Fri, 24 Nov 2017

Package tscount updated to version 1.4.1 with previous version 1.4.0 dated 2017-09-30

Title: Analysis of Count Time Series
Description: Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided. Models with the identity and with the logarithmic link function are allowed. The conditional distribution can be Poisson or Negative Binomial.
Author: Tobias Liboschik [aut, cre], Roland Fried [aut], Konstantinos Fokianos [aut], Philipp Probst [aut], Jonathan Rathjens [ctb]
Maintainer: Tobias Liboschik <liboschik@statistik.tu-dortmund.de>

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Package TrajDataMining updated to version 0.1.4 with previous version 0.1.3 dated 2017-11-23

Title: Trajectories Data Mining
Description: Contains a set of methods for trajectory data preparation, such as filtering, compressing and clustering, and for trajectory pattern discovery.
Author: Diego Monteiro [aut, cre], Karine Reis [ctb], Carlos Alberto [ctb], Felipe Carvalho [ctb]
Maintainer: Diego Monteiro <dvm1607@gmail.com>

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Package ThresholdROC updated to version 2.6 with previous version 2.5 dated 2017-08-01

Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>

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Package tgram updated to version 0.2-3 with previous version 0.2-2 dated 2013-07-24

Title: Compute and Plot Tracheidograms
Description: Functions to compute and plot tracheidograms, as in De Soto et al. (2011) <doi:10.1139/x11-045>.
Author: Marcelino de la Cruz and Lucia DeSoto
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>

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Package SNFtool updated to version 2.2.1 with previous version 2.2 dated 2014-09-08

Title: Similarity Network Fusion
Description: Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.
Author: Bo Wang, Aziz Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg
Maintainer: Daniel Cole <goldenberglab@gmail.com>

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Package Rramas updated to version 0.1-5 with previous version 0.1-4 dated 2014-01-28

Title: Matrix Population Models
Description: Imitating the 'Ramas' (c) software, analyzes and predicts from matrix population models, (Caswell 2006) <doi:10.1002/9781118445112.stat07481>.
Author: Marcelino de la Cruz
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>

Diff between Rramas versions 0.1-4 dated 2014-01-28 and 0.1-5 dated 2017-11-24

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Package rmcfs updated to version 1.2.7 with previous version 1.2.6 dated 2017-07-03

Title: The MCFS-ID Algorithm for Feature Selection and Interdependency Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M.Draminski, A.Rada-Iglesias, S.Enroth, C.Wadelius, J. Koronacki, J.Komorowski (2008) <doi:10.1093/bioinformatics/btm486>.
Author: Michal Draminski [aut, cre], Jacek Koronacki [aut], Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>

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Package Rdimtools updated to version 0.1.3 with previous version 0.1.2 dated 2017-11-13

Title: Dimension Reduction and Estimation Methods
Description: We provide a rich collection of linear and nonlinear dimension reduction techniques implemented using 'RcppArmadillo'. The question on what we should use as the target dimension is addressed by intrinsic dimension estimation methods introduced as well. For more details on dimensionality techniques, see the paper by Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in statistical approach, or Engel, Huttenberger, and Hamann (2012) <doi:10.4230/OASIcs.VLUDS.2011.135> for a broader cross-disciplinary overview.
Author: Kisung You [aut, cre], Donggun Kim [ctb], Yoon Mo Jung [ctb]
Maintainer: Kisung You <kyou@nd.edu>

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Package inferference updated to version 1.0.0 with previous version 0.5.4 dated 2017-09-25

Title: Methods for Causal Inference with Interference
Description: Provides methods for estimating causal effects in the presence of interference described in B. Saul and M. Hugdens (2017) <doi:10.18637/jss.v082.i02>. Currently it implements the inverse-probability weighted (IPW) estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele (2012) <doi:10.1177/0962280210386779>.
Author: Bradley Saul
Maintainer: Bradley Saul <bradleysaul@gmail.com>

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Package ecespa updated to version 1.1-9 with previous version 1.1-8 dated 2015-07-04

Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on 'spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>

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Package dixon updated to version 0.0-6 with previous version 0.0-5 dated 2013-03-13

Title: Nearest Neighbour Contingency Table Analysis
Description: Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002) <doi:10.1080/11956860.2002.11682700>. Some 'Fortran' code has been included to the original dixon2002() function of the 'ecespa' package to improve speed.
Author: Marcelino de la Cruz Rot and Philip M. Dixon
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>

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Package venn updated to version 1.5 with previous version 1.2 dated 2016-05-10

Title: Draw Venn Diagrams
Description: Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set intersections.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

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Package replicatedpp2w updated to version 0.1-2 with previous version 0.1-1 dated 2015-04-29

Title: Two-Way ANOVA-Like Method to Analyze Replicated Point Patterns
Description: Test for effects of both individual factors and their interaction on replicated spatial patterns in a two factorial design, as explained in Ramon et al. (2016) <doi:10.1111/ecog.01848>.
Author: Marcelino de la Cruz Rot
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>

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Package unitizer updated to version 1.4.5 with previous version 1.4.4 dated 2017-09-01

Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test code with earlier versions of those same objects. If objects are unchanged the tests pass, otherwise execution stops with error details. If in interactive mode, tests can be reviewed through the provided interactive environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>

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Package tmaptools updated to version 1.2-2 with previous version 1.2-1 dated 2017-05-11

Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

Diff between tmaptools versions 1.2-1 dated 2017-05-11 and 1.2-2 dated 2017-11-24

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Package reticulate updated to version 1.3.1 with previous version 1.3 dated 2017-11-16

Title: R Interface to Python
Description: R interface to Python modules, classes, and functions. When calling into Python R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types. Compatible with all versions of Python >= 2.7.
Author: JJ Allaire [aut, cre], Kevin Ushey [ctb], RStudio [cph, fnd], Yuan Tang [aut, cph], Dirk Eddelbuettel [ctb, cph], Bryan Lewis [ctb, cph], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package RcppThread updated to version 0.1.2 with previous version 0.1.1 dated 2017-11-07

Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>

Diff between RcppThread versions 0.1.1 dated 2017-11-07 and 0.1.2 dated 2017-11-24

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Package LAM updated to version 0.1-22 with previous version 0.0-17 dated 2017-05-11

Title: Some Latent Variable Models
Description: Contains some procedures for latent variable modelling with a particular focus on multilevel data. The LAM package contains mean and covariance structure modelling for multivariate normally distributed data ('mlnormal'), a general Metropolis-Hastings algorithm ('amh') and penalized maximum likelihood estimation ('pmle').
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between LAM versions 0.0-17 dated 2017-05-11 and 0.1-22 dated 2017-11-24

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Package covTestR updated to version 0.1.1 with previous version 0.1.0 dated 2017-11-22

Title: Covariance Matrix Tests
Description: Testing functions for Covariance Matrices. These tests include high-dimension homogeneity of covariance matrix testing described by Schott (2007) <doi:10.1016/j.csda.2007.03.004> and high-dimensional one-sample tests of covariance matrix structure described by Fisher, et al. (2010) <doi:10.1016/j.jmva.2010.07.004>. Covariance matrix tests use C++ to speed performance and allow larger data sets.
Author: Ben Barnard [aut, cre], Dean Young [aut]
Maintainer: Ben Barnard <ben_barnard@outlook.com>

Diff between covTestR versions 0.1.0 dated 2017-11-22 and 0.1.1 dated 2017-11-24

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More information about covTestR at CRAN
Permanent link

