 2018-09-10

Title: An R-Tool for Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>), Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>), Cochrane Library (<http://www.cochranelibrary.com/>) and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>

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Package colorplaner (with last version 0.1.3) was removed from CRAN

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

2016-11-01 0.1.3
2016-10-04 0.1.2
2016-09-21 0.1.1

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Package PAC updated to version 1.1.0 with previous version 1.0.10 dated 2018-03-06

Title: Partition-Assisted Clustering and Multiple Alignments of Networks
Description: Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.
Author: Ye Henry Li, Dangna Li
Maintainer: Ye Henry Li <hlowl2@gmail.com>

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Package mindr updated to version 1.1.5 with previous version 1.1.0 dated 2017-07-19

Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into FreeMind mindmap ('.mm') files, and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package dglars updated to version 2.1.0 with previous version 2.0.1 dated 2018-04-24

Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

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Package nucim updated to version 1.0.6 with previous version 1.0.0 dated 2016-12-05

Title: Nucleome Imaging Toolbox
Description: Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.
Author: Volker Schmid [aut, cre]
Maintainer: Volker Schmid <stats@volkerschmid.de>

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Package funData updated to version 1.3-2 with previous version 1.3-1 dated 2018-10-02

Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with utility functions.
Author: Clara Happ [aut, cre]
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>

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Package reReg updated to version 1.1.5 with previous version 1.1.4 dated 2018-05-30

Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time data. Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>, Lin et al. (2000) <doi:10.1111/1467-9868.00259>, Wang et al. (2001) <doi:10.1198/016214501753209031>, Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>, Huang and Wang (2004) <doi:10.1198/016214504000001033>, and more.
Author: Sy Han (Steven) Chiou [aut, cre], Chiung-Yu Huang [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>

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Package rmgarch updated to version 1.3-5 with previous version 1.3-0 dated 2015-12-28

Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

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Package Bolstad updated to version 0.2-40 with previous version 0.2-39 dated 2018-08-29

Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to Bayesian Statistics, Bolstad, W.M. (2017), John Wiley & Sons ISBN 978-1-118-09156-2.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>

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Package aphid updated to version 1.3.0 with previous version 1.2.0 dated 2018-08-14

Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>

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Mon, 08 Oct 2018

Package cladoRcpp updated to version 0.15 with previous version 0.14.4 dated 2014-05-18

Title: C++ Implementations of Phylogenetic Cladogenesis Calculations
Description: Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.
Author: Nicholas J. Matzke [aut, cre, cph]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>

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Package pmml updated to version 1.5.6 with previous version 1.5.5 dated 2018-07-06

Title: Generate PMML for Various Models
Description: The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms.
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler (arules), Software AG, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha, Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@softwareag.com>

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Package funHDDC updated to version 2.2.0 with previous version 2.1.0 dated 2018-08-13

Title: Univariate and Multivariate Model-Based Clustering in Group-Specific Functional Subspaces
Description: The funHDDC algorithm (Schmutz et al., 2018) allows to cluster functional univariate or multivariate data by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

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Package weathercan updated to version 0.2.8 with previous version 0.2.7 dated 2018-07-05

Title: Download Weather Data from the Environment and Climate Change Canada Website
Description: Provides means for downloading historical weather data from the Environment and Climate Change Canada website (<http://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). Data can be downloaded from multiple stations and over large date ranges and automatically processed into a single dataset. Tools are also provided to identify stations either by name or proximity to a location.
Author: Steffi LaZerte [aut, cre] (<https://orcid.org/0000-0002-7690-8360>), Sam Albers [ctb] (<https://orcid.org/0000-0002-9270-7884>)
Maintainer: Steffi LaZerte <steffi@steffi.ca>

Diff between weathercan versions 0.2.7 dated 2018-07-05 and 0.2.8 dated 2018-10-08

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Package billboarder updated to version 0.2.4 with previous version 0.2.3 dated 2018-08-07

Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between billboarder versions 0.2.3 dated 2018-08-07 and 0.2.4 dated 2018-10-08

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New package vamc with initial version 0.1.0
Package: vamc
Type: Package
Title: A Monte Carlo Valuation Framework for Variable Annuities
Version: 0.1.0
Authors@R: c( person("Hengxin", "Li", email = "h343li@uwaterloo.ca", role = c("aut", "cph")), person("Ben", "Feng", email = "ben.feng@uwaterloo.ca", role = c("aut", "cph", "cre")), person("GuoJun", "Gan", email = "Guojun.Gan@uconn.edu", role = c("ctb")))
Description: Implementation of a Monte Carlo simulation engine for valuing synthetic portfolios of variable annuities, which reflect realistic features of common annuity contracts in practice. It aims to facilitate the development and dissemination of research related to the efficient valuation of a portfolio of large variable annuities. The main valuation methodology was proposed by Gan (2017) <doi:10.1515/demo-2017-0021>.
Depends: R (>= 3.3.0)
License: GPL-2
LazyData: true
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Imports: stats (>= 3.3.0), utils (>= 3.3.0), Rdpack (>= 0.4)
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2018-10-01 16:23:19 UTC; thecoolestman
Author: Hengxin Li [aut, cph], Ben Feng [aut, cph, cre], GuoJun Gan [ctb]
Maintainer: Ben Feng <ben.feng@uwaterloo.ca>
Repository: CRAN
Date/Publication: 2018-10-08 18:30:03 UTC

