Wed, 27 Jul 2016

Package SimSCRPiecewise updated to version 0.1.1 with previous version 0.1.0 dated 2016-07-27

Title: 'Simulates Univariate and Semi-Competing Risks Data Given Covariates and Piecewise Exponential Baseline Hazards'
Description: Contains two functions for simulating survival data from piecewise exponential hazards with a proportional hazards adjustment for covariates. The first function SimUNIVPiecewise simulates univariate survival data based on a piecewise exponential hazard, covariate matrix and true regression vector. The second function SimSCRPiecewise semi-competing risks data based on three piecewise exponential hazards, three true regression vectors and three matrices of patient covariates (which can be different or the same). This simulates from the Semi-Markov model of Lee et al (2015) given patient covariates, regression parameters, patient frailties and baseline hazard functions.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <Andrew.G.Chapple@rice.edu>

Diff between SimSCRPiecewise versions 0.1.0 dated 2016-07-27 and 0.1.1 dated 2016-07-27

 DESCRIPTION             |    6 +++---
 MD5                     |   10 +++++-----
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 6 files changed, 15 insertions(+), 21 deletions(-)

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Package sEparaTe updated to version 0.2.1 with previous version 0.1.2 dated 2016-07-24

Title: Maximum Likelihood Estimation and Likelihood Ratio Test Functions for Separable Variance-Covariance Structures
Description: It combines maximum likelihood estimation of the parameters of matrix and 3rd-order tensor normal distributions with unstructured factor variance-covariance matrices, two procedures, and unbiased modified likelihood ratio testing of simple and double separability for variance-covariance structures, two procedures.
Author: Ameur Manceur [aut], Timothy Schwinghamer [aut, cre], Pierre Dutilleul [aut, cph]
Maintainer: Timothy Schwinghamer <schwinghamer@hotmail.com>

Diff between sEparaTe versions 0.1.2 dated 2016-07-24 and 0.2.1 dated 2016-07-27

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 6 files changed, 753 insertions(+), 552 deletions(-)

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Package plsVarSel updated to version 0.9 with previous version 0.8 dated 2016-06-15

Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least Squares. The methods include filter methods, wrapper methods and embedded methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between plsVarSel versions 0.8 dated 2016-06-15 and 0.9 dated 2016-07-27

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New package placement with initial version 0.1.1
Package: placement
Type: Package
Title: Tools for Accessing the Google Maps API
Version: 0.1.1
Author: Derek Darves
Maintainer: Derek Darves <darves@gmail.com>
Description: The main functions in this package are drive_time (used for calculating distances between physical addresses or coordinates) and geocode_url (used for estimating the lat/long coordinates of a physical address). Optionally, it generates the cryptographic signatures necessary for making API calls with a Google for Work/Premium account within the geocoding process. These accounts have larger quota limits than the "standard_api" and, thus, this package may be useful for individuals seeking to submit large batch jobs within R to the Google Maps API. Placement also provides methods for accessing the standard API using a (free) Google API key (see: <https://developers.google.com/maps/documentation/javascript/get-api-key#get-an-api-key>).
License: MIT + file LICENSE
LazyData: TRUE
Imports: RCurl, jsonlite, base64enc, digest, urltools, stringi
URL: https://github.com/derekyves/placement
BugReports: https://github.com/derekyves/placement/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 21:59:44 UTC; ddarves
Repository: CRAN
Date/Publication: 2016-07-28 00:07:05

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Package neotoma updated to version 1.6.0 with previous version 1.5.1 dated 2016-05-06

Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (http://api.neotomadb.org/). The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>

Diff between neotoma versions 1.5.1 dated 2016-05-06 and 1.6.0 dated 2016-07-27

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 24 files changed, 309 insertions(+), 242 deletions(-)

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New package MWLasso with initial version 1.3
Package: MWLasso
Type: Package
Title: Penalized Moving-Window Lasso Method for Genome-Wide Association Studies
Version: 1.3
Date: 2016-07-27
Author: Minli Bao
Maintainer: Minli Bao <minli-bao@uiowa.edu>
Description: The Moving-Window Lasso (MWLasso) method for genome-wide association studies. A window scans the design matrix. For predictors in the same window, their coefficients estimates are smoothed.
License: GPL
Packaged: 2016-07-27 19:48:18 UTC; Minli
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-07-27 23:50:35

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Package kyotil updated to version 2016.7-27 with previous version 2016.7-9 dated 2016-07-11

Title: Utility Functions by Youyi, Krisz and Others
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>

Diff between kyotil versions 2016.7-9 dated 2016-07-11 and 2016.7-27 dated 2016-07-27

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 8 files changed, 151 insertions(+), 137 deletions(-)

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Package GLDEX updated to version 2.0.0.4 with previous version 2.0.0.3 dated 2015-07-04

Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su <allegro.su@gmail.com>

Diff between GLDEX versions 2.0.0.3 dated 2015-07-04 and 2.0.0.4 dated 2016-07-27

 DESCRIPTION                  |    8 ++++----
 MD5                          |   19 ++++++++++---------
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Package etl updated to version 0.3.3 with previous version 0.3.1 dated 2016-06-13

Title: Extract-Transform-Load Framework for Medium Data
Description: A framework for loading medium-sized data from the Internet to a local or remote relational database management system. This package itself doesn't do much more than provide a toy example and set up the method structure. Packages that depend on this package will facilitate the construction and maintenance of their respective databases.
Author: Ben Baumer [aut, cre], Carson Sievert [ctb]
Maintainer: Ben Baumer <ben.baumer@gmail.com>

Diff between etl versions 0.3.1 dated 2016-06-13 and 0.3.3 dated 2016-07-27

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Package bibliometrix updated to version 1.0 with previous version 0.8 dated 2016-06-20

Title: Bibliometric and Co-Citation Analysis Tool
Description: Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from SCOPUS and Thomson Reuters' ISI Web of Knowledge databases, performing bibliometric analysis and building data matrices for co-citation, coupling and scientific collaboration analysis.
Author: Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>

Diff between bibliometrix versions 0.8 dated 2016-06-20 and 1.0 dated 2016-07-27

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 32 files changed, 502 insertions(+), 101 deletions(-)

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Package archivist updated to version 2.1 with previous version 2.0.4 dated 2016-05-12

Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut], Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between archivist versions 2.0.4 dated 2016-05-12 and 2.1 dated 2016-07-27

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 49 files changed, 366 insertions(+), 187 deletions(-)

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Package IsoplotR updated to version 0.6 with previous version 0.5 dated 2016-07-03

Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using the 'York' approach. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Calculates 40A/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Future versions will include functionality for the Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, ternary diagrams, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app at http://isoplotr.london-geochron.com. Offline access to this interface will be provided at a later point in time.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 0.5 dated 2016-07-03 and 0.6 dated 2016-07-27

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 30 files changed, 530 insertions(+), 275 deletions(-)