Package cctools updated to version 0.1.1 with previous version 0.1.0 dated 2017-04-26

Title: Tools for the Continuous Convolution Trick in Nonparametric Estimation
Description: Implements the uniform scaled beta distribution and the continuous convolution kernel density estimator.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

Diff between cctools versions 0.1.0 dated 2017-04-26 and 0.1.1 dated 2017-11-24

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Package STARTS updated to version 0.2-10 with previous version 0.1-51 dated 2017-08-27

Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>, <DOI:10.1037/10409-008>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between STARTS versions 0.1-51 dated 2017-08-27 and 0.2-10 dated 2017-11-24

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New package gpHist with initial version 0.1
Package: gpHist
Type: Package
Title: Gaussian Process with Histogram Intersection Kernel
Version: 0.1
Date: 2017-11-24
Author: Dennis Becker
Maintainer: Dennis Becker <dbecker@leuphana.de>
Description: Provides an implementation of a Gaussian process regression with a histogram intersection kernel (HIK) and utilizes approximations to speed up learning and prediction. In contrast to a squared exponential kernel, an HIK provides advantages such as linear memory and learning time requirements. However, the HIK only provides a piecewise-linear approximation of the function. Furthermore, the number of estimated eigenvalues is reduced. The eigenvalues and vectors are required for the approximation of the log-likelihood function as well as the approximation of the predicted variance of new samples. This package provides approximations for a single eigenvalue as well as multiple. Further information of the variance and log-likelihood approximation, as well as the Gaussian process with HIK, can be found in the paper by Rodner et al. (2016) <doi:10.1007/s11263-016-0929-y>.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2017-11-24 13:19:29 UTC; dennis
Repository: CRAN
Date/Publication: 2017-11-24 14:03:57 UTC

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New package fmriqa with initial version 0.1.0
Package: fmriqa
Type: Package
Title: Functional MRI Quality Assurance Routines
Version: 0.1.0
Date: 2017-11-22
Authors@R: person("Martin", "Wilson", email = "martin@pipegrep.co.uk", role = c("cre","aut"))
Description: Methods for performing fMRI quality assurance (QA) measurements of test objects. Heavily based on the fBIRN procedures detailed by Friedman and Glover (2006) <doi:10.1002/jmri.20583>.
BugReports: https://github.com/martin3141/fmriqa/issues
License: GPL-3
LazyData: true
RoxygenNote: 6.0.1
Imports: viridisLite, RNifti, ggplot2, reshape2, gridExtra, grid, tidyr, optparse, tcltk, RcppEigen, pracma
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2017-11-24 09:40:04 UTC; wilsonmp
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Repository: CRAN
Date/Publication: 2017-11-24 13:51:41 UTC

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Package fDMA updated to version 2.2.1 with previous version 2.2 dated 2017-11-15

Title: Dynamic Model Averaging and Dynamic Model Selection for Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>

Diff between fDMA versions 2.2 dated 2017-11-15 and 2.2.1 dated 2017-11-24

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Package Aoptbdtvc updated to version 0.0.2 with previous version 0.0.1 dated 2017-11-22

Title: A-Optimal Block Designs for Comparing Test Treatments with Controls
Description: A collection of functions to construct A-optimal block designs for comparing test treatments with one or more control(s). Mainly A-optimal balanced treatment incomplete block designs, weighted A-optimal balanced treatment incomplete block designs, A-optimal group divisible treatment designs and A-optimal balanced bipartite block designs can be constructed using the package. The designs are constructed using algorithms based on linear integer programming. To the best of our knowledge, these facilities to construct A-optimal block designs for comparing test treatments with one or more controls are not available in the existing R packages. For more details on designs for tests versus control(s) comparisons, please see Hedayat, A. S. and Majumdar, D. (1984) <doi:10.1080/00401706.1984.10487989> A-Optimal Incomplete Block Designs for Control-Test Treatment Comparisons, Technometrics, 26, 363-370 and Mandal, B. N. , Gupta, V. K., Parsad, Rajender. (2017) <doi:10.1080/03610926.2015.1071394> Balanced treatment incomplete block designs through integer programming. Communications in Statistics - Theory and Methods 46(8), 3728-3737.
Author: Baidya Nath Mandal [aut, cre], Sukanta Dash [aut], Rajender Parsad [aut]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>

Diff between Aoptbdtvc versions 0.0.1 dated 2017-11-22 and 0.0.2 dated 2017-11-24

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Package vdmR updated to version 0.2.5 with previous version 0.2.4 dated 2017-06-23

Title: Visual Data Mining Tools
Description: This provides web-based visual data-mining tools by adding interactive functions to 'ggplot2' graphics. Brushing and linking between the multiple plots is one of the main feature of this package. Currently scatter plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>

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Package tmap updated to version 1.11 with previous version 1.10 dated 2017-05-11

Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre], Joel Gombin [ctb], Sebastian Jeworutzki [ctb], Kent Russell [ctb], Richard Zijdeman [ctb], John Clouse [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

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Package qle updated to version 0.16-6 with previous version 0.16-5 dated 2017-11-16

Title: Simulation-Based Quasi-Likelihood Estimation
Description: A simulation-based quasi-likelihood method (Baaske, M., Ballani, F., v.d. Boogaart, K.G. (2014) <doi:10.5566/ias.v33.p107-119>) for parameter estimation of parametric statistical models for which closed-form representations of distributional characteristics are unavailable and can only be obtained by computationally intensive simulations of the model.
Author: Markus Baaske [aut, cre, cph], K. Gerald van den Boogaart [ths]
Maintainer: Markus Baaske <markus.baaske@uni-jena.de>

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Package loa updated to version 0.2.43.1 with previous version 0.2.38 dated 2016-03-01

Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework. The plots, which include loaPlot(), GoogleMap() and trianglePlot(), use panelPal(), a function that extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel and panel-to-key synchronization/management.
Author: Karl Ropkins
Maintainer: Karl Ropkins <k.ropkins@its.leeds.ac.uk>

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Package ANN2 updated to version 1.4 with previous version 1.3 dated 2017-11-16

Title: Artificial Neural Networks for Anomaly Detection
Description: Training of general classification and regression neural networks using gradient descent. Special features include a function for training replicator neural networks and a function for training autoencoders. Multiple activation and cost functions (including Huber and pseudo-Huber) are supported, as well as L1 and L2 regularization, momentum, early stopping and the possibility to specify a learning rate schedule. The package contains a vectorized gradient descent implementation which facilitates faster training through batch learning.
Author: Bart Lammers
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>

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Package lime updated to version 0.3.1 with previous version 0.3.0 dated 2017-09-15

Title: Local Interpretable Model-Agnostic Explanations
Description: When building complex models, it is often difficult to explain why the model should be trusted. While global measures such as accuracy are useful, they cannot be used for explaining why a model made a specific prediction. 'lime' (a port of the 'lime' 'Python' package) is a method for explaining the outcome of black box models by fitting a local model around the point in question an perturbations of this point. The approach is described in more detail in the article by Ribeiro et al. (2016) <arXiv:1602.04938>.
Author: Thomas Lin Pedersen [cre, aut], Michaël Benesty [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package galts updated to version 1.3.1 with previous version 1.3 dated 2013-02-07

