Wed, 25 Feb 2015

New package SurvCorr with initial version 1.0
Package: SurvCorr
Type: Package
Title: Correlation of Bivariate Survival Times
Version: 1.0
Date: 2015-02-25
Author: Meinhard Ploner, Alexandra Kaider and Georg Heinze
Maintainer: Georg Heinze
Depends: R (>= 3.0.2)
Imports: survival, fields
Description: Estimates correlation coefficients with associated confidence limits for bivariate, partially censored survival times. Uses the iterative multiple imputation approach proposed by Schemper, Kaider, Wakounig and Heinze, Statistics in Medicine 2013. Provides a scatterplot function to visualize the bivariate distribution, either on the original time scale or as copula.
License: GPL
Packaged: 2015-02-25 16:02:48 UTC; Georg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-26 02:18:35

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Package PRROC updated to version 1.1 with previous version 1.0 dated 2014-12-16

Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau

Diff between PRROC versions 1.0 dated 2014-12-16 and 1.1 dated 2015-02-25

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Package hergm updated to version 2.2-0 with previous version 2.1-1 dated 2015-01-11

Title: Hierarchical Exponential-Family Random Graph Models
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger [aut, cre], Mark S. Handcock [ctb], Pamela Luna [ctb]
Maintainer: Michael Schweinberger

Diff between hergm versions 2.1-1 dated 2015-01-11 and 2.2-0 dated 2015-02-25

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Package frailtypack updated to version 2.7.4 with previous version 2.7.2 dated 2014-10-16

Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction
Description: Frailtypack fits several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation. 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 joint modelling for recurrent events with terminal event for clustered data or not. 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 a gamma distribution, but you can switch to a log-normal in shared and joint models. Now, you can also consider time-varying covariates effects in Cox, shared and joint models. 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-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau

Diff between frailtypack versions 2.7.2 dated 2014-10-16 and 2.7.4 dated 2015-02-25

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New package dplRCon with initial version 1.0
Package: dplRCon
Type: Package
Title: Concordance for Dendroclimatology
Version: 1.0
Date: 2015-01-16
Author: Maryann Pirie
Maintainer: M R Pirie
Description: The concordance method is a non-parametric method based on bootstrapping that is used to test the hypothesis that two subsets of time series are similar in terms of mean, variance or both. This method was developed to address a concern within dendroclimatology that young trees may produce a differing climate response to older more established trees. Details of this method are available in Pirie, M. (2013). The Climate of New Zealand reconstructed from kauri tree rings: Enhancement through the use of novel statistical methodology. PhD. Dissertation, School of Environment and Department of Statistics, University of Auckland, New Zealand. This package also produces a figure with 3 panels, each panel is for a different climate variable. An example of this figure in included in "On the influence of tree size on the climate - growth relationship of New Zealand kauri (Agathis australis): insights from annual, monthly and daily growth patterns. J Wunder, AM Fowler, ER Cook, M Pirie, SPJ McCloskey. Trees 27 (4), 937-948". For further R functions for loading your own dendroclimatology datasets and performing dendrochronology analysis refer to the R package "dplR: Dendrochronology Program Library in R". The concordance procedure is intended to add to the standard dendrochronology techniques provided in "dplR".
License: GPL
LazyLoad: yes
LazyData: yes
Depends: R (>= 2.10)
Packaged: 2015-02-25 20:43:10 UTC; piriem
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-26 01:56:47

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Package diseasemapping updated to version 1.1.7 with previous version 1.1.5 dated 2015-01-15

Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown

Diff between diseasemapping versions 1.1.5 dated 2015-01-15 and 1.1.7 dated 2015-02-25

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Package visreg updated to version 2.1-1 with previous version 2.1-0 dated 2014-11-27

Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

Diff between visreg versions 2.1-0 dated 2014-11-27 and 2.1-1 dated 2015-02-25

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Package survMisc updated to version 0.4.5 with previous version 0.4.4 dated 2015-01-06

Title: Miscellaneous Functions for Survival Data
Description: A collection of functions for analysis of survival data. These extend the methods available in the survival package.
Author: Chris Dardis
Maintainer: Chris Dardis

Diff between survMisc versions 0.4.4 dated 2015-01-06 and 0.4.5 dated 2015-02-25

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Package multitaper updated to version 1.0-11 with previous version 1.0-10 dated 2015-02-18