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Permanent link

New package iDOS with initial version 1.0.0
Package: iDOS
Type: Package
Title: Integrated Discovery of Oncogenic Signatures
Version: 1.0.0
Date: 2016-07-27
Author: Syed Haider, Francesca M Buffa
Maintainer: Syed Haider <Syed.Haider@oncology.ox.ac.uk>
Depends: R (>= 2.15.0), VennDiagram (>= 1.6.5)
Description: Integrate molecular profiles to discover candidate oncogenic drivers.
License: GPL-2
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-07-27 17:31:11 UTC; shaider
Repository: CRAN
Date/Publication: 2016-07-27 20:25:35

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New package SimSCRPiecewise with initial version 0.1.0
Package: SimSCRPiecewise
Type: Package
Title: 'Simulates Univariate and Semi-Competing Risks Data Given Covariates and Piecewise Exponential Baseline Hazards'
Version: 0.1.0
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <Andrew.G.Chapple@rice.edu>
Description: Contains two functions for simulating survival data from piecewise exponential hazards with a proportional hazards adjustment for covariates. The first function SimUNIVPiecewise simulates univariate survival data based on a piecewise exponential hazard, covariate matrix and true regression vector. The second function SimSCRPiecewise semi-competing risks data based on three piecewise exponential hazards, three true regression vectors and three matrices of patient covariates (which can be different or the same). This simulates from the Semi-Markov model of Lee et al (2015) given patient covariates, regression parameters, patient frailties and baseline hazard functions.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 15:22:49 UTC; Andrew
Repository: CRAN
Date/Publication: 2016-07-27 19:03:16

More information about SimSCRPiecewise at CRAN
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Package metricTester updated to version 1.3.0 with previous version 1.2.2 dated 2016-06-25

Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and performance of phylogenetic metrics and null models.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>

Diff between metricTester versions 1.2.2 dated 2016-06-25 and 1.3.0 dated 2016-07-27

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Package maps updated to version 3.1.1 with previous version 3.1.0 dated 2016-02-13

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg. Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between maps versions 3.1.0 dated 2016-02-13 and 3.1.1 dated 2016-07-27

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New package BayesPiecewiseICAR with initial version 0.1.0
Package: BayesPiecewiseICAR
Type: Package
Title: Hierarchical Bayesian Model for a Hazard Function
Version: 0.1.0
Author: person("Andrew", "Chapple", email = "Andrew.G.Chapple@rice.edu", role = c("aut", "cre"))
Maintainer: Andrew Chapple <Andrew.G.Chapple@rice.edu>
Description: Fits a piecewise exponential hazard to survival data using a Hierarchical Bayesian model with an Intrinsic Conditional Autoregressive formulation for the spatial dependency in the hazard rates for each piece. This function uses Metropolis- Hastings-Green MCMC to allow the number of split points to vary. This function outputs graphics that display the histogram of the number of split points and the trace plots of the hierarchical parameters. The function outputs a list that contains the posterior samples for the number of split points, the location of the split points, and the log hazard rates corresponding to these splits. Additionally, this outputs the posterior samples of the two hierarchical parameters, Mu and Sigma^2.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
Depends: mvtnorm
NeedsCompilation: no
Packaged: 2016-07-27 15:16:18 UTC; Andrew
Repository: CRAN
Date/Publication: 2016-07-27 19:00:54

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Package vipor updated to version 0.4.3 with previous version 0.4.2 dated 2016-07-03

Title: Plot Categorical Data Using Quasirandom Noise and Density Estimates
Description: Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Author: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>

Diff between vipor versions 0.4.2 dated 2016-07-03 and 0.4.3 dated 2016-07-27

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Package hunspell updated to version 1.4.3 with previous version 1.4.2 dated 2016-07-13

Title: Morphological Analysis and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for languages with rich morphology and complex word compounding or character encoding. The package can check and analyze individual words as well as search for incorrect words within a text, latex or manual document. Use the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between hunspell versions 1.4.2 dated 2016-07-13 and 1.4.3 dated 2016-07-27

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Package Surrogate updated to version 0.1-74 with previous version 0.1-73 dated 2016-05-16

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 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

Diff between Surrogate versions 0.1-73 dated 2016-05-16 and 0.1-74 dated 2016-07-27

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Package kinn updated to version 0.2 with previous version 0.1 dated 2016-05-22

Title: An Implementation of 'kinn' Algorithm, a Graph Based Regression Model
Description: A graph based regression model from flat unstructured dataset. Each line in the input data set is treated as a node from which an edge to another line (node) can be formed. In the training process, a model is created which contains sparse graph adjacency matrix. This model is then used for prediction by taking a predictor and the model as inputs and outputs a prediction which is an average of the most similar node and its neighbours in the model graph.
Author: Yossi Keshet
Maintainer: Yossi Keshet <jossiekat@icloud.com>

Diff between kinn versions 0.1 dated 2016-05-22 and 0.2 dated 2016-07-27

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New package MortHump with initial version 0.1
Package: MortHump
Type: Package
Title: Measure the Young Adult Mortality Hump
Version: 0.1
Date: 2016-06-20
Author: Adrien Remund, Carlo G Camarda, Tim Riffe
Maintainer: Adrien Remund <adrien.remund@unige.ch>
Description: Fit diverse models of mortality graduation, parametric or not, in order to isolate the hump that is often observed in the age-specific death rates during adolescence and early adulthood in human populations. Can handle either all-cause or cause-specific data.
License: GPL-2
Imports: HMDHFDplus, MortalitySmooth, RColorBrewer, WeightedCluster, demography, minpack.lm, Matrix
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 09:16:54 UTC; remunda
Repository: CRAN
Date/Publication: 2016-07-27 11:58:17

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New package EvaluationMeasures with initial version 1.1.0
Package: EvaluationMeasures
Type: Package
Title: Collection of Model Evaluation Measure Functions
Version: 1.1.0
Authors@R: c(person(given = "Babak", family = "Khorsand", role = c("aut", "cre"), email = "khorsand@yahoo.com"), person(given = "Javad", family = "Zahiri", role = "ths", email = "zahiri@modares.ac.ir"), person(given = "Abdorreza", family = "Savadi", role = "ths", email = "savadi@um.ac.ir"))
Maintainer: Babak Khorsand <khorsand@yahoo.com>
Description: Provides Some of the most important evaluation measures for evaluating a model. Just by giving the real and predicted class, measures such as accuracy, sensitivity, specificity, ppv, npv, fmeasure, mcc and ... will be returned.
License: GPL
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 09:48:27 UTC; Challenger1980
Author: Babak Khorsand [aut, cre], Javad Zahiri [ths], Abdorreza Savadi [ths]
Repository: CRAN
Date/Publication: 2016-07-27 12:03:25

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Package bnspatial updated to version 1.0 with previous version 0.9 dated 2016-06-02