Title: Genetic Algorithms and C-Steps Based LTS (Least Trimmed Squares) Estimation
Description: Includes the ga.lts() function that estimates LTS (Least Trimmed Squares) parameters using genetic algorithms and C-steps. ga.lts() constructs a genetic algorithm to form a basic subset and iterates C-steps as defined in Rousseeuw and van-Driessen (2006) to calculate the cost value of the LTS criterion. OLS (Ordinary Least Squares) regression is known to be sensitive to outliers. A single outlying observation can change the values of estimated parameters. LTS is a resistant estimator even the number of outliers is up to half of the data. This package is for estimating the LTS parameters with lower bias and variance in a reasonable time. Version >=1.3 includes the function medmad for fast outlier detection in linear regression.
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>

Diff between galts versions 1.3 dated 2013-02-07 and 1.3.1 dated 2017-11-24

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New package SteinerNet with initial version 2.0
Package: SteinerNet
Version: 2.0
Date: 2017-11-23
Title: Steiner Tree Approach for Graph Analysis
License: GPL-3
Author: Afshin Sadeghi
Maintainer: Afshin Sadeghi <sadeghi.afshin@gmail.com>
Depends: R (>= 3.1)
Imports: igraph, limma, RBGL, graph, grDevices, stats, utils, graphics
Description: A set of graph functions to find Steiner trees on graphs. It provides tools for analysing Steiner tree application on networks. It has applications in biological pathway network analysis (Sadeghi 2013) <doi:10.1186/1471-2105-14-144>.
Packaged: 2017-11-23 18:08:11 UTC; afshin
Repository: CRAN
Date/Publication: 2017-11-24 09:16:38 UTC
NeedsCompilation: no
X-CRAN-Comment: Archived on 2013-09-07: it was never updated from igraph0 to igraph despite several reminders.

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Package DLMtool updated to version 5.0.1 with previous version 5.0 dated 2017-10-24

Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management procedures for data-limited fisheries (see Carruthers et al (2014) <doi:10.1016/j.fishres.2013.12.014>).
Author: Tom Carruthers [aut, cre], Adrian Hordyk [aut]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>

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More information about DLMtool at CRAN
Permanent link

Thu, 23 Nov 2017

Package packcircles updated to version 0.3.0 with previous version 0.2.0 dated 2017-04-06

Title: Circle Packing
Description: Simple algorithms for circle packing.
Author: Michael Bedward [aut, cre], David Eppstein [aut] (Author of Python code for graph-based circle packing ported to C++ for this package), Peter Menzel [aut] (Author of C code for progressive circle packing ported to C++ for this package)
Maintainer: Michael Bedward <michael.bedward@gmail.com>

Diff between packcircles versions 0.2.0 dated 2017-04-06 and 0.3.0 dated 2017-11-23

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 packcircles-0.3.0/packcircles/LICENSE                           |    2 
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More information about packcircles at CRAN
Permanent link

Package GFGM.copula updated to version 1.0.1 with previous version 1.0.0 dated 2017-10-27

Title: Generalized Farlie-Gumbel-Morgenstern Copula
Description: Compute bivariate dependence measures and perform bivariate competing risks analysis under the generalized Farlie-Gumbel-Morgenstern (FGM) copula. See Shih and Emura (2016) <doi:10.1007/s00362-016-0865-5> and Shih and Emura (2017, in re-submission) for details.
Author: Jia-Han Shih
Maintainer: Jia-Han Shih <tommy355097@gmail.com>

Diff between GFGM.copula versions 1.0.0 dated 2017-10-27 and 1.0.1 dated 2017-11-23

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More information about GFGM.copula at CRAN
Permanent link

Package PracTools updated to version 0.7 with previous version 0.6 dated 2017-07-26

Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>

Diff between PracTools versions 0.6 dated 2017-07-26 and 0.7 dated 2017-11-23

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More information about PracTools at CRAN
Permanent link

Package sirt updated to version 2.3-57 with previous version 2.2-14 dated 2017-09-20

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R, including multidimensional compensatory and noncompensatory IRT models, MCMC for hierarchical IRT models and testlet models, NOHARM, Rasch copula model, faceted and hierarchical rater models, ordinal IRT model (ISOP), DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between sirt versions 2.2-14 dated 2017-09-20 and 2.3-57 dated 2017-11-23

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 sirt-2.3-57/sirt/MD5                                                     | 1143 +++++-----
 sirt-2.3-57/sirt/NAMESPACE                                               |    6 
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 sirt-2.3-57/sirt/R/Probtrace_sirt.R                                      |    1 
 sirt-2.3-57/sirt/R/Q3.R                                                  |    6 
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 sirt-2.3-57/sirt/R/R2conquest.R                                          |    1 
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 sirt-2.3-57/sirt/R/R2noharm.EAP.R                                        |    1 
 sirt-2.3-57/sirt/R/R2noharm.R                                            |    1 
 sirt-2.3-57/sirt/R/R2noharm.jackknife.R                                  |    1 
 sirt-2.3-57/sirt/R/RcppExports.R                                         |    1 
 sirt-2.3-57/sirt/R/Rhat_sirt.R                                           |    1 
 sirt-2.3-57/sirt/R/amh_plot.R                                            |    1 
 sirt-2.3-57/sirt/R/anova_sirt.R                                          |    1 
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 sirt-2.3-57/sirt/R/btm.R                                                 |    1 
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 sirt-2.3-57/sirt/R/btm_fit_combine_tables.R                              |    1 
 sirt-2.3-57/sirt/R/categorize.R                                          |    1 
 sirt-2.3-57/sirt/R/ccov.np.R                                             |    1 
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 sirt-2.3-57/sirt/R/conf.detect.R                                         |    1 
 sirt-2.3-57/sirt/R/confint.xxirt.R                                       |    1 
 sirt-2.3-57/sirt/R/create.ccov.R                                         |    1 
 sirt-2.3-57/sirt/R/data.prep.R                                           |    1 
 sirt-2.3-57/sirt/R/data.wide2long.R                                      |    1 
 sirt-2.3-57/sirt/R/decategorize.R                                        |    1 
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 sirt-2.3-57/sirt/R/diag2.R                                               |    1 
 sirt-2.3-57/sirt/R/dif.logisticregression.R                              |    1 
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 sirt-2.3-57/sirt/R/equating.rasch.R                                      |    1 
 sirt-2.3-57/sirt/R/expl.detect.R                                         |    1 
 sirt-2.3-57/sirt/R/f1d.irt.R                                             |    1 
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 sirt-2.3-57/sirt/R/fit.logistic_alg.R                                    |    1 
 sirt-2.3-57/sirt/R/fuzcluster.R                                          |    1 
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 sirt-2.3-57/sirt/R/fuzdiscr.R                                            |    1 
 sirt-2.3-57/sirt/R/ginverse_sym.R                                        |    1 
 sirt-2.3-57/sirt/R/gom.em.R                                              |    1 
 sirt-2.3-57/sirt/R/gom.em.alg.R                                          |    1 
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 sirt-2.3-57/sirt/R/logLik_sirt.R                                         |    1 
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 sirt-2.3-57/sirt/src/eigenvaluessirt.cpp                                 |   77 
 sirt-2.3-57/sirt/src/evm_comp_matrix_poly.cpp                            |  509 ++--
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 sirt-2.3-57/sirt/src/xxirt_functions.cpp                                 |  103 
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Package Rcpp updated to version 0.12.14 with previous version 0.12.13 dated 2017-09-28

Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2017, <doi:10.7287/peerj.preprints.3188v1>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between Rcpp versions 0.12.13 dated 2017-09-28 and 0.12.14 dated 2017-11-23

 ChangeLog                               |   58 +++++++++++++++++++
 DESCRIPTION                             |   13 ++--
 MD5                                     |   68 +++++++++++-----------
 build/Rcpp.pdf                          |binary
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Package mrfDepth updated to version 1.0.6 with previous version 1.0.5 dated 2017-10-13

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, cre], Mia Hubert [aut], Peter Rousseeuw [aut], Jakob Raymaekers [aut], Kaveh Vakili [ctb]
Maintainer: Pieter Segaert <Pieter.Segaert@kuleuven.be>

Diff between mrfDepth versions 1.0.5 dated 2017-10-13 and 1.0.6 dated 2017-11-23

 DESCRIPTION   |    8 ++++----
 MD5           |    8 ++++----
 R/Misc.R      |    2 +-
 inst/NEWS.Rd  |   11 +++++++++++
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 5 files changed, 22 insertions(+), 12 deletions(-)

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Package Compositional updated to version 2.7 with previous version 2.6 dated 2017-10-07

Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. The standard textbook for such data is John Aitchison's (1986). "The statistical analysis of compositional data". Chapman & Hall.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 2.6 dated 2017-10-07 and 2.7 dated 2017-11-23

 DESCRIPTION                  |   10 +-
 MD5                          |   99 ++++++++++----------
 NAMESPACE                    |    3 
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Package bioinactivation updated to version 1.2.0 with previous version 1.1.5 dated 2017-01-29

Title: Simulation of Dynamic Microbial Inactivation
Description: Prediction and adjustment to experimental data of microbial inactivation. Several models available in the literature are implemented.
Author: Alberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>

Diff between bioinactivation versions 1.1.5 dated 2017-01-29 and 1.2.0 dated 2017-11-23

 DESCRIPTION                           |   12 +-
 MD5                                   |  107 +++++++++---------
 NAMESPACE                             |    9 +
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Permanent link

New package TrajDataMining with initial version 0.1.3
Package: TrajDataMining
Type: Package
Title: Trajectories Data Mining
Version: 0.1.3
Authors@R: c( person("Diego","Monteiro",role=c("aut","cre"),email="dvm1607@gmail.com"), person("Karine", "Reis", role = "ctb",email="karine.ferreira@inpe.br"), person("Carlos", "Alberto", role = "ctb",email="carlos.noronha@inpe.br"), person("Felipe", "Carvalho", role = "ctb",email="lipecaso@gmail.com") )
Description: Contains a set of methods for trajectory data preparation, such as filtering, compressing and clustering, and for trajectory pattern discovery.
License: MIT + file LICENSE
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 3.3.3)
Imports: sp, trajectories, rgdal, xts, spacetime, RPostgreSQL, geosphere, methods, ggplot2, magrittr
Suggests: testthat, knitr, rmarkdown, covr
VignetteBuilder: knitr
URL: https://github.com/INPEtrajectories/TrajDataMining
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-11-23 18:31:45 UTC; asainpe
Author: Diego Monteiro [aut, cre], Karine Reis [ctb], Carlos Alberto [ctb], Felipe Carvalho [ctb]
Maintainer: Diego Monteiro <dvm1607@gmail.com>
Repository: CRAN
Date/Publication: 2017-11-23 18:51:24 UTC

More information about TrajDataMining at CRAN
Permanent link

New package Ternary with initial version 0.1.1
Package: Ternary
Version: 0.1.1
Date: 2017-11-23
Title: Plot Ternary Diagrams
Description: Plots ternary diagrams using the standard graphics functions. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
URL: https://github.com/ms609/Ternary
BugReports: https://github.com/ms609/Ternary/issues
Authors@R: c(person("Martin R.", 'Smith', email="martins@gmail.com", role=c("aut", "cre", "cph"), comment=c(ORCID = "0000-0001-5660-1727")) )
License: GPL (>= 2)
Depends: R (>= 3.2.0)
Suggests: knitr, rmarkdown, testthat
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-11-23 18:16:11 UTC; ms609
Author: Martin R. Smith [aut, cre, cph] (0000-0001-5660-1727)
Maintainer: Martin R. Smith <martins@gmail.com>
Repository: CRAN
Date/Publication: 2017-11-23 18:41:58 UTC

More information about Ternary at CRAN
Permanent link

Package stplanr updated to version 0.2.1 with previous version 0.1.9 dated 2017-07-12

Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning, including origin-destination analysis, route allocation and modelling travel patterns.
Author: Robin Lovelace [aut, cre] (0000-0001-5679-6536), Richard Ellison [aut], Barry Rowlingson [ctb] (Author of overline), Nick Bearman [ctb] (Co-author of gclip), Malcolm Morgan [ctb] (Co-author of angle_diff), Nikolai Berkoff [ctb] (Co-author of line2route), Scott Chamberlin [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10)
Maintainer: Robin Lovelace <rob00x@gmail.com>

Diff between stplanr versions 0.1.9 dated 2017-07-12 and 0.2.1 dated 2017-11-23

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Package ecospat updated to version 2.2.0 with previous version 2.1.1 dated 2016-11-02

Title: Spatial Ecology Miscellaneous Methods
Description: Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre-, core and post- modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann [aut], Valeria Di Cola [cre, aut], Blaise Petitpierre [ctb], Frank Breiner [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb], Robin Engler [ctb], Wim Hordijk [ctb], Julien Pottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb], Dorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis [ctb], Daniel Scherrer [ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte Ndiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb], Antoine Guisan [aut]
Maintainer: Valeria Di Cola <valeriadicola@gmail.com>

Diff between ecospat versions 2.1.1 dated 2016-11-02 and 2.2.0 dated 2017-11-23

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Package MVar.pt updated to version 1.9.9 with previous version 1.9.8 dated 2017-04-18

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, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MVar.pt versions 1.9.8 dated 2017-04-18 and 1.9.9 dated 2017-11-23

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Package embryogrowth updated to version 7.1 with previous version 7.0 dated 2017-09-26

Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between embryogrowth versions 7.0 dated 2017-09-26 and 7.1 dated 2017-11-23

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Package CopulaDTA updated to version 1.0.0 with previous version 0.0.6 dated 2017-10-11

Title: Copula Based Bivariate Beta-Binomial Model for Diagnostic Test Accuracy Studies
Description: Modelling of sensitivity and specificity on their natural scale using copula based bivariate beta-binomial distribution to yield marginal mean sensitivity and specificity. The intrinsic negative correlation between sensitivity and specificity is modelled using a copula function. A forest plot can be obtained for categorical covariates or for the model with intercept only. Nyaga VN, Arbyn M, Aerts M (2017) <doi:10.18637/jss.v082.c01>.
Author: Victoria N Nyaga [aut, cre]
Maintainer: Victoria N Nyaga <victoria.nyaga@outlook.com>

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Package lawstat updated to version 3.2 with previous version 3.1 dated 2017-01-16

Title: Tools for Biostatistics, Public Policy, and Law
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness, measures of relative variability etc, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.
Author: Joseph L. Gastwirth [aut], Yulia R. Gel [aut], W. L. Wallace Hui [aut], Vyacheslav Lyubchich [aut, cre], Weiwen Miao [aut], Kimihiro Noguchi [aut]
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>

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Package joint.Cox updated to version 2.14 with previous version 2.13 dated 2017-09-03

