Sun, 23 Nov 2014

Package mediation updated to version 4.4.3 with previous version 4.4.2 dated 2014-08-27

Title: Causal Mediation Analysis
Description: mediation allows both parametric and nonparametric causal mediation analysis. It implements the methods and suggestions in Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley , Teppei Yamamoto , Kentaro Hirose , Luke Keele , Kosuke Imai
Maintainer: Teppei Yamamoto

Diff between mediation versions 4.4.2 dated 2014-08-27 and 4.4.3 dated 2014-11-23

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More information about mediation at CRAN
Permanent link

Package BiodiversityR updated to version 2.5-1 with previous version 2.4-4 dated 2014-05-15

Title: GUI for biodiversity, suitability and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt

Diff between BiodiversityR versions 2.4-4 dated 2014-05-15 and 2.5-1 dated 2014-11-23

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Sat, 22 Nov 2014

Package TAM updated to version 1.2 with previous version 1.1 dated 2014-10-19

Title: Test Analysis Modules
Description: The package includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models, Cognitive Diagnostic Models), fit statistics and person parameter estimation.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch

Diff between TAM versions 1.1 dated 2014-10-19 and 1.2 dated 2014-11-22

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Package robustbase updated to version 0.92-2 with previous version 0.92-1 dated 2014-11-18

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably Peter Rousseeuw and Christophe Croux, see file 'Copyrights'; Valentin Todorov , Andreas Ruckstuhl , Matias Salibian-Barrera , Tobias Verbeke , Manuel Koller , Martin Maechler
Maintainer: Martin Maechler

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Package magrittr updated to version 1.5 with previous version 1.0.1 dated 2014-05-15

Title: A Forward-Pipe Operator for R
Description: Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe."
Author: Stefan Milton Bache and Hadley Wickham
Maintainer: Stefan Milton Bache

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Package classyfire updated to version 0.1-1 with previous version 0.1-0 dated 2014-09-04

Title: Robust multivariate classification using highly optimised SVM ensembles
Description: A collection of functions for the creation and application of highly optimised, robustly evaluated ensembles of support vector machines (SVMs). The package takes care of training individual SVM classifiers using a fast parallel heuristic algorithm, and combines individual classifiers into ensembles. Robust metrics of classification performance are offered by bootstrap resampling and permutation testing.
Author: Eleni Chatzimichali and Conrad Bessant
Maintainer: Eleni Chatzimichali

Diff between classyfire versions 0.1-0 dated 2014-09-04 and 0.1-1 dated 2014-11-22

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Package BIFIEsurvey updated to version 1.1 with previous version 1.0 dated 2014-10-12

Title: Some Tools for Survey Statistics in Educational Assessment, Developed by BIFIE
Description: Some Tools for Survey Statistics in Educational Assessment, Developed by BIFIE. Bundesinstitut fuer Bildungsforschung, Entwicklung und Innovation im oesterreichischen Schulwesen; Federal Institute for Educational Research, Innovation and Development of the Austrian School System; Salzburg, Austria.
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre], Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch

Diff between BIFIEsurvey versions 1.0 dated 2014-10-12 and 1.1 dated 2014-11-22

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Fri, 21 Nov 2014

Package yhatr updated to version 0.13.1 with previous version 0.12.1 dated 2014-07-19

Title: R binder for the Yhat API
Description: yhatr lets you deploy, maintain, and invoke models via the Yhat REST API.
Author: Greg Lamp , Eric Chiang
Maintainer: Greg Lamp

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Package RadOnc updated to version 1.0.9 with previous version 1.0.8 dated 2014-05-31

Title: Analytical Tools for Radiation Oncology
Description: This package is designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology. The tools herein enable import of DVH information from Varian's Aria/Eclipse platform and 3D structural representations and dosimetric information from DICOM-RT files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson
Maintainer: Reid F. Thompson

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Package pxweb updated to version 0.5.2 with previous version 0.4 dated 2014-09-04

Title: R interface to the PX-Web/PC-Axis API
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API is used by organizations such as Statistics Sweden and Statistics Finland to disseminate data. The R package can interact with all PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract metadata and extract and parse statistics to R data.frame format. PX-Web is a solution to disseminate PC-Axis data files in dynamic tables on the web. Since 2013 PX-Web contains an API to disseminate PC-Axis files. PX-Web/PC-Axis API information can be found at: http://www.scb.se/Grupp/OmSCB/API/API-description.pdf
Author: Mans Magnusson, Leo Lahti, Love Hansson
Maintainer: Mans Magnusson