Title: Spatial Implementation of Bayesian Networks and Mapping
Description: Package for the spatial implementation of Bayesian Networks and mapping in geographical space. It makes maps of expected value (or most likely state) given known and unknown conditions, maps of uncertainty measured as coefficient of variation or Shannon index (entropy), maps of probability associated to any states of any node of the network. Some additional features are provided as well: parallel processing options, data discretization routines and function wrappers designed for users with minimal knowledge of the R language. Outputs can be exported to any common GIS format. Development was funded by the European Union FP7 (2007-2013), under project ROBIN (agreement 283093).
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dmasan@ceh.ac.uk>

Diff between bnspatial versions 0.9 dated 2016-06-02 and 1.0 dated 2016-07-27

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Package RecordLinkage updated to version 0.4-10 with previous version 0.4-9 dated 2016-05-03

Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain.
Author: Andreas Borg <borga@uni-mainz.de>, Murat Sariyar <murat.sariyar@charite.de>
Maintainer: Andreas Borg <borga@uni-mainz.de>

Diff between RecordLinkage versions 0.4-9 dated 2016-05-03 and 0.4-10 dated 2016-07-27

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Package ordinalNet updated to version 1.5 with previous version 1.4 dated 2015-12-10

Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty. Supported models include cumulative logit, probit, cauchit, and complementary log-log. The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Michael Wurm [aut, cre], Bret Hanlon [ths]
Maintainer: Michael Wurm <wurm@wisc.edu>

Diff between ordinalNet versions 1.4 dated 2015-12-10 and 1.5 dated 2016-07-27

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Package oec updated to version 1.0.2 with previous version 1.0 dated 2016-07-26

Title: The Observatory of Economic Complexity
Description: Use The Observatory of Economic Complexity's API from R console to obtain international trade data to create spreadsheets (csv format) and D3Plus visualizations.
Author: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>
Maintainer: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>

Diff between oec versions 1.0 dated 2016-07-26 and 1.0.2 dated 2016-07-27

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Package dggridR updated to version 0.1.8 with previous version 0.1.7 dated 2016-07-23

Title: Discrete Global Grids for R
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut, cre], Kevin Sahr [ctb], Gerald Evenden [ctb], Angus Johnson [ctb], Frank Warmerdam [ctb]
Maintainer: Richard Barnes <rbarnes@umn.edu>

Diff between dggridR versions 0.1.7 dated 2016-07-23 and 0.1.8 dated 2016-07-27

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Package ddalpha updated to version 1.2.0.1 with previous version 1.2.0 dated 2016-07-25

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

Diff between ddalpha versions 1.2.0 dated 2016-07-25 and 1.2.0.1 dated 2016-07-27

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Package ph2bye updated to version 0.1.2 with previous version 0.1.1 dated 2016-07-25

Title: Phase II Clinical Trial Design Using Bayesian Methods
Description: Calculate the Bayesian posterior/predictive probability and determine the sample size and stopping boundaries for single-arm Phase II design.
Author: Yalin Zhu, Rui Qin
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>

Diff between ph2bye versions 0.1.1 dated 2016-07-25 and 0.1.2 dated 2016-07-27

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Package list updated to version 8.1 with previous version 8.0 dated 2015-05-19

Title: Statistical Methods for the Item Count Technique and List Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011), Blair and Imai (2012), Blair, Imai, and Lyall (2013), Imai, Park, and Greene (2014), and Aronow, Coppock, Crawford, and Green (2015). This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, and a method for combining list experiments with direct questions. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Kosuke Imai [aut, cre], Bethany Park [ctb], Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

Diff between list versions 8.0 dated 2015-05-19 and 8.1 dated 2016-07-27

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Package birk updated to version 2.1.2 with previous version 2.1.1 dated 2016-07-14

Title: MA Birk's Functions
Description: Collection of tools to make R more convenient. Includes tools to summarize data using statistics not available with base R and manipulate objects for analyses.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>

Diff between birk versions 2.1.1 dated 2016-07-14 and 2.1.2 dated 2016-07-27

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Tue, 26 Jul 2016

Package zoib updated to version 1.4.1 with previous version 1.4.0 dated 2016-07-11

Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong
Maintainer: Fang Liu <fang.liu.131@nd.edu>

Diff between zoib versions 1.4.0 dated 2016-07-11 and 1.4.1 dated 2016-07-26

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New package StableEstim with initial version 2.1
Package: StableEstim
Type: Package
Title: Estimate the Four Parameters of Stable Laws using Different Methods
Version: 2.1
Date: 2016-07-26
Depends: R(>= 2.10.0),methods,Matrix,stats,utils,stabledist,testthat
Imports: numDeriv, xtable, fBasics, MASS
Author: Tarak Kharrat, Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Description: Estimate the four parameters of stable laws using maximum likelihood method, generalised method of moments with finite and continuum number of points, iterative Koutrouvelis regression and Kogon-McCulloch method. The asymptotic properties of the estimators (covariance matrix, confidence intervals) are also provided.
License: GPL (>= 2)
Collate: cte.R ExternalPackageInterface.R ToolsFct.R Interpolation.R RegularInverse.R stableCF.R CFbasedMoment.R WeightingMatrix.R eCFfirstZero.R tSchemes.R MultiDimIntegral.R InitialGuess.R KoutParamsEstim.R MLParamsEstim.R GMMParamsEstim.R CgmmParamsEstim.R OutputFileManip.R CheckPoint.R BestT_Class.R Estim_Class.R Estim.R Simulation.R BestT.R
NeedsCompilation: no
Packaged: 2016-07-26 18:19:43 UTC; mcbssgb2
Repository: CRAN
Date/Publication: 2016-07-27 03:50:56

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Package SNPMClust updated to version 1.3 with previous version 1.2 dated 2016-03-28

Title: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays
Description: Bivariate Gaussian genotype clustering and calling for Illumina microarrays, building on the package 'mclust'. Pronounced snip-em-clust.
Author: Stephen W. Erickson and Joshua C. Callaway
Maintainer: Joshua C. Callaway <joshcllw@gmail.com>

Diff between SNPMClust versions 1.2 dated 2016-03-28 and 1.3 dated 2016-07-26

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New package RcppHoney with initial version 0.1.0
Package: RcppHoney
Type: Package
Title: Iterator Based Expression Template Expansion of Standard Operators
Version: 0.1.0
Author: Daniel C. Dillon
Maintainer: Daniel C. Dillon <dcdillon@gmail.com>
Description: Creates an easy way to use expression templates with R semantics on any iterator based structure.
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.12.5)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-07-26 20:06:27 UTC; dcdillon
Repository: CRAN
Date/Publication: 2016-07-27 03:40:51

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Package nCal updated to version 2016.7-26 with previous version 2015.3-3 dated 2015-03-04