Title: Penalized Likelihood Estimation and Dynamic Prediction under the Joint Frailty-Copula Models Between Tumour Progression and Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction methods under the joint frailty-copula model between tumour progression and death for meta-analysis. A penalized likelihood is employed for estimating model parameters, where the baseline hazard functions are approximated by smoothing splines. The methods are applicable for meta-analytic data combining several studies. The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression). See Emura et al. (2015) <doi:10.1177/0962280215604510> and Emura et al. (2017) <doi:10.1177/0962280216688032> for details. Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

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Package s20x updated to version 3.1-25 with previous version 3.1-23 dated 2017-08-08

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

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More information about s20x at CRAN
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Package Rnightlights updated to version 0.1.4 with previous version 0.1.3 dated 2017-11-21

Title: Satellite Nightlight Data Extraction
Description: The Rnightlights package 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], Henrik Bengtsson [ctb] (data setup, https://cran.r-project.org/package=R.cache), Black Guru [ctb] (gdal zonal, http://www.guru-gis.net/efficient-zonal-statistics-using-r-and-gdal/), Jeff Chen [ctb] (masq function, https://commercedataservice.github.io/tutorial_viirs_part1/), Star Ying [ctb] (masq function, https://commercedataservice.github.io/tutorial_viirs_part1/), Chris Elvidge [ctb] (information + masq function)
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>

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New package distcrete with initial version 1.0.3
Package: distcrete
Title: Discrete Distribution Approximations
Version: 1.0.3
Authors@R: c( person("Steph","Locke", role="cre", email = "steph@itsalocke.com"), person("Rich", "FitzJohn", role = c("aut"), email = "rich.fitzjohn@gmail.com"), person("Anne", "Cori", role = "aut"), person("Thibaut", "Jombart", role = "aut"))
Description: Creates discretised versions of continuous distribution functions by mapping continuous values to an underlying discrete grid, based on a (uniform) frequency of discretisation, a valid discretisation point, and an integration range. For a review of discretisation methods, see Chakraborty (2015) <doi:10.1186/s40488-015-0028-6>.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/reconhub/distcrete
BugReports: https://github.com/reconhub/distcrete/issues
Suggests: knitr, rmarkdown, testthat
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-11-23 12:44:36 UTC; steph
Author: Steph Locke [cre], Rich FitzJohn [aut], Anne Cori [aut], Thibaut Jombart [aut]
Maintainer: Steph Locke <steph@itsalocke.com>
Repository: CRAN
Date/Publication: 2017-11-23 13:50:05 UTC

More information about distcrete at CRAN
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Package iClick updated to version 1.3 with previous version 1.2 dated 2016-02-24

Title: A Button-Based GUI for Financial and Economic Data Analysis
Description: A GUI designed to support the analysis of financial-economic time series data.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@mail.shu.edu.tw>

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New package adjustedcranlogs with initial version 0.1.0
Package: adjustedcranlogs
Type: Package
Title: Remove Automated and Repeated Downloads from 'RStudio' 'CRAN' Download Logs
Version: 0.1.0
Authors@R: c(person("Tyler", "Morgan-Wall", email = "tylermw@gmail.com", role = c("aut", "cre")))
Date: 2017-11-22
Description: Adjusts output of 'cranlogs' package to account for 'CRAN'-wide daily automated downloads and re-downloads caused by package updates.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: cranlogs, xml2, lubridate, dplyr, rvest
Depends: R (>= 2.10)
URL: https://github.com/tylermorganwall/adjustedcranlogs
BugReports: https://github.com/tylermorganwall/adjustedcranlogs/issues
NeedsCompilation: no
Packaged: 2017-11-22 22:20:56 UTC; tyler
Author: Tyler Morgan-Wall [aut, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Repository: CRAN
Date/Publication: 2017-11-23 12:35:35 UTC

More information about adjustedcranlogs at CRAN
Permanent link

Package phuse (with last version 0.1.4) was removed from CRAN

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

2017-09-26 0.1.4

Permanent link
Package powdist updated to version 0.1.4 with previous version 0.1.3 dated 2017-08-16

Title: Power and Reversal Power Distributions
Description: Density, distribution function, quantile function and random generation for the family of power and reversal power distributions.
Author: Susan Anyosa [aut, cre], Jorge Luis Bazán Guzmán [aut], Artur Lemonte [aut]
Maintainer: Susan Anyosa <susanaliciach@gmail.com>

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Package palm updated to version 1.1.0 with previous version 1.0.0 dated 2017-01-30

Title: Fitting Point Process Models via the Palm Likelihood
Description: Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008) <DOI:10.1002/bimj.200610339>, maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package is chiefly focused on Neyman-Scott point processes, but can also fit void processes. The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a clustered point process. As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys.
Author: Ben Stevenson <ben.stevenson@auckland.ac.nz>
Maintainer: Ben Stevenson <ben.stevenson@auckland.ac.nz>

Diff between palm versions 1.0.0 dated 2017-01-30 and 1.1.0 dated 2017-11-23

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Package forega updated to version 1.0.3 with previous version 1.0.2 dated 2017-09-22

Title: Floating-Point Genetic Algorithms with Statistical Forecast Based Inheritance Operator
Description: The implemented algorithm performs a floating-point genetic algorithm search with a statistical forecasting operator that generates offspring which probably will be generated in future generations. Use of this operator enhances the search capabilities of floating-point genetic algorithms because offspring generated by usual genetic operators rapidly forecasted before performing more generations.
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>

Diff between forega versions 1.0.2 dated 2017-09-22 and 1.0.3 dated 2017-11-23

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Package CorporaCoCo updated to version 1.1-0 with previous version 1.0-2 dated 2017-03-31

Title: Corpora Co-Occurrence Comparison
Description: A set of functions used to compare co-occurrence between two corpora.
Author: Anthony Hennessey [aut, cre], Viola Wiegand [aut], Michaela Mahlberg [aut], Christopher R. Tench [aut], Jamie Lentin [aut]
Maintainer: Anthony Hennessey <anthony.hennessey@nottingham.ac.uk>

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Package BinaryEPPM updated to version 2.1 with previous version 2.0 dated 2016-11-28

Title: Mean and Variance Modeling of Binary Data
Description: Modeling under- and over-dispersed binary data using extended Poisson process models (EPPM) as in the article MJ Faddy and DM Smith (2012) <doi:10.1002/bimj.201100214> .
Author: David M Smith, Malcolm J Faddy
Maintainer: David M. Smith <smithdm1@us.ibm.com>

Diff between BinaryEPPM versions 2.0 dated 2016-11-28 and 2.1 dated 2017-11-23

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New package JMcmprsk with initial version 0.9
Package: JMcmprsk
Type: Package
Title: Joint Models for Longitudinal Measurements and Competing Risks Failure Time Data
Version: 0.9
Date: 2017-11-22
Author: Hong Wang<wh@csu.edu.cn>, Ning Li<nli@biomath.ucla.edu> and Gang Li<vli@ucla.edu>
Maintainer: Hong Wang <wh@csu.edu.cn>
Description: Parameter models for the joint modeling of longitudinal (continuous or ordinal) data and time-to-event data with competing risks. For a detailed information, see Robert Elashoff, Gang li and Ning Li (2016, ISBN:9781439807828) ; Robert M. Elashoff,Gang Li and Ning Li (2008) <doi:10.1111/j.1541-0420.2007.00952.x> ; Ning Li, Robert Elashoff, Gang Li and Jeffrey Saver (2010) <doi:10.1002/sim.3798> .
License: GPL (>= 2)
Imports: Rcpp,MASS,stats,utils
LinkingTo: Rcpp
SystemRequirements: GNU GSL
NeedsCompilation: yes
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2017-11-23 00:35:01 UTC; wh
Repository: CRAN
Date/Publication: 2017-11-23 09:54:33 UTC