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Package PoweR updated to version 1.0.4 with previous version 1.0.3 dated 2014-10-07

Title: Computation of Power and Level Tables for Hypothesis Tests
Description: Functions for the computation of power and level tables for hypothesis tests, in LaTeX format, functions to build explanatory graphs for studying power of test statistics.
Author: Pierre Lafaye de Micheaux , Viet Anh Tran
Maintainer: P. Lafaye de Micheaux

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Package nodiv updated to version 0.9.3 with previous version 0.9.2 dated 2014-11-18

Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution). DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard

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Package mkin updated to version 0.9-34 with previous version 0.9-33 dated 2014-10-11

Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers and a choice of the optimisation methods made available by the FME package. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke

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Package bpcp updated to version 1.2.4 with previous version 1.1.0 dated 2014-04-30

Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay

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Package bayesTFR updated to version 4.0-11 with previous version 4.0-9 dated 2014-11-07

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

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Package arfima updated to version 1.2-7 with previous version 1.2-6 dated 2014-07-01

Title: Fractional ARIMA Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time series, possibly mixed with ARMA, regression, transfer-function components. Exact methods (MLE, forecasting simulation) are used.
Author: Justin Q. Veenstra, A.I. McLeod
Maintainer: A.I. McLeod

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Package SciencesPo updated to version 0.11.21 with previous version 0.05.21 dated 2014-05-27

Title: A tool set for political behaviour data
Description: SciencesPo is a facility package for the political science crowd. It provides sound functions for analyzing random and nonrandom data, future updates will focus on innovative techniques published on relevant journals in the field of political science.
Author: Daniel Marcelino
Maintainer: Daniel Marcelino

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Package quantspec updated to version 1.0-2 with previous version 1.0-1 dated 2014-06-05

Title: Quantile-based Spectral Analysis of Time Series
Description: Methods to determine, smooth and plot quantile (i. e., Laplace or copula) periodograms for univariate time series.
Author: Tobias Kley [aut, cre]
Maintainer: Tobias Kley

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Package pdc updated to version 1.0.2 with previous version 1.0.1 dated 2014-11-10

Title: Permutation Distribution Clustering
Description: Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.
Author: Andreas M. Brandmaier
Maintainer: Andreas M. Brandmaier

Diff between pdc versions 1.0.1 dated 2014-11-10 and 1.0.2 dated 2014-11-21

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Package MAPA updated to version 1.9 with previous version 1.8 dated 2014-10-03

Title: Multiple Aggregation Prediction Algorithm
Description: This package contains functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts time series at multiple temporal aggregation levels, thus strengthening and attenuating the various time series components for better holistic estimation of its structure.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes

Diff between MAPA versions 1.8 dated 2014-10-03 and 1.9 dated 2014-11-21

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Permanent link

Package lmerTest updated to version 2.0-20 with previous version 2.0-11 dated 2014-07-24

Title: Tests in Linear Mixed Effects Models
Description: Tests on lmer objects (of lme4 package). The tests comprise type 3 and type 1 F tests with approximation methods for degrees of freedom for the fixed effects, LR tests for the random effects, calculation of population means for fixed factors with confidence intervals and corresponding plots. Package also provides backward elimination of non-significant effects
Author: Alexandra Kuznetsova [aut, cre], Per Bruun Brockhoff [aut, ths], Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova

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Package LambertW updated to version 0.5 with previous version 0.2.9.9.5 dated 2014-03-09

Title: Analyze and Gaussianize heavy-tailed, skewed data
Description: Lambert W x F distributions are a generalized framework to analyze skewed, heavy-tailed data. They are based on an input/output system, where the input random variable (RV) X ~ F, and the output Y is a non-linearly transformed version of X with similar properties, but slightly skewed and/or heavy-tailed. This transformed RV Y has a Lambert W x F distribution. This package contains functions to model and analyze skewed, heavy-tailed data the Lambert Way: simulate random samples, estimate parameters, compute quantiles, and plot/print results nicely. Probably the most important function is 'Gaussianize', which works similarly to 'scale', but actually makes the data Gaussian. A do-it-yourself toolkit allows users to define their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg

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Package Hmisc updated to version 3.14-6 with previous version 3.14-5 dated 2014-09-12

Title: Harrell Miscellaneous
Description: The Hmisc package contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.
Author: Frank E Harrell Jr , with contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr

Diff between Hmisc versions 3.14-5 dated 2014-09-12 and 3.14-6 dated 2014-11-21

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Package greport updated to version 0.5-2 with previous version 0.5-1 dated 2014-04-16

Title: Graphical Reporting for Clinical Trials
Description: The greport package contains many functions useful for monitoring and reporting the results of clinical trials and other experiments in which treatments are compared. LaTeX is used to typeset the resulting reports, recommended to be in the context of knitr. The Hmisc and lattice packages are used by greport for high-level graphics.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr

Diff between greport versions 0.5-1 dated 2014-04-16 and 0.5-2 dated 2014-11-21

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Package CDM updated to version 4.0 with previous version 3.4-21 dated 2014-08-31

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous data. This package enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the multidimensional linear compensatory item response model and the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch

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Package glmvsd updated to version 1.1 with previous version 1.0 dated 2014-10-22

Title: Variable Selection Deviation (VSD) Measures and Instability Tests for High-dimensional Generalized Linear Models
Description: Variable selection deviation measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan , Yi Yang , Yuhong Yang
Maintainer: Yi Yang

Diff between glmvsd versions 1.0 dated 2014-10-22 and 1.1 dated 2014-11-21

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Package ivivc updated to version 0.2.2 with previous version 0.2.1 dated 2014-09-23

Title: A Data Analysis Tool for In Vitro-In Vivo Correlation (IVIVC)
Description: a menu-driven package for IVIVC model building, data analysis and model validation (only internal validation) based on Wagner-Nelson Method (only for the one-compartment PK model) for Level A correlation
Author: Hsin-ya Lee, Yung-jin Lee
Maintainer: Yung-jin Lee

Diff between ivivc versions 0.2.1 dated 2014-09-23 and 0.2.2 dated 2014-11-21

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Thu, 20 Nov 2014

Package lmms updated to version 1.2 with previous version 1.1 dated 2014-09-11

Title: Linear mixed effect model splines for modelling and analysis of time course data
Description: The package implements linear mixed effect model splines for modelling and differential expression for highly dimensional data sets: investNoise for quality control and filterNoise for removing non-informative trajectories; lmmSpline to model time course expression profiles and lmmsDE performs differential expression analysis to identify differential expression between groups, time and/or time x group interaction.
Author: Jasmin Straube, Kim-Anh Le Cao and Emma Huang with contributions of Dominique Gorse
Maintainer: Jasmin Straube

Diff between lmms versions 1.1 dated 2014-09-11 and 1.2 dated 2014-11-20

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Package bayesPop updated to version 5.2-1 with previous version 5.1-5 dated 2014-08-13

Title: Probabilistic Population Projection
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova

Diff between bayesPop versions 5.1-5 dated 2014-08-13 and 5.2-1 dated 2014-11-20

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Package aprof updated to version 0.2.4 with previous version 0.2.1 dated 2014-07-02

Title: Amdahl's profiler, directed optimization made easy.
Description: Assists the evaluation of whether and where to focus code optimization, using Amdahl's law and visual aids based on line profiling. Amdahl's profiler organises profiling output files (will soon include memory profiling) in a visually appealing way. It is meant to help to balance development vs. execution time by helping to identify the most promising sections of code to optimize and projecting potential gains. The package is an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser

Diff between aprof versions 0.2.1 dated 2014-07-02 and 0.2.4 dated 2014-11-20

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Package ROracle updated to version 1.1-12 with previous version 1.1-11 dated 2014-03-04

Title: OCI based Oracle database interface for R
Description: Oracle database interface (DBI) driver for R. This is a DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Denis Mukhin

Diff between ROracle versions 1.1-11 dated 2014-03-04 and 1.1-12 dated 2014-11-20

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Package plotmo updated to version 2.0.0 with previous version 1.3-3 dated 2014-02-04

Title: Plot a Model's Response While Varying the Values of the Predictors
Description: Plot a model's response when varying one or two predictors while holding the other predictors constant. A poor man's partial dependence plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