Title: Nonlinear Calibration
Description: Performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>, Xuesong Yu <xyu@scharp.org>
Maintainer: Youyi Fong <yfong@fhcrc.org>

Diff between nCal versions 2015.3-3 dated 2015-03-04 and 2016.7-26 dated 2016-07-26

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Package MVar.pt updated to version 1.9.3 with previous version 1.9.2 dated 2016-07-17

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MVar.pt versions 1.9.2 dated 2016-07-17 and 1.9.3 dated 2016-07-26

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New package microseq with initial version 1.0
Package: microseq
Type: Package
Title: Basic Biological Sequence Analysis
Version: 1.0
Date: 2016-07-26
Author: Lars Snipen, Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Description: Basic functions for microbial sequence data analysis. In some cases the functions use the corresponding functions in the 'Biostrings' package from Bioconductor <http://www.bioconductor.org/>, but provide an easier interface.
License: GPL-2
RoxygenNote: 5.0.1
Depends: R (>= 3.2.1)
Imports: Biostrings
NeedsCompilation: no
Packaged: 2016-07-26 07:33:56 UTC; larssn
Repository: CRAN
Date/Publication: 2016-07-27 03:49:42

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New package measurements with initial version 1.0.0
Package: measurements
Type: Package
Title: Tools for Units of Measurement
Version: 1.0.0
Date: 2016-07-26
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Description: Collection of tools to make working with physical measurements easier. Convert between metric and imperial units, or calculate a dimension's unknown value from other dimensions' measurements.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-26 20:15:48 UTC; matthewbirk
Repository: CRAN
Date/Publication: 2016-07-27 03:38:30

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New package l0ara with initial version 0.1.2
Package: l0ara
Type: Package
Title: Sparse Generalized Linear Model with L0 Approximation for Feature Selection
Version: 0.1.2
Date: 2016-06-28
Author: Wenchuan Guo, Zhenqiu Liu, Fengzhu Sun, Dermot P McGovern, Sandra Orsulic
Maintainer: Wenchuan Guo <wguo007@ucr.edu>
Description: An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.
License: GPL-2
Imports: Rcpp (>= 0.12.6)
LinkingTo: Rcpp, RcppArmadillo
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-07-26 23:42:59 UTC; Wenchuan
Repository: CRAN
Date/Publication: 2016-07-27 03:45:52

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Package ipdw updated to version 0.2-5 with previous version 0.2-4 dated 2016-03-03

Title: Spatial Interpolation by Inverse Path Distance Weighting
Description: Functions are provided to interpolate georeferenced point data via Inverse Path Distance Weighting. Useful for coastal marine applications where barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek <stachel2@msu.edu>
Maintainer: Joseph Stachelek <stachel2@msu.edu>

Diff between ipdw versions 0.2-4 dated 2016-03-03 and 0.2-5 dated 2016-07-26

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New package GEEaSPU with initial version 1.0.1
Package: GEEaSPU
Type: Package
Title: Adaptive Association Tests for Multiple Phenotypes using Generalized Estimating Equations (GEE)
Version: 1.0.1
Date: 2016-07-26
Author: Junghi Kim and Wei Pan
Maintainer: Junghi Kim <junghikim0@gmail.com>
Description: Provides adaptive association tests for SNP level, gene level and pathway level analyses.
License: GNU General Public License (>= 3)
Depends: R (>= 2.10), gee, stats
Imports: Rcpp (>= 0.12.6)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-07-26 16:53:50 UTC; junghikim
Repository: CRAN
Date/Publication: 2016-07-27 03:39:48

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New package FIT with initial version 0.0.1
Package: FIT
Title: Transcriptomic Dynamics Models in Field Conditions
Version: 0.0.1
Authors@R: c(person("Koji", "Iwayama", email = "fieldtranscriptome@gmail.com", role = c("cre")), person("Yuri", "Aisaka", email = "aisaka@lpixel.net", role = c("aut")))
Description: Provides functionality for constructing statistical models of transcriptomic dynamics in field conditions. It further offers the function to predict expression of a gene given the attributes of samples and meteorological data.
Depends: R (>= 3.2.2)
Imports: methods, Rcpp (>= 0.11.2), XML, gglasso, MASS
License: MPL (>= 2) | file LICENSE
LazyData: true
LinkingTo: Rcpp, RcppEigen (>= 0.3.2.1.2)
SystemRequirements: C++11
NeedsCompilation: yes
RoxygenNote: 5.0.1
Packaged: 2016-07-25 02:07:37 UTC; ec2-user
Author: Koji Iwayama [cre], Yuri Aisaka [aut]
Maintainer: Koji Iwayama <fieldtranscriptome@gmail.com>
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2016-07-27 03:44:52

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Package fasteraster updated to version 1.0.4 with previous version 1.0 dated 2016-07-21

Title: Raster Image Processing and Vector Recognition
Description: If there is a need to recognise edges on a raster image or a bitmap or any kind of a matrix, one can find packages that does only 90 degrees vectorization. Typically the nature of artefact images is linear and can be vectorized in much more efficient way than draw a series of 90 degrees lines. The fasteraster package does recognition of lines using only one pass.
Author: Andy Bosyi
Maintainer: Andy Bosyi <andy@bosyi.com>

Diff between fasteraster versions 1.0 dated 2016-07-21 and 1.0.4 dated 2016-07-26

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Package cellranger updated to version 1.1.0 with previous version 1.0.0 dated 2015-06-20

Title: Translate Spreadsheet Cell Ranges to Rows and Columns
Description: Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.
Author: Jennifer Bryan [cre, aut], Hadley Wickham [ctb]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>

Diff between cellranger versions 1.0.0 dated 2015-06-20 and 1.1.0 dated 2016-07-26

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Package PortfolioEffectEstim updated to version 1.3 with previous version 1.2 dated 2016-02-04

Title: High Frequency Price Estimators by PortfolioEffect
Description: R interface to PortfolioEffect cloud service for estimating high frequency price variance, quarticity, microstructure noise variance, and other metrics in both aggregate and rolling window flavors. Constructed estimators could use client-side market data or access HF intraday price history for all major US Equities. See https://www.portfolioeffect.com/ for more information on the PortfolioEffect high frequency portfolio analytics platform.
Author: Andrey Kostin [aut, cre], Aleksey Zemnitskiy [aut], Oleg Nechaev [aut]
Maintainer: Andrey Kostin <andrey.kostin@portfolioeffect.com>

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Package palr updated to version 0.0.6 with previous version 0.0-4 dated 2015-06-11

Title: Colour Palettes for Data
Description: Colour palettes for data, based on some well known public data sets.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package lsl updated to version 0.5.5 with previous version 0.5.1 dated 2015-12-01

Title: Latent Structure Learning
Description: Conduct structural equation modeling via penalized likelihood.
Author: Po-Hsien Huang [aut, cre]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>