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New package TPMplt with initial version 0.1.0
Package: TPMplt
Type: Package
Title: Tool-Kit for Dynamic Materials Model and Thermal Processing Maps
Version: 0.1.0
Date: 2018-09-30
Authors@R: person("ZHANG_Chen", "Developer", email = "447974102@qq.com", role = c("aut", "com", "cre"))
Description: Provides a simple approach for constructing dynamic materials modeling suggested by Prasad and Gegel <doi:10.1007/BF02664902>. It can easily generate various processing-maps based on this model as well. The calculation result in this package contains full materials constants, information about power dissipation efficiency factor, and rheological properties, can be exported completely also, through which further analysis and customized plots will be applicable as well.
License: GPL-3
URL: https://github.com/CubicZebra/TPMplt
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: VBTree, ggplot2, rgl, e1071, qpcR, grDevices, rowr, graphics, stats
Depends: R (>= 2.10)
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-01 15:30:18 UTC; chen_zhang
Author: ZHANG_Chen Developer [aut, com, cre]
Maintainer: ZHANG_Chen Developer <447974102@qq.com>
Repository: CRAN
Date/Publication: 2018-10-08 18:40:03 UTC

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Package sommer updated to version 3.6 with previous version 3.5 dated 2018-07-02

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for multiple random effects allowing the specification of variance-covariance structures for random effects and allowing the fit of heterogeneous variance models (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson, and Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) to include multiple relationship matrices or other covariance structures. Spatial models can be fitted using the two-dimensional spline functionality in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

Diff between sommer versions 3.5 dated 2018-07-02 and 3.6 dated 2018-10-08

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New package nlgeocoder with initial version 0.1.3
Package: nlgeocoder
Title: Geocoding for the Netherlands
Version: 0.1.3
Authors@R: c(person("Willy", "Tadema", role = c("aut")), person("Egge-Jan", "Pollé", role = c("aut")) ,person("Edwin", "de Jonge", email = "edwindjonge@gmail.com", role = c("aut", "cre")) ,person("Juris", "Breidaks", role = c("ctb")))
Description: R interface to the open location server API of 'Publieke Diensten Op de Kaart' (<http://www.pdok.nl>). It offers geocoding, address suggestions and lookup of geographical objects. Included is an utility function for displaying leaflet tiles restricted to the Netherlands.
Depends: R (>= 3.4)
License: GPL-2
BugReports: https://github.com/uRos2018/nlgeocoder/issues
URL: https://github.com/uRos2018/nlgeocoder
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: testthat, knitr, rmarkdown, sf, shiny, leaflet
VignetteBuilder: knitr
Imports: jsonlite
NeedsCompilation: no
Packaged: 2018-10-01 12:37:12 UTC; edwin
Author: Willy Tadema [aut], Egge-Jan Pollé [aut], Edwin de Jonge [aut, cre], Juris Breidaks [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-08 18:30:06 UTC

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Package ndtv updated to version 0.12.3 with previous version 0.12.2 dated 2018-05-13

Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut], Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>

Diff between ndtv versions 0.12.2 dated 2018-05-13 and 0.12.3 dated 2018-10-08

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New package IntrinioStockAPI with initial version 0.0.1
Package: IntrinioStockAPI
Title: Wrapper for the 'Intrinio Stock API'
Version: 0.0.1
Maintainer: Kenneth Miller <kmiller@intrinio.com>
Description: Download financial data from the free 'Intrinio Stock API' (<https://intrinio.com/>). 'Intrinio' offers a REST API which provides financial markets data including intra-day stock prices, historical stock prices, technical indicators, company fundamentals, and more. Complete documentation for the 'Intrinio Stock API' is available here: <https://intrinio.com/documentation/api/>. To access the 'Intrinio Stock API', simply create a free account <https://intrinio.com/>.
Author: Intrinio
Depends: R (>= 3.0.1)
Imports: stringr, httr, jsonlite, gtools
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/intrinio/r-sdk
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-01 16:14:15 UTC; kgmiller
Repository: CRAN
Date/Publication: 2018-10-08 18:50:07 UTC

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Package CopyDetect updated to version 1.3 with previous version 1.2 dated 2016-04-27

Title: Computing Response Similarity Indices for Multiple-Choice Tests
Description: Contains several IRT and non-IRT based response similarity indices proposed in the literature for multiple-choice examinations such as the Omega index, Wollack (1997) <doi:10.1177/01466216970214002>; Generalized Binomial Test, van der Linden & Sotaridona (2006) <doi:10.3102/10769986031003283>; K index, K1 and K2 indices, Sotaridona & Meijer (2002) <doi:10.1111/j.1745-3984.2002.tb01138.x>; and S1 and S2 indices, Sotaridona & Meijer (2003) <doi:10.1111/j.1745-3984.2003.tb01096.x>.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <c.zopluoglu@miami.edu>