Diff between plotmo versions 1.3-3 dated 2014-02-04 and 2.0.0 dated 2014-11-20

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 34 files changed, 2125 insertions(+), 1675 deletions(-)

More information about plotmo at CRAN
Permanent link

Package RAPIDR updated to version 0.1.1 with previous version 0.1 dated 2014-03-07

Title: Reliable Accurate Prenatal non-Invasive Diagnosis R package
Description: Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA
Author: Kitty Lo
Maintainer: Kitty Lo

Diff between RAPIDR versions 0.1 dated 2014-03-07 and 0.1.1 dated 2014-11-20

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More information about RAPIDR at CRAN
Permanent link

Package BACprior updated to version 2.0 with previous version 1.2.1 dated 2013-02-16

Title: Choice of the Hyperparameter Omega in the Bayesian Adjustment for Confounding (BAC) Algorithm
Description: The BACprior package provides an approximate sensitivity analysis of the Bayesian Adjustment for Confounding (BAC) algorithm (Wang et al., 2012) with regards to the hyperparameter omega. The package also provides functions to guide the user in their choice of an appropriate omega value. The method is based on Lefebvre, Atherton and Talbot (2014).
Author: Denis Talbot, Genevičve Lefebvre, Juli Atherton
Maintainer: Denis Talbot

Diff between BACprior versions 1.2.1 dated 2013-02-16 and 2.0 dated 2014-11-20

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More information about BACprior at CRAN
Permanent link

Package tsintermittent updated to version 1.5 with previous version 1.4 dated 2014-10-03

Title: Intermittent Time Series Forecasting
Description: This package contains functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes

Diff between tsintermittent versions 1.4 dated 2014-10-03 and 1.5 dated 2014-11-20

 ChangeLog    |    3 +++
 DESCRIPTION  |    8 ++++----
 MD5          |    6 +++---
 R/crost.ma.R |    6 +++---
 4 files changed, 13 insertions(+), 10 deletions(-)

More information about tsintermittent at CRAN
Permanent link

Package deltaPlotR updated to version 1.5 with previous version 1.4 dated 2014-07-22

Title: Identification of dichotomous differential item functioning (DIF) using Angoff's Delta Plot method
Description: The deltaPlotR package proposes an implementation of Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported.
Author: David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France)
Maintainer: David Magis

Diff between deltaPlotR versions 1.4 dated 2014-07-22 and 1.5 dated 2014-11-20

 DESCRIPTION               |    8 +--
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 NEWS                      |   23 +++++++--
 R/diagPlot.R              |    4 -
 man/adjustExtreme.Rd      |   36 ++++-----------
 man/deltaPlot.Rd          |  108 ++++++++++++++--------------------------------
 man/deltaPlotR-package.Rd |    7 +-
 man/diagPlot.Rd           |   31 ++++---------
 man/verbal.rd             |   12 +----
 9 files changed, 95 insertions(+), 150 deletions(-)

More information about deltaPlotR at CRAN
Permanent link

Package ReporteRs updated to version 0.7.0 with previous version 0.6.0 dated 2014-08-13

Title: Microsoft Word, Microsoft Powerpoint and HTML documents generation from R
Description: An R package for creating Microsoft Word document (>=2007), Microsoft Powerpoint document (>=2007) and HTML documents from R. There are several features to let you format and present R outputs ; e.g. Editable Vector Graphics, functions for complex tables reporting, reuse of corporate template document (*.docx and *.pptx). You can use the package as a tool for fast reporting and as a tool for reporting automation. The package does not require any installation of Microsoft product to be able to write Microsoft files (docx and pptx).
Author: David Gohel [aut, cre], Bootstrap [ctb, cph] (Bootstrap development team), jQuery [ctb, cph] (The jQuery Foundation), Dmitry Baranovskiy [ctb, cph] (raphael and g.raphael javascript libraries)
Maintainer: David Gohel

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Package x12GUI updated to version 0.13.0 with previous version 0.12.0 dated 2014-02-24

Title: X12 - Graphical User Interface
Description: A graphical user interface for the x12 package
Author: Daniel Schopfhauser, Alexander Kowarik , Angelika Meraner
Maintainer: Alexander Kowarik

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Package x12 updated to version 1.6.0 with previous version 1.5.0 dated 2014-02-24