Diff between lsl versions 0.5.1 dated 2015-12-01 and 0.5.5 dated 2016-07-26

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Package JAGUAR updated to version 3.0.1 with previous version 3.0.0 dated 2015-09-24

Title: Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map Expression Quantitative Trait Loci (eQTL)
Description: Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.
Author: Chaitanya R. Acharya and Andrew S. Allen
Maintainer: Chaitanya Acharya <c.acharya@duke.edu>

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Package ghit updated to version 0.2.10 with previous version 0.2.5 dated 2016-03-15

Title: Lightweight GitHub Package Installer
Description: A lightweight, vectorized drop-in replacement for 'devtools::install_github()' that uses native git and R methods to clone and install a package from GitHub.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package georob updated to version 0.2-4 with previous version 0.2-3 dated 2016-03-02

Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust and Gaussian (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift kriging predictions, along with utility functions for variogram modelling in ad-hoc geostatistical analyses, model building, model evaluation by cross-validation and for unbiased back-transformation of kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut], Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>

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Package EGRET updated to version 2.6.0 with previous version 2.4.3 dated 2016-03-04

Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

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Package DoseFinding updated to version 0.9-15 with previous version 0.9-14 dated 2016-02-02

Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis of dose-finding experiments (with focus on pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models (using Bayesian and non-Bayesian estimation), calculating optimal designs and an implementation of the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp <bbnkmp@gmail.com>

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Package dataRetrieval updated to version 2.5.10 with previous version 2.5.5 dated 2016-04-20

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from the National Water Information System (NWIS) tools. Both EPA and USGS water quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut], Jordan Read [ctb], Lindsay Carr [ctb], David Watkins [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

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Package Rdpack updated to version 0.4-20 with previous version 0.4-18 dated 2015-07-15

Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of Rd objects, including function reprompt() for updating existing Rd documentation for functions, methods and classes and function rebib() for import of references from 'bibtex' files. There is also a macro for importing 'bibtex' references which an be used in Rd files and 'roxygen' comments without importing this package.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package mirtCAT updated to version 1.0 with previous version 0.9 dated 2016-06-24

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R. Package also contains tools useful for performing Monte Carlo simulations for studying the behaviour of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Permanent link

Package MonoPhy updated to version 1.2 with previous version 1.1 dated 2016-03-11

Title: Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups in a Phylogeny
Description: Requires rooted resolved phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways.
Author: Orlando Schwery
Maintainer: Orlando Schwery <oschwery@vols.utk.edu>

Diff between MonoPhy versions 1.1 dated 2016-03-11 and 1.2 dated 2016-07-26

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Package curl updated to version 1.1 with previous version 1.0 dated 2016-07-23

Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [cre, aut], Hadley Wickham [ctb], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between curl versions 1.0 dated 2016-07-23 and 1.1 dated 2016-07-26

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More information about curl at CRAN
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Package ChannelAttribution updated to version 1.8 with previous version 1.7 dated 2016-07-19

Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>

Diff between ChannelAttribution versions 1.7 dated 2016-07-19 and 1.8 dated 2016-07-26

 DESCRIPTION                       |    8 +--
 MD5                               |    6 +-
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 4 files changed, 56 insertions(+), 48 deletions(-)

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Package psychotools updated to version 0.4-1 with previous version 0.4-0 dated 2015-01-19

Title: Infrastructure for Psychometric Modeling
Description: Infrastructure for psychometric modeling such as data classes (for item response data and paired comparisons), basic model fitting functions (for Bradley-Terry, Rasch, partial credit, rating scale, multinomial processing tree models), extractor functions for different types of parameters (item, person, threshold, discrimination), unified inference and visualizations, and various datasets for illustration. Intended as a common lightweight and efficient toolbox for psychometric modeling and a common building block for fitting psychometric mixture models in package "psychomix" and psychometric tree models in package "psychotree".
Author: Achim Zeileis [aut, cre], Carolin Strobl [aut], Florian Wickelmaier [aut], Basil Abou El-Komboz [aut], Julia Kopf [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

Diff between psychotools versions 0.4-0 dated 2015-01-19 and 0.4-1 dated 2016-07-26

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Package corr2D updated to version 0.1.10 with previous version 0.1.9 dated 2016-06-06

Title: Implementation of 2D Correlation Analysis
Description: Implementation of two-dimensional (2D) correlation analysis based on the Fourier-transformation approach described by Isao Noda (I. Noda (1993) <DOI:10.1366/0003702934067694>). Additionally there are two plot functions for the resulting correlation matrix: The first one creates colored 2D plots, while the second one generates 3D plots.
Author: Robert Geitner [cre, aut], Robby Fritzsch [aut], Thomas Bocklitz [aut], Juergen Popp [ctb, cph]
Maintainer: Robert Geitner <robert.geitner@uni-jena.de>

Diff between corr2D versions 0.1.9 dated 2016-06-06 and 0.1.10 dated 2016-07-26

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Package Bchron updated to version 4.2.4 with previous version 4.2.2 dated 2016-06-21

Title: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling
Description: Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM). The package includes a vignette which can be accessed via the vignette.
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>

Diff between Bchron versions 4.2.2 dated 2016-06-21 and 4.2.4 dated 2016-07-26

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Package AmostraBrasil updated to version 1.2 with previous version 1.1 dated 2016-06-15

Title: Generates Samples or Complete List of Brazilian IBGE (Instituto Brasileiro De Geografia e Estatistica) Census Households, Geocoding it by Google Maps
Description: Generates samples or complete list of Brazilian IBGE (Instituto Brasileiro de Geografia e Estatistica, see <http://www.ibge.gov.br/> for more information) census households, geocoding it by Google Maps. The package connects IBGE site and downloads maps and census data.
Author: Celso Stephan;Ricardo Cordeiro
Maintainer: Celso Stephan <celso.stephan@gmail.com>

Diff between AmostraBrasil versions 1.1 dated 2016-06-15 and 1.2 dated 2016-07-26

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Package SizeEstimation updated to version 1.1.1 with previous version 1.1.0 dated 2016-07-13

Title: Estimating the Sizes of Populations at Risk of HIV Infection from Multiple Data Sources Using a Bayesian Hierarchical Model
Description: This function develops an algorithm for presenting a Bayesian hierarchical model for estimating the sizes of local and national drug injected populations in Bangladesh. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion.
Author: Le Bao, Adrian E. Raftery, Kyongwon Kim
Maintainer: Kyongwon Kim<kbk5206@psu.edu>

Diff between SizeEstimation versions 1.1.0 dated 2016-07-13 and 1.1.1 dated 2016-07-26

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Package SIDES updated to version 1.3 with previous version 1.2 dated 2016-07-12

Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between SIDES versions 1.2 dated 2016-07-12 and 1.3 dated 2016-07-26

 DESCRIPTION          |    6 +++---
 MD5                  |    8 ++++----
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Package random.polychor.pa updated to version 1.1.4-2 with previous version 1.1.4-1 dated 2014-08-12