Title: Multitaper Spectral Analysis Tools
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim , Wesley S. Burr
Maintainer: Karim Rahim

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Package MuMIn updated to version 1.13.4 with previous version 1.12.1 dated 2014-12-17

Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria (AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń

Diff between MuMIn versions 1.12.1 dated 2014-12-17 and 1.13.4 dated 2015-02-25

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Package bamboo (with last version 0.9.5) was removed from CRAN

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

2014-08-14 0.9.5

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Package jvmr (with last version 2.11.2.1) was removed from CRAN

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

2014-08-30 2.11.2.1
2014-06-25 2.11.1.1
2013-07-16 1.0.4
2013-06-25 1.0.3

Permanent link
New package momentchi2 with initial version 0.1.0
Package: momentchi2
Title: Moment-Matching Methods for Weighted Sums of Chi-Squared Random Variables
Version: 0.1.0
Author: Dean Bodenham
Maintainer: Dean Bodenham
Description: A collection of moment-matching methods for computing the cumulative distribution function of a positively-weighted sum of chi-squared random variables. Methods include the Satterthwaite-Welch method, Hall-Buckley-Eagleson method, Wood's F method, and the Lindsay-Pilla-Basak method.
Depends: R (>= 3.1.2)
License: GPL-2 | GPL-3
LazyData: true
Packaged: 2015-02-25 10:34:38 UTC; dean
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-25 11:54:43

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Package BoolNet updated to version 2.1.1 with previous version 2.1.0 dated 2015-02-23

Title: Construction, Simulation and Analysis of Boolean Networks
Description: Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb] (contributed PicoSAT code), Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler

Diff between BoolNet versions 2.1.0 dated 2015-02-23 and 2.1.1 dated 2015-02-25

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Package SDD updated to version 1.2 with previous version 1.1 dated 2014-02-27

Title: Serial Dependence Diagrams
Description: Allows for computing (and by default plotting) different types of serial dependence diagrams.
Author: Luca Bagnato, Lucio De Capitani, Angelo Mazza and Antonio Punzo
Maintainer: Angelo Mazza

Diff between SDD versions 1.1 dated 2014-02-27 and 1.2 dated 2015-02-25

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Package lgcp updated to version 1.3-9 with previous version 1.3-8 dated 2015-02-04

Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor

Diff between lgcp versions 1.3-8 dated 2015-02-04 and 1.3-9 dated 2015-02-25

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Package FGSG updated to version 1.0.2 with previous version 1.0 dated 2014-04-13

Title: Feature Grouping and Selection Over an Undirected Graph
Description: Implement algorithms for feature grouping and selection over an undirected graph, solves problems like graph fused lasso, graph OSCAR and so on.
Author: Xiaotong Shen, Yiwen Sun, Julie Langou
Maintainer: Yiwen Sun

Diff between FGSG versions 1.0 dated 2014-04-13 and 1.0.2 dated 2015-02-25

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Package soilDB updated to version 1.5-2 with previous version 1.5 dated 2015-02-20

Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette

Diff between soilDB versions 1.5 dated 2015-02-20 and 1.5-2 dated 2015-02-25

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Package sgt updated to version 1.1 with previous version 1.0 dated 2015-02-16

Title: Skewed Generalized T Distribution
Description: Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.
Author: Carter Davis
Maintainer: Carter Davis

Diff between sgt versions 1.0 dated 2015-02-16 and 1.1 dated 2015-02-25

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Package R.matlab updated to version 3.2.0 with previous version 3.1.1 dated 2014-10-10

Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files (via 'Rcompression'), sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson

Diff between R.matlab versions 3.1.1 dated 2014-10-10 and 3.2.0 dated 2015-02-25

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Package npmv updated to version 2.2 with previous version 2.1 dated 2013-12-04

Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis

Diff between npmv versions 2.1 dated 2013-12-04 and 2.2 dated 2015-02-25

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Package multiPIM updated to version 1.4-3 with previous version 1.4-1 dated 2014-04-14