Diff between CopyDetect versions 1.2 dated 2016-04-27 and 1.3 dated 2018-10-08

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Package stylo updated to version 0.6.8 with previous version 0.6.7 dated 2018-05-26

Title: Stylometric Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>

Diff between stylo versions 0.6.7 dated 2018-05-26 and 0.6.8 dated 2018-10-08

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Package InvariantCausalPrediction updated to version 0.7-2 with previous version 0.7-1 dated 2017-10-03

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

Diff between InvariantCausalPrediction versions 0.7-1 dated 2017-10-03 and 0.7-2 dated 2018-10-08

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Package cdata updated to version 1.0.2 with previous version 1.0.1 dated 2018-09-22

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

Diff between cdata versions 1.0.1 dated 2018-09-22 and 1.0.2 dated 2018-10-08

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Package useful updated to version 1.2.6 with previous version 1.2.5 dated 2018-06-09

Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a data.frame, constructing formulas from text and building design and response matrices.
Author: Jared P. Lander [cre, aut], Nicholas Galasinao [ctb], Joshua Kraut [ctb], Daniel Chen [ctb]
Maintainer: Jared P. Lander <packages@jaredlander.com>

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Package bookdownplus updated to version 1.5.1 with previous version 1.4.6 dated 2018-09-10

Title: Generate Assorted Books and Documents with R 'bookdown' Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in 'YAML' and 'LaTeX'.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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 bookdownplus-1.5.1/bookdownplus/man/share.Rd         |   17 
 24 files changed, 218 insertions(+), 668 deletions(-)

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Package solvebio updated to version 2.6.0 with previous version 2.5.1 dated 2018-07-10

Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs. For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>

Diff between solvebio versions 2.5.1 dated 2018-07-10 and 2.6.0 dated 2018-10-08

 DESCRIPTION              |   10 -
 MD5                      |   13 +-
 NAMESPACE                |    1 
 NEWS.md                  |    5 
 R/shiny.R                |  294 +++++++++++++++++++++++++++++++++++++----------
 README.md                |    9 +
 man/protectedServer.Rd   |    2 
 man/protectedServerJS.Rd |only
 8 files changed, 261 insertions(+), 73 deletions(-)

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New package processcheckR with initial version 0.1.0
Package: processcheckR
Type: Package
Title: Rule-Based Conformance Checking of Business Process Event Data
Version: 0.1.0
Date: 2018-10-01
Authors@R: person("Gert","Janssenswillen", email = "gert.janssenswillen@uhasselt.be", role = c("aut","cre"))
Description: Check compliance of event data from (business) processes with respect to specified rules. Rules supported are of three types: frequency (activities that should (not) happen x number of times), order (succession between activities) and exclusiveness (and and exclusive choice between activities).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, bupaR, rlang, edeaR, stringr, glue
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, eventdataR
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-01 12:55:00 UTC; lucp8407
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Repository: CRAN
Date/Publication: 2018-10-08 14:20:03 UTC

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New package epos with initial version 0.1.0
Package: epos
Type: Package
Title: Epilepsy Ontology Similarities
Version: 0.1.0
Author: Bernd Müller
Maintainer: Bernd Mueller <bernd.mueller@zbmed.de>
Depends: R (>= 2.10)
Description: Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the corpus of LIVIVO. The ranked result lists of neurological drug terms co-occurring with named entities from the epilepsy ontologies EpSO, ESSO, and EPILONT are aggregated in order to generate two different results: an overview table of drugs that are relevant to epilepsy created with the method createNeuroTable, and a plot of tanimoto similarity coefficients between the aggregated list of drug terms against the list of drug terms from each of the ontologies created with the method createTanimotoBaseline(). The alignment of the Top-K Ranked Lists is conducted using the R-package TopKLists <https://cran.r-project.org/package=TopKLists>. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558> and Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: hashmap, ggplot2, tidyr, dplyr, testthat, gridExtra, TopKLists, stringr, xtable
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-10-08 10:27:05 UTC; muellerb
Repository: CRAN
Date/Publication: 2018-10-08 14:20:06 UTC

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New package crossrun with initial version 0.1.0
Package: crossrun
Version: 0.1.0
Title: Joint Distribution of Number of Crossings and Longest Run
Authors@R: c(person("Tore","Wentzel-Larsen",email="tore.wentzellarsen@gmail.com",role=c("aut","cre")), person("Jacob", "Anhøj", email="jacob@anhoej.net", role="aut"))
Description: Joint distribution of number of crossings and the longest run in a series of independent Bernoulli trials. The computations uses an iterative procedure where computations are based on results from shorter series. The procedure conditions on the start value and partitions by further conditioning on the position of the first crossing (or none).
Depends: R (>= 3.5)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/ToreWentzel-Larsen/crossrun
LazyData: true
Imports: Rmpfr (>= 0.7-1)
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-01 09:50:57 UTC; Tore Admin
Author: Tore Wentzel-Larsen [aut, cre], Jacob Anhøj [aut]
Maintainer: Tore Wentzel-Larsen <tore.wentzellarsen@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-08 14:20:10 UTC

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