Title: A Parallel Analysis with Polychoric Correlation Matrices
Description: The Function performs a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from both the randomly generated and the real data polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. Random data sets are simulated assuming or a uniform or a multinomial distribution or via the bootstrap method of resampling (i.e., random permutations of cases). Also Multigroup Parallel analysis is made available for random (uniform and multinomial distribution and with or without difficulty factor) and bootstrap methods. An option to choose between default or full output is also available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA, RMR and BIC) for the factor solutions indicated by the Parallel Analysis.
Author: Fabio Presaghi [aut, cre], Marta Desimoni [ctb]
Maintainer: Fabio Presaghi <fabio.presaghi@uniroma1.it>

Diff between random.polychor.pa versions 1.1.4-1 dated 2014-08-12 and 1.1.4-2 dated 2016-07-26

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More information about random.polychor.pa at CRAN
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Package preprosim updated to version 0.2.0 with previous version 0.1.0 dated 2016-05-28

Title: Lightweight Data Quality Simulation for Classification
Description: Data quality simulation can be used to check the robustness of data analysis findings and learn about the impact of data quality contaminations on classification. This package helps to add contaminations (noise, missing values, outliers, low variance, irrelevant features, class swap (inconsistency), class imbalance and decrease in data volume) to data and then evaluate the simulated data sets for classification accuracy. As a lightweight solution simulation runs can be set up with no or minimal up-front effort.
Author: Markus Vattulainen [aut, cre]
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>

Diff between preprosim versions 0.1.0 dated 2016-05-28 and 0.2.0 dated 2016-07-26

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New package oec with initial version 1.0
Package: oec
Type: Package
Title: The Observatory of Economic Complexity
Version: 1.0
Date: 2016-07-25
Author: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>
Maintainer: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>
URL: http://atlas.media.mit.edu/en/, https://github.com/pachamaltese/oec/
Description: Use The Observatory of Economic Complexity's API from R console to obtain international trade data to create spreadsheets (csv format) and D3Plus visualizations.
License: MIT + file LICENSE
LazyData: TRUE
Depends: curl, data.table, jsonlite, plyr, servr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-26 02:01:58 UTC; pacha
Repository: CRAN
Date/Publication: 2016-07-26 12:12:18

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New package MethyBayes with initial version 0.1.0
Package: MethyBayes
Title: Full Bayesian Partition Model for Identifying Differentially Methylated Loci
Version: 0.1.0
Authors@R: c( person("Henan", "Wang", email = "hwg58@mail.missouri.edu", role = c("cre", "aut")), person("Yuchen", "Wang", email = "ycwang0712@gmail.com", role = "aut") )
Description: A full Bayesian partition model is implemented to identify differentially methylated loci from single-nucleotide resolution sequencing data.
Depends: R (>= 3.2)
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-07-26 03:29:26 UTC; yuchen
Author: Henan Wang [cre, aut], Yuchen Wang [aut]
Maintainer: Henan Wang <hwg58@mail.missouri.edu>
Repository: CRAN
Date/Publication: 2016-07-26 12:30:19

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Package lightsout updated to version 0.3 with previous version 0.2.1 dated 2016-01-06

Title: Implementation of the 'Lights Out' Puzzle Game
Description: Lights Out is a puzzle game consisting of a grid of lights that are either on or off. Pressing any light will toggle it and its adjacent lights. The goal of the game is to switch all the lights off. This package provides an interface to play the game on different board sizes, both through the command line or with a visual application. Puzzles can also be solved using the automatic solver included. View a demo online at http://daattali.com/shiny/lightsout/.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between lightsout versions 0.2.1 dated 2016-01-06 and 0.3 dated 2016-07-26

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Package LARF updated to version 1.4 with previous version 1.3 dated 2015-02-09

Title: Local Average Response Functions for Instrumental Variable Estimation of Treatment Effects
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An <weihuaan@indiana.edu>

Diff between LARF versions 1.3 dated 2015-02-09 and 1.4 dated 2016-07-26

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New package intubate with initial version 0.99.1
Package: intubate
Type: Package
Title: Interface to Popular R Functions for Data Science Pipelines
Version: 0.99.1
Date: 2016-07-26
Author: Roberto Bertolusso
Maintainer: Roberto Bertolusso <rbertolusso@rice.edu>
Description: Interface to popular R functions with formulas, such as 'lm', so they can be included painlessly in data science pipelines implemented by 'magrittr' with the operator %>%.
License: GPL (>= 2)
Imports: graphics, magrittr, MASS, stats
NeedsCompilation: no
Packaged: 2016-07-26 05:48:07 UTC; mame
Repository: CRAN
Date/Publication: 2016-07-26 12:34:36

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New package denoiseR with initial version 1.0
Package: denoiseR
Version: 1.0
Date: 2016-07-09
Type: Package
Title: Regularized Low Rank Matrix Estimation
Author: Julie Josse, Sylvain Sardy, Stefan Wager
Maintainer: Julie Josse <julie.josserennes@gmail.com>
Imports: irlba, Matrix, FactoMineR, stats
Suggests: missMDA
Description: Estimate a low rank matrix from noisy data using singular values thresholding and shrinking functions. Impute missing values with matrix completion.
License: GPL (>= 2)
RoxygenNote: 5.0.1
Depends: R(>= 2.10)
NeedsCompilation: no
Packaged: 2016-07-10 10:39:33 UTC; josse
Repository: CRAN
Date/Publication: 2016-07-26 12:40:37

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Mon, 25 Jul 2016

Package vcfR updated to version 1.2.0 with previous version 1.1.0 dated 2016-05-26

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

Diff between vcfR versions 1.1.0 dated 2016-05-26 and 1.2.0 dated 2016-07-25

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 tests/testthat/test_heatmapbp.R    |    9 +
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 49 files changed, 1157 insertions(+), 546 deletions(-)

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New package jacpop with initial version 0.5
Package: jacpop
Type: Package
Title: Jaccard Index for Population Structure Identification
Description: Uses the Jaccard similarity index to account for population structure in sequencing studies. This method was specifically designed to detect population stratification based on rare variants, hence it will be especially useful in rare variant analysis.
Version: 0.5
Author: Dmitry Prokopenko
Maintainer: Dmitry Prokopenko <dmitry.prokopenko@uni-bonn.de>
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-25 22:22:57 UTC; Dmitry
Repository: CRAN
Date/Publication: 2016-07-26 02:11:59