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Package odk updated to version 1.4 with previous version 1.3 dated 2017-11-02

Title: Convert 'ODK' or 'XLSForm' to 'SPSS' Data Frame
Description: After develop a 'ODK' <https://opendatakit.org/> frame, we can link the frame to 'Google Sheets' <https://www.google.com/sheets/about/> and collect data through 'Android' <https://www.android.com/>. This data uploaded to a 'Google sheets'. odk2spss() function help to convert the 'odk' frame into 'SPSS' <https://www.ibm.com/analytics/us/en/technology/spss/> frame. Also able to add downloaded 'Google sheets' data or read data from 'Google sheets' by using 'ODK' frame 'submission_url'.
Author: Muntashir-Al-Arefin
Maintainer: Muntashir-Al-Arefin <muntashir.a2i@gmail.com>

Diff between odk versions 1.3 dated 2017-11-02 and 1.4 dated 2017-11-23

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Package wtest updated to version 2.0 with previous version 1.0 dated 2016-08-05

Title: The W-Test on Genetic Interactions Testing
Description: Perform the calculation of W-test, diagnostic checking, calculate minor allele frequency (MAF) and odds ratio.
Author: Rui Sun, Maggie Haitian Wang
Maintainer: Rui Sun <rsunzju@gmail.com>

Diff between wtest versions 1.0 dated 2016-08-05 and 2.0 dated 2017-11-23

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Package RSurvey updated to version 0.9.2 with previous version 0.9.1 dated 2017-02-24

Title: Geographic Information System Application
Description: A geographic information system (GIS) graphical user interface (GUI) that provides data viewing, management, and analysis tools.
Author: Jason C. Fisher [aut, cre] (0000-0001-9032-8912)
Maintainer: Jason C. Fisher <jfisher@usgs.gov>

Diff between RSurvey versions 0.9.1 dated 2017-02-24 and 0.9.2 dated 2017-11-23

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Package MHTdiscrete updated to version 1.0.0 with previous version 0.1.3 dated 2017-02-08

Title: Multiple Hypotheses Testing for Discrete Data
Description: A comprehensive tool for almost all existing multiple testing methods for discrete data. The package also provides some novel multiple testing procedures controlling FWER/FDR for discrete data. Given discrete p-values and their domains, the [method].p.adjust function returns adjusted p-values, which can be used to compare with the nominal significant level alpha and make decisions. For users' convenience, the functions also provide the output option for printing decision rules.
Author: Yalin Zhu, Wenge Guo
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>

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Wed, 22 Nov 2017

Package IDCard updated to version 0.3.0 with previous version 0.2.0 dated 2017-11-08

Title: Update Chinese ID Card Number to Eighteen Digits
Description: The digits of the old version (before 2000 year) of 'Chinese ID Card Number' is 15, this package aims to update to the current version of 18 digits. Besides, this package can help check whether the given 'ID' is right or not.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

Diff between IDCard versions 0.2.0 dated 2017-11-08 and 0.3.0 dated 2017-11-22

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Package boclust updated to version 0.1.1 with previous version 0.1.0 dated 2017-11-15

Title: A Clustering Method Based on Boosting on Single Attributes
Description: An overlap clustering algorithm for categorical ultra-dimension data.
Author: Peng Zhang [aut], Kaixiu Jin [aut, cre]
Maintainer: Kaixiu Jin <jinkaixiu@zju.edu.cn>

Diff between boclust versions 0.1.0 dated 2017-11-15 and 0.1.1 dated 2017-11-22

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Package TempleMetrics updated to version 1.1.0 with previous version 1.0.0 dated 2017-11-10

Title: Estimating Conditional Distributions
Description: Estimates conditional distributions and conditional quantiles. The versions of the methods in this package are primarily for use in multiple step procedures where the first step is to estimate a conditional distribution. In particular, there are functions for implementing distribution regression, quantile regression, and versions of local linear distribution regression; all in a unified framework. Distribution regression provides a way to flexibly model the distribution of some outcome Y conditional on covariates X without imposing parametric assumptions on the conditional distribution but providing more structure than fully nonparametric estimation (See Foresi and Peracchi (1995) <doi:10.2307/2291056> and Chernozhukov, Fernandez-Val, and Melly (2013) <doi:10.3982/ECTA10582>).
Author: Brantly Callaway [aut, cre], Weige Huang [aut]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>

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Package sn updated to version 1.5-1 with previous version 1.5-0 dated 2017-02-10

Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and model diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package sjstats updated to version 0.13.0 with previous version 0.12.0 dated 2017-10-16

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

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Package mgm updated to version 1.2-2 with previous version 1.2-1 dated 2017-06-20

Title: Estimating Time-Varying k-Order Mixed Graphical Models
Description: Estimation of k-Order time-varying Mixed Graphical Models and mixed VAR(p) models via elastic-net regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>

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Package hms updated to version 0.4.0 with previous version 0.3 dated 2016-11-22

Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre], The R Consortium [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package entropart updated to version 1.4-8 with previous version 1.4-7 dated 2017-03-29

Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon [aut, cre], Bruno Herault [aut]
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>

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Package d3r updated to version 0.7.1 with previous version 0.7.0 dated 2017-10-11

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

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Package LocalControl updated to version 1.1.0 with previous version 1.0.1 dated 2017-06-03

Title: Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence
Description: Implements novel nonparametric approaches to address biases and confounding when comparing treatments or exposures in observational studies of outcomes. While designed and appropriate for use in studies involving medicine and the life sciences, the package can be used in other situations involving outcomes with multiple confounders. The package implements a family of methods for nonparametric bias correction when comparing treatments in cross-sectional, case-control, and survival analysis settings, including competing risks with censoring. The approach extends to bias-corrected personalized predictions of treatment outcome differences, and analysis of heterogeneity of treatment effect-sizes across patient subgroups.
Author: Nicolas R. Lauve [aut], Stuart J. Nelson [aut], S. Stanley Young [aut], Robert L. Obenchain [aut], Melania Pintilie [ctb], Martin Kutz [ctb], Christophe G. Lambert [aut, cre]
Maintainer: Christophe G. Lambert <cglambert@unm.edu>

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Package ExplainPrediction updated to version 1.2.3 with previous version 1.1.8 dated 2017-04-03

Title: Explanation of Predictions for Classification and Regression Models
Description: Generates explanations for classification and regression models and visualizes them. Explanations are generated for individual predictions as well as for models as a whole. Two explanation methods are included, EXPLAIN and IME. The EXPLAIN method is fast but might miss explanations expressed redundantly in the model. The IME method is slower as it samples from all feature subsets. For the EXPLAIN method see Robnik-Sikonja and Kononenko (2008) <doi:10.1109/TKDE.2007.190734>, and the IME method is described in Strumbelj and Kononenko (2010, JMLR, vol. 11:1-18). All models in package 'CORElearn' are natively supported, for other prediction models a wrapper function is provided and illustrated for models from packages 'randomForest', 'nnet', and 'e1071'.
Author: Marko Robnik-Sikonja
Maintainer: Marko Robnik-Sikonja <marko.robnik@fri.uni-lj.si>