Title: Variable Importance Analysis with Population Intervention Models
Description: Performs variable importance analysis using a causal inference approach. This is done by fitting Population Intervention Models. The default is to use a Targeted Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and Graphical Computation (G-COMP) estimators. Inference can be obtained from the influence curve (plug-in) or by bootstrapping.
Author: Stephan Ritter , Alan Hubbard , Nicholas Jewell
Maintainer: Stephan Ritter

Diff between multiPIM versions 1.4-1 dated 2014-04-14 and 1.4-3 dated 2015-02-25

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Package lessR updated to version 3.2 with previous version 3.1.1 dated 2014-09-23

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate descriptive statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function and color themes. The function Help provides a help system that suggests specific analyses and functions. Variable labels are available. A confirmatory factor analysis of multiple indicator measurement models is also available as is a pedagogical routines for data simulation such as for the Central Limit Theorem.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing

Diff between lessR versions 3.1.1 dated 2014-09-23 and 3.2 dated 2015-02-25

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Package iqLearn updated to version 1.3 with previous version 1.2 dated 2014-03-04

Title: Interactive Q-Learning
Description: Estimate an optimal dynamic treatment regime using Interactive Q-learning.
Author: Kristin A. Linn, Eric B. Laber, Leonard A. Stefanski
Maintainer: Kristin A. Linn

Diff between iqLearn versions 1.2 dated 2014-03-04 and 1.3 dated 2015-02-25

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New package ihs with initial version 1.0
Package: ihs
Version: 1.0
Type: Package
Title: Inverse Hyperbolic Sine Distribution
Date: 2015-02-24
Author: Carter Davis
Maintainer: Carter Davis
Depends: R (>= 2.4.0), maxLik (>= 1.2-4)
Description: Density, distribution function, quantile function and random generation for the inverse hyperbolic sine distribution. This package also provides a function that can fit data to the inverse hyperbolic sine distribution using maximum likelihood estimation.
License: GPL (>= 3)
Repository: CRAN
Packaged: 2015-02-25 05:40:24 UTC; carterdavis
NeedsCompilation: no
Date/Publication: 2015-02-25 08:12:31

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New package GAabbreviate with initial version 1.0
Package: GAabbreviate
Type: Package
Version: 1.0
Date: 2015-02-25
Title: Abbreviating Questionnaires (or Other Measures) Using Genetic Algorithms
Description: The GAabbreviate uses Genetic Algorithms as an optimization tool to create abbreviated forms of lengthy questionnaires (or other measures) that maximally capture the variance in the original data of the long form of the measure.
Authors@R: c(person("Luca", "Scrucca", role = "aut"), person("Baljinder K.", "Sahdra", role = c("aut", "cre"), email = "baljinder.sahdra@acu.edu.au"))
Depends: R (>= 3.0), GA (>= 2.0), psych (>= 1.4.3)
License: GPL (>= 2)
ByteCompile: true
LazyLoad: yes
Author: Luca Scrucca [aut], Baljinder K. Sahdra [aut, cre]
Maintainer: Baljinder K. Sahdra
Packaged: 2015-02-25 06:41:06 UTC; basahdra
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-25 08:05:20

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Package dunn.test updated to version 1.2.3 with previous version 1.2.2 dated 2015-01-03

Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno

Diff between dunn.test versions 1.2.2 dated 2015-01-03 and 1.2.3 dated 2015-02-25

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New package BayesSummaryStatLM with initial version 1.0
Package: BayesSummaryStatLM
Type: Package
Title: MCMC Sampling of Bayesian Linear Models via Summary Statistics
Version: 1.0
Date: 2015-01-01
Author: Evgeny Savel'ev, Alexey Miroshnikov, Erin Conlon
Maintainer: Evgeny Savel'ev
Description: Methods for generating Markov Chain Monte Carlo (MCMC) posterior samples of Bayesian linear regression model parameters that require only summary statistics of data as input. Summary statistics are useful for systems with very limited amounts of physical memory. The package provides two functions: one function that computes summary statistics of data and one function that carries out the MCMC posterior sampling for Bayesian linear regression models where summary statistics are used as input. The function read.regress.data.ff utilizes the R package 'ff' to handle data sets that are too large to fit into a user's physical memory, by reading in data in chunks.
Depends: mvnfast, ff
License: GPL (>= 2)
Packaged: 2015-02-25 03:36:21 UTC; evgeny
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-25 08:05:16

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