More information about jacpop at CRAN
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New package Infusion with initial version 1.0.0
Package: Infusion
Type: Package
Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated.
Encoding: UTF-8
Version: 1.0.0
Date: 2016-07-26
Imports: spaMM (>= 1.9.14), proxy, geometry, Matrix, rcdd, blackbox, mvtnorm, Rmixmod (>= 2.0.4), methods, numDeriv, viridis
Suggests: ks, mclust, caret, testthat
Depends: R (>= 3.1.0)
Authors@R: c(person("François", "Rousset", role = c("aut", "cre", "cph"), email = "francois.rousset@umontpellier.fr"))
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
License: CeCILL-2
URL: http://www.r-project.org, http://kimura.univ-montp2.fr/~rousset/Infusion.htm
NeedsCompilation: no
Packaged: 2016-07-25 22:29:40 UTC; rousset
Author: François Rousset [aut, cre, cph]
Repository: CRAN
Date/Publication: 2016-07-26 02:19:40

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Package DDRTree updated to version 0.1.4 with previous version 0.1.3 dated 2016-02-02

Title: Learning Principal Graphs with DDRTree
Description: Project data into a reduced dimensional space and construct a principal graph from the reduced dimension.
Author: Xiaojie Qiu, Cole Trapnell, Qi Mao, Li Wang
Maintainer: Xiaojie Qiu <xqiu@uw.edu>

Diff between DDRTree versions 0.1.3 dated 2016-02-02 and 0.1.4 dated 2016-07-25

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Package boral updated to version 1.0.1 with previous version 1.0 dated 2016-06-17

Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>

Diff between boral versions 1.0 dated 2016-06-17 and 1.0.1 dated 2016-07-25

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New package timevis with initial version 0.1
Package: timevis
Title: Create Interactive Timeline Visualizations in R
Version: 0.1
Authors@R: c( person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"), comment = "R interface"), person(family = "Almende B.V.", role = c("aut", "cph"), comment = "vis.js library, http://visjs.org, http://www.almende.com/home") )
Description: Create rich and fully interactive timeline visualizations. Timelines can be included in Shiny apps and R markdown documents, or viewed from the R console and RStudio Viewer. 'timevis' includes an extensive API to manipulate a timeline after creation, and supports getting data out of the visualization into R. Based on the 'vis.js' Timeline module and the 'htmlwidgets' R package.
URL: https://github.com/daattali/timevis, http://daattali.com/shiny/timevis-demo/
BugReports: https://github.com/daattali/timevis/issues
Depends: R (>= 3.1.0)
Imports: htmltools (>= 0.2.6), htmlwidgets (>= 0.6), jsonlite, rmarkdown, shiny
Suggests: knitr (>= 1.7), testthat (>= 0.9.1),
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-25 17:14:09 UTC; Dean
Author: Dean Attali [aut, cre] (R interface), Almende B.V. [aut, cph] (vis.js library, http://visjs.org, http://www.almende.com/home)
Maintainer: Dean Attali <daattali@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-25 22:49:33

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New package ph2bye with initial version 0.1.1
Package: ph2bye
Type: Package
Title: Phase II Clinical Trial Design Using Bayesian Methods
Version: 0.1.1
Author: Yalin Zhu
Maintainer: Yalin Zhu <yalin.zhu@outlook.com><yalin.zhu@regeneron.com>
Description: Calculate the Bayesian posterior/predictive probability and determine the sample size and stopping boundaries for single-arm Phase II design.
License: GPL (>= 2)
LazyData: TRUE
Depends: stats, graphics, animation
Imports: base, ph2bayes, VGAM
Suggests: clinfun, gsDesign, survival
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-25 14:25:37 UTC; yalin.zhu
Repository: CRAN
Date/Publication: 2016-07-25 22:44:05

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Package VCA updated to version 1.3.2 with previous version 1.3.1 dated 2016-04-04

Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>

Diff between VCA versions 1.3.1 dated 2016-04-04 and 1.3.2 dated 2016-07-25

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Package texmexseq updated to version 0.3 with previous version 0.2 dated 2016-05-26

Title: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>

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Package runjags updated to version 2.0.4-2 with previous version 2.0.3-2 dated 2016-03-31

Title: Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.
Author: Matthew Denwood [aut, cre], Martyn Plummer [cph] (Copyright holder of the code in /src/distributions/jags, src/distributions/DPar1.*, configure.ac, and original copyright holder of some modified code where indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>

Diff between runjags versions 2.0.3-2 dated 2016-03-31 and 2.0.4-2 dated 2016-07-25

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Package longpower updated to version 1.0-16 with previous version 1.0-15 dated 2016-05-17

Title: Sample Size Calculations for Longitudinal Data
Description: The longpower package contains functions for computing power and sample size for linear models of longitudinal data based on the formula due to Liu and Liang (1997) and Diggle et al (2002). Either formula is expressed in terms of marginal model or Generalized Estimating Equations (GEE) parameters. This package contains functions which translate pilot mixed effect model parameters (e.g. random intercept and/or slope) into marginal model parameters so that the formulas of Diggle et al or Liu and Liang formula can be applied to produce sample size calculations for two sample longitudinal designs assuming known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue <mdonohue@usc.edu>

Diff between longpower versions 1.0-15 dated 2016-05-17 and 1.0-16 dated 2016-07-25

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Package ifaTools updated to version 0.11 with previous version 0.10 dated 2016-05-16

Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between ifaTools versions 0.10 dated 2016-05-16 and 0.11 dated 2016-07-25

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Package frailtypack updated to version 2.9.4 with previous version 2.9.3.1 dated 2016-07-08

Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>

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Package HK80 updated to version 0.0.2 with previous version 0.0.1 dated 2014-05-02

Title: Conversion Tools for HK80 Geographical Coordinate System
Description: This is a collection of functions for converting coordinates between WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems used in Hong Kong SAR, based on the algorithms described in Explanatory Notes on Geodetic Datums in Hong Kong by Survey and Mapping Office Lands Department, Hong Kong Government (1995).
Author: Jinlong Zhang [aut, cre]
Maintainer: Jinlong Zhang <jinlongzhang01@gmail.com>

Diff between HK80 versions 0.0.1 dated 2014-05-02 and 0.0.2 dated 2016-07-25

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Package equateIRT updated to version 2.0-1 with previous version 2.0 dated 2016-03-30

Title: Direct, Chain and Average Equating Coefficients with Standard Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>

Diff between equateIRT versions 2.0 dated 2016-03-30 and 2.0-1 dated 2016-07-25

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Package ddalpha updated to version 1.2.0 with previous version 1.1.3.1 dated 2015-07-24

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

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Package CORElearn updated to version 1.48.0 with previous version 1.47.1 dated 2015-09-04

Title: Classification, Regression and Feature Evaluation
Description: This is a suite of machine learning algorithms written in C++ with R interface. It contains several machine learning model learning techniques in classification and regression, for example classification and regression trees with optional constructive induction and models in the leaves, random forests, kNN, naive Bayes, and locally weighted regression. All predictions obtained with these models can be explained and visualized with ExplainPrediction package. The package is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, and DKM. These methods can be used for example to discretize numeric attributes. Its additional feature is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class, enabling analysis according to the Kano model of customer satisfaction. Several algorithms support parallel multithreaded execution via OpenMP. The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>