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Package domino updated to version 0.3.1 with previous version 0.3.0 dated 2016-07-10

Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite. 'Domino' is a service that makes it easy to run your code on scalable hardware, with integrated version control and collaboration features designed for analytical workflows (see <http://www.dominodatalab.com> for more information).
Author: Jacek Glodek <jacek@theiterators.com>
Maintainer: Nick Elprin <nick@dominodatalab.com>

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Package plsVarSel updated to version 0.9.3 with previous version 0.9.2 dated 2017-11-09

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>

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Package KMgene updated to version 1.2 with previous version 1.1 dated 2017-11-09

Title: Gene-Based Association Analysis for Complex Traits
Description: Gene based association test between a group of SNPs and traits including familial (both continuous and binary) traits, multivariate continuous (both independent and familial) traits, longitudinal continuous traits and survival traits. Part of methods were previously published in Maity et al (2012) <doi:10.1002/gepi.21663>, Chen et al (2013) <doi:10.1002/gepi.21703>, Chen et al (2014) <doi:10.1002/gepi.21791>, Yan et al (2015) <doi:10.1159/000375409>, Yan et al (2015) <doi:10.1534/genetics.115.178590> and Yan et al (2015) <doi:10.1159/000445057>.
Author: Qi Yan
Maintainer: Qi Yan <qiy17@pitt.edu>

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Package futility updated to version 0.2 with previous version 0.1 dated 2017-07-28

Title: Interim Analysis of Operational Futility in Randomized Trials with Time-to-Event Endpoints and Fixed Follow-Up
Description: Randomized clinical trials commonly follow participants for a time-to-event efficacy endpoint for a fixed period of time. Consequently, at the time when the last enrolled participant completes their follow-up, the number of observed endpoints is a random variable. Assuming data collected through an interim timepoint, simulation-based estimation and inferential procedures in the standard right-censored failure time analysis framework are conducted for the distribution of the number of endpoints--in total as well as by treatment arm--at the end of the follow-up period. The future (i.e., yet unobserved) enrollment, endpoint, and dropout times are generated according to mechanisms specified in the simTrial() function in the 'seqDesign' package. A Bayesian model for the endpoint rate, offering the option to specify a robust mixture prior distribution, is used for generating future data (see the vignette for details).
Author: Yingying Zhuang and Michal Juraska, with contributions from Doug Grove, Peter B. Gilbert, Alexander R. Luedtke, Sanne Roels, and An Vandebosch
Maintainer: Michal Juraska <mjuraska@fredhutch.org>

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Package Nippon updated to version 0.6.4 with previous version 0.6.3-1 dated 2016-04-13

Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com> [aut, cre], Hironobu Takahashi [cph], Hajime Baba [cph], Takatsugu Nokubi [cph]
Maintainer: Susumu Tanimura <aruminat@gmail.com>

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Package ggfan updated to version 0.1.1 with previous version 0.1.0 dated 2017-11-14

Title: Summarise a Distribution Through Coloured Intervals
Description: Implements the functionality of the 'fanplot' package as 'geoms' for 'ggplot2'. Designed for summarising MCMC samples from a posterior distribution, where a visualisation is desired for several values of a continuous covariate. Increasing posterior intervals of the sampled quantity are mapped to a continuous colour scale.
Author: Jason Hilton [aut, cre]
Maintainer: Jason Hilton <jason_hilton@yahoo.com>

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New package bucky with initial version 1.0.3
Package: bucky
Type: Package
Title: Bucky's Archive for Data Analysis in the Social Sciences
Version: 1.0.3
Date: 2017-11-20
Author: Alexander Tahk [aut, cre]
Maintainer: Alexander Tahk <tahk@alum.mit.edu>
Authors@R: c(person("Alexander", "Tahk", role = c("aut", "cre"), email = "tahk@alum.mit.edu"))
Depends: R (>= 3.1.0), methods, sandwich, lmtest
Suggests: MASS, parallel, Amelia
Enhances: texreg, stargazer
Description: Provides functions for various statistical techniques commonly used in the social sciences, including functions to compute clustered robust standard errors, combine results across multiply-imputed data sets, and simplify the addition of robust and clustered robust standard errors. The package was originally developed, in part, to assist porting of replication code from 'Stata' and attempts to replicate default options from 'Stata' where possible.
License: GPL-3
NeedsCompilation: no
Packaged: 2017-11-22 13:50:11 UTC; tahk
Repository: CRAN
Date/Publication: 2017-11-22 18:18:46 UTC

More information about bucky at CRAN
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Package blscrapeR updated to version 3.1.1 with previous version 3.0.1 dated 2017-10-05

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

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Package dynamichazard updated to version 0.5.0 with previous version 0.4.0 dated 2017-09-16

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.
Author: Benjamin Christoffersen [cre, aut], Alan Miller [cph], Anthony Williams [cph], Boost developers [cph], R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>

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Package bssm updated to version 0.1.2 with previous version 0.1.1-1 dated 2017-07-12

Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo and parallel importance sampling type weighted Markov chain Monte Carlo. Gaussian, Poisson, binomial, or negative binomial observation densities, stochastic volatility models with Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.
Author: Jouni Helske, Matti Vihola
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package miic updated to version 1.0 with previous version 0.1 dated 2017-10-09

Title: Multivariate Information Inductive Causation
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Verny et al. Plos Comput Biol. (2017) <doi:10.1371/journal.pcbi.1005662>.
Author: Nadir Sella [aut, cre], Louis Verny [aut], Severine Affeldt [aut], Hervé Isambert [aut]
Maintainer: Nadir Sella <nadir.sella@curie.fr>

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Package DVHmetrics updated to version 0.3.7 with previous version 0.3.6 dated 2016-07-29

Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics as well as generalized equivalent uniform dose (gEUD), biologically effective dose (BED), equivalent dose in 2 Gy fractions (EQD2), normal tissue complication probability (NTCP), and tumor control probability (TCP). Show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre], Heiko Karle [aut], Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>

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Package clustermq (with last version 0.8.0) was removed from CRAN

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

2017-11-11 0.8.0
2017-08-28 0.7.0

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Package SELF updated to version 0.1.1 with previous version 0.1.0 dated 2017-11-13

Title: A Structural Equation Embedded Likelihood Framework for Causal Discovery
Description: Provides the SELF criteria to learn causal structure. Please cite "Ruichu Cai, Jie Qiao, Zhenjie Zhang, Zhifeng Hao. SELF: Structural Equational Embedded Likelihood Framework for Causal Discovery. AAAI. 2018."
Author: Ruichu Cai [ths, aut], Jie Qiao [aut, cre], Zhenjie Zhang [ths, aut], Zhifeng Hao [ths, aut]
Maintainer: Jie Qiao <qiaojie2004@vip.qq.com>

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Package ManifoldOptim updated to version 0.1.4 with previous version 0.1.3 dated 2017-03-31

Title: An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization
Description: An R interface to version 0.3 of the 'ROPTLIB' optimization library (see <http://www.math.fsu.edu/~whuang2> for more information). Optimize real- valued functions over manifolds such as Stiefel, Grassmann, and Symmetric Positive Definite matrices.
Author: Kofi P. Adragni [aut, cph], Sean R. Martin [aut, cre, cph], Andrew M. Raim [aut, cph], Wen Huang [aut, cph]
Maintainer: Sean R. Martin <smarti1@umbc.edu>