Diff between CORElearn versions 1.47.1 dated 2015-09-04 and 1.48.0 dated 2016-07-25

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Package condformat updated to version 0.4.0 with previous version 0.2.0 dated 2016-03-07

Title: Conditional Formatting in Data Frames
Description: Apply and visualize conditional formatting to data frames in R. It renders a data frame with cells formatted according to criteria defined by rules, using a syntax similar to 'ggplot2'. The table is printed either opening a web browser or within the 'RStudio' viewer if available. The conditional formatting rules allow to highlight cells matching a condition or add a gradient background to a given column. This package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and exporting to an 'xlsx' file.
Author: Sergio Oller Moreno [aut, cph, cre]
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>

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Package Chaos01 updated to version 1.0.1 with previous version 1.0.0 dated 2016-07-18

Title: 0-1 Test for Chaos
Description: Computes and plot the results of the 0-1 test for chaos proposed by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is available in parallel for the independent values of parameter c.
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>

Diff between Chaos01 versions 1.0.0 dated 2016-07-18 and 1.0.1 dated 2016-07-25

 DESCRIPTION          |    6 +++---
 MD5                  |    6 +++---
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Package CALF updated to version 0.1.3 with previous version 0.1.2 dated 2016-03-25

Title: Coarse Approximation Linear Function
Description: Contains a greedy algorithm for coarse approximation linear function.
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>

Diff between CALF versions 0.1.2 dated 2016-03-25 and 0.1.3 dated 2016-07-25

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New package bigReg with initial version 0.1.2
Package: bigReg
Type: Package
Title: Generalized Linear Models (GLM) for Large Data Sets
Version: 0.1.2
Date: 2016-07-23
Author: Chibisi Chima-Okereke <chibisi@active-analytics.com>
Maintainer: Chibisi Chima-Okereke <chibisi@active-analytics.com>
Description: Allows the user to carry out GLM on very large data sets. Data can be created using the data_frame() function and appended to the object with object$append(data); data_frame and data_matrix objects are available that allow the user to store large data on disk. The data is stored as doubles in binary format and any character columns are transformed to factors and then stored as numeric (binary) data while a look-up table is stored in a separate .meta_data file in the same folder. The data is stored in blocks and GLM regression algorithm is modified and carries out a MapReduce- like algorithm to fit the model. The functions bglm(), and summary() and bglm_predict() are available for creating and post-processing of models. The library requires Armadillo installed on your system. It probably won't function on windows since multi-core processing is done using mclapply() which forks R on Unix/Linux type operating systems.
License: GPL (>= 2)
Depends: R (>= 3.2.0), Rcpp (>= 0.12.3), parallel, methods, stats, uuid (>= 0.1-2), MASS (>= 7.3-39)
LinkingTo: Rcpp, RcppArmadillo (>= 0.5.200.1.0)
OS_type: unix
Collate: 'RcppExports.R' 'data_frame.r' 'data_matrix.r' 'family.r' 'map_reg.r'
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-07-25 09:31:12 UTC; chib
Repository: CRAN
Date/Publication: 2016-07-25 19:16:58

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Package BacArena updated to version 1.5.1 with previous version 1.5.0 dated 2016-07-14

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

Diff between BacArena versions 1.5.0 dated 2016-07-14 and 1.5.1 dated 2016-07-25

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New package MSCMT with initial version 1.0.0
Package: MSCMT
Type: Package
Version: 1.0.0
Date: 2016-07-25
Title: Multivariate Synthetic Control Method Using Time Series
Authors@R: c(person("Martin","Becker", role = c("aut","cre"), email = "martin.becker@mx.uni-saarland.de"), person("Stefan","Kloessner", role = c("aut"), email = "S.Kloessner@mx.uni-saarland.de"), person("Karline","Soetaert", role = c("com"), email = "karline.soetaert@nioz.nl"), person("LAPACK authors", role = "cph"))
Depends: R (>= 3.0.0)
Imports: stats, utils, optimx, lpSolve, parallel, DEoptim, rgenoud, ggplot2
Suggests: Synth, knitr, rmarkdown
Description: Multivariate Synthetic Control Method Using Time Series. Two generalizations of the synthetic control method (which has already an implementation in package 'Synth') are implemented: first, 'MSCMT' allows for using multiple outcome variables, second, time series can be supplied as economic predictors. Much effort has been taken to make the implementation as stable as possible (including edge cases) without losing computational efficiency.
License: GPL
Copyright: inst/COPYRIGHTS
LazyData: yes
RoxygenNote: 5.0.1
VignetteBuilder: knitr
BuildVignettes: yes
NeedsCompilation: yes
Packaged: 2016-07-25 06:20:22 UTC; mabe003
Author: Martin Becker [aut, cre], Stefan Kloessner [aut], Karline Soetaert [com], LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Repository: CRAN
Date/Publication: 2016-07-25 15:15:12

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Package mvst updated to version 1.0.1 with previous version 1.0 dated 2016-07-20

Title: Bayesian Inference for the Multivariate Skew-t Model
Description: Estimates the multivariate skew-t and nested models, as described in the articles Liseo, B., Parisi, A. (2013). Bayesian inference for the multivariate skew-normal model: a population Monte Carlo approach. Comput. Statist. Data Anal. <doi:10.1016/j.csda.2013.02.007> and in Parisi, A., Liseo, B. Objective Bayesian analysis for the multivariate skew-t model (to appear).
Author: Antonio Parisi [aut, cre], Brunero Liseo [aut], Dirk Eddelbuettel [ctb], Romain Francois [ctb]
Maintainer: Antonio Parisi <antonio.parisi@uniroma2.it>

Diff between mvst versions 1.0 dated 2016-07-20 and 1.0.1 dated 2016-07-25

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Package jomo updated to version 2.2-0 with previous version 2.1-2 dated 2016-04-04

Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>

Diff between jomo versions 2.1-2 dated 2016-04-04 and 2.2-0 dated 2016-07-25

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New package wordcloud2 with initial version 0.2.0
Package: wordcloud2
Type: Package
Title: Create Word Cloud by htmlWidget
Version: 0.2.0
Author: Dawei Lang
Description: A fast visualization tool for creating wordcloud by using wordcloud2.js.
License: GPL-2
Depends: R (>= 3.1.0)
LazyData: TRUE
VignetteBuilder: knitr
Imports: htmlwidgets, base64enc, grDevices, graphics
Suggests: knitr
Enhances: shiny (>= 0.12)
URL: https://github.com/lchiffon/wordcloud2
BugReports: https://github.com/lchiffon/wordcloud2/issues
Maintainer: Dawei Lang <chiffonlang@icloud.com>
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-25 02:03:03 UTC; dawei_lang
Repository: CRAN
Date/Publication: 2016-07-25 09:56:48

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Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.