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 ManifoldOptim-0.1.4/ManifoldOptim/src/Makevars.win                                           |    3 
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/BrockettProblem.cpp                      |   36 +
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ManifoldOptim.cpp                        |   34 -
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ManifoldOptim.h                          |   13 
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ManifoldOptimModule.cpp                  |    7 
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ProblemAdapter.cpp                       |  188 ----------
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ProblemAdapter.h                         |   16 
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/RProblem.cpp                             |   39 +-
 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/RProblem.h                               |    8 
 ManifoldOptim-0.1.4/ManifoldOptim/src/MyRcppExports.cpp                                      |   12 
 ManifoldOptim-0.1.4/ManifoldOptim/src/Others/RegisterDynamicSymbol.cpp                       |only
 36 files changed, 475 insertions(+), 358 deletions(-)

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Package LCF updated to version 1.7.0 with previous version 1.6-6 dated 2017-02-17

Title: Linear Combination Fitting
Description: Baseline correction, normalization and linear combination fitting (LCF) of X-ray absorption near edge structure (XANES) spectra. The package includes data loading of .xmu files exported from 'ATHENA' (Ravel and Newville, 2005) <doi:10.1107/S0909049505012719>. Loaded spectra can be background corrected and all standards can be fitted at once. Two linear combination fitting functions can be used: (1) fit_athena(): Simply fitting combinations of standards as in ATHENA, (2) fit_float(): Fitting all standards with changing baseline correction and edge-step normalization parameters.
Author: Florian Werner [aut, cre]
Maintainer: Florian Werner <florian.werner@wzw.tum.de>

Diff between LCF versions 1.6-6 dated 2017-02-17 and 1.7.0 dated 2017-11-22

 DESCRIPTION          |   10 +++++-----
 MD5                  |   28 ++++++++++++++--------------
 R/LC_fit.R           |    2 +-
 R/initial_load.R     |    7 ++++---
 R/read_raw_spec.R    |   24 +++++++++++++++++++++---
 man/LCF_solve_QP.Rd  |    1 -
 man/LC_fit.Rd        |    3 +--
 man/bkg_corr.Rd      |    1 -
 man/fit_athena.Rd    |    1 -
 man/fit_float.Rd     |    1 -
 man/initial_load.Rd  |    7 ++++---
 man/plot_LCF.Rd      |    1 -
 man/read_raw_spec.Rd |    7 ++++---
 man/specdat.Rd       |    1 -
 man/std_df.Rd        |    1 -
 15 files changed, 54 insertions(+), 41 deletions(-)

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Package bfork (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:

2016-01-04 0.1.1
2016-01-04 0.1.2

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Package reactR updated to version 0.1.4 with previous version 0.1.3 dated 2017-10-12

Title: React Helpers
Description: Make it easy to use 'React' in R with helper dependency functions, embedded 'Babel' transpiler, and examples.
Author: Facebook Inc [aut, cph] (React library in lib, https://facebook.github.io/react; see AUTHORS for full list of contributors), Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between reactR versions 0.1.3 dated 2017-10-12 and 0.1.4 dated 2017-11-22

 reactR-0.1.3/reactR/inst/www/react/LICENSE          |only
 reactR-0.1.4/reactR/DESCRIPTION                     |   16 
 reactR-0.1.4/reactR/LICENSE                         |    2 
 reactR-0.1.4/reactR/MD5                             |   25 -
 reactR-0.1.4/reactR/NEWS.md                         |    4 
 reactR-0.1.4/reactR/R/meta.R                        |    2 
 reactR-0.1.4/reactR/inst/doc/intro_reactR.Rmd       |    4 
 reactR-0.1.4/reactR/inst/doc/intro_reactR.html      |   12 
 reactR-0.1.4/reactR/inst/examples/antd.R            |    2 
 reactR-0.1.4/reactR/inst/examples/office-fabric.R   |   64 ++-
 reactR-0.1.4/reactR/inst/examples/semiotic.R        |only
 reactR-0.1.4/reactR/inst/www/react/LICENSE.txt      |only
 reactR-0.1.4/reactR/inst/www/react/react-dom.min.js |  393 +++++++++-----------
 reactR-0.1.4/reactR/inst/www/react/react.min.js     |   43 +-
 reactR-0.1.4/reactR/vignettes/intro_reactR.Rmd      |    4 
 15 files changed, 304 insertions(+), 267 deletions(-)

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Package provenance updated to version 1.8 with previous version 1.7 dated 2017-05-18

Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov- Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between provenance versions 1.7 dated 2017-05-18 and 1.8 dated 2017-11-22

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 R/gui.R     |    5 ++---
 3 files changed, 8 insertions(+), 9 deletions(-)

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Package wTO updated to version 1.4.1 with previous version 1.4.0 dated 2017-11-12

Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks (Nowick et al. (2009) <doi:10.1073/pnas.0911376106>) 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.
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 1.4.0 dated 2017-11-12 and 1.4.1 dated 2017-11-22

 DESCRIPTION                |    6 
 MD5                        |   36 ++--
 NAMESPACE                  |    1 
 R/Correlation.Overlap.R    |    2 
 R/Cut.off2.R               |    1 
 R/NetVis.R                 |  326 +++++++++++++++++++++++----------------------
 R/sample_ind.R             |    1 
 R/wTO.Complete2.R          |    1 
 R/wTO.Consensus.R          |   11 -
 R/wTO.R                    |   59 ++++----
 R/wTO.in.line.R            |   81 +++++------
 man/Correlation.Overlap.Rd |    3 
 man/Cut.off.Rd             |    3 
 man/NetVis.Rd              |    3 
 man/sample_ind.Rd          |    3 
 man/wTO.Complete.Rd        |    3 
 man/wTO.Consensus.Rd       |    4 
 man/wTO.Rd                 |    3 
 man/wTO.in.line.Rd         |    3 
 19 files changed, 297 insertions(+), 253 deletions(-)

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Package dyads updated to version 1.1 with previous version 1.0 dated 2017-10-10

Title: Dyadic Network Analysis
Description: Contains functions for dyadic network analysis.
Author: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Maintainer: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>

Diff between dyads versions 1.0 dated 2017-10-10 and 1.1 dated 2017-11-22

 DESCRIPTION                |   10 -
 MD5                        |   14 +
 NAMESPACE                  |   27 ++-
 R/internalFunctionsDyads.R |  337 ++++++++++++++++++++++++++++++++-------------
 R/j2.R                     |only
 build/partial.rdb          |binary
 man/dyads-package.Rd       |   10 -
 man/j2.Rd                  |only
 man/p2.Rd                  |    7 
 9 files changed, 286 insertions(+), 119 deletions(-)

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Package dng updated to version 0.1.1 with previous version 0.1.0 dated 2017-09-20

Title: Distributions and Gradients
Description: Provides density, distribution function, quantile function and random generation for the split-t distribution, and computes the mean, variance, skewness and kurtosis for the split-t distribution (Li, F, Villani, M. and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>).
Author: Feng Li, Jiayue Zeng
Maintainer: Jiayue Zeng <zengjiayue@126.com>

Diff between dng versions 0.1.0 dated 2017-09-20 and 0.1.1 dated 2017-11-22

 DESCRIPTION          |    8 ++++----
 MD5                  |    4 ++--
 src/rcpp_dsplitt.cpp |    2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

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