Title: x12 - wrapper function and structure for batch processing
Description: A wrapper function and GUI for the X12 binaries
Author: Alexander Kowarik , Angelika Meraner
Maintainer: Alexander Kowarik

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Package crmn updated to version 0.0.20 with previous version 0.0.19 dated 2012-07-13

Title: CCMN and other noRMalizatioN methods for metabolomics data
Description: Implements the Cross-contribution Compensating Multiple standard Normalization (CCMN) method and other normalization algorithms.
Author: Henning Redestig
Maintainer: Henning Redestig

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Package bayesLife updated to version 2.1-3 with previous version 2.1-2 dated 2014-11-13

Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova, Adrian Raftery; original WinBugs code written by Jennifer Chunn
Maintainer: Hana Sevcikova

Diff between bayesLife versions 2.1-2 dated 2014-11-13 and 2.1-3 dated 2014-11-20

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Wed, 19 Nov 2014

Package gset updated to version 1.1.0 with previous version 1.0 dated 2014-05-19

Title: Group Sequential Design in Equivalence Studies
Description: calculate equivalence and futility boundaries based on the exact bivariate $t$ test statistics for group sequential designs in studies with equivalence hypotheses.
Author: Fang Liu [aut, cre]
Maintainer: Fang Liu

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Package adaptivetau updated to version 2.2 with previous version 2.1 dated 2014-05-08

Title: Tau-leaping stochastic simulation
Description: Implements adaptive tau leaping to approximate the trajectory of a continuous-time stochastic process as described by Cao et al. (2007) The Journal of Chemical Physics. This package is based upon work supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson and NIH R01-AI049334 to Rustom Antia.
Author: Philip Johnson
Maintainer: Philip Johnson

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Package meta updated to version 4.0-1 with previous version 3.8-0 dated 2014-09-12

Title: Meta-Analysis with R
Description: User-friendly general package providing standard methods for meta-analysis: - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from RevMan 5; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer

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Package cocorresp updated to version 0.2-3 with previous version 0.2-1 dated 2013-12-13

Title: Co-correspondence Analysis Methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson. Function simpls based on simpls.fit (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Maintainer: Gavin L. Simpson

Diff between cocorresp versions 0.2-1 dated 2013-12-13 and 0.2-3 dated 2014-11-19

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Package sqlutils updated to version 1.2 with previous version 1.1.2 dated 2014-05-02

Title: Utilities for working with SQL files.
Description: This package provides utilities for working with a library of SQL files.
Author: Jason Bryer
Maintainer: Jason Bryer

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Package sjPlot updated to version 1.6 with previous version 1.5 dated 2014-09-10

Title: Data Visualization for Statistics in Social Science
Description: Collection of several plotting / table output functions for visualizing data and utility functions.
Author: Daniel LĂĽdecke
Maintainer: Daniel Luedecke

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Package rpart.plot updated to version 1.4-5 with previous version 1.4-4 dated 2014-02-05

Title: Plot rpart models. An enhanced version of plot.rpart.
Description: Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

Diff between rpart.plot versions 1.4-4 dated 2014-02-05 and 1.4-5 dated 2014-11-19

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 12 files changed, 16664 insertions(+), 13964 deletions(-)

More information about rpart.plot at CRAN
Permanent link

Package pedometrics updated to version 0.3-0 with previous version 0.1-9 dated 2014-08-08

Title: Pedometric Tools and Techniques
Description: This package contains functions to employ many tools and techniques used in the field of pedometrics (see http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics). These functions were developed to fulfil the demands created by the PhD research project (2012-2016) entitled Contribution to the Construction of Models for Predicting Soil Properties, developed by Alessandro Samuel-Rosa under the supervision of Dr Lucia HC Anjos (Universidade Federal Rural do Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Solos, Brazil), and Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands). The project is supported by the CAPES, Ministério da Educação, Brasília - DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions are simple wrapper functions that extend the functionalities of other functions commonly used for the analysis of pedometric data. It should be noted that changes are likely to occur quite often and using this package as a dependency for other packages is strongly discouraged.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths], Gustavo de Mattos Vasques [ths], Gerard B. M. Heuvelink [ths], Tony Olsen [ctb], Tom Kincaid [ctb], Juan Carlos Ruiz Cuetos [ctb], Maria Eugenia Polo Garcia [ctb], Pablo Garcia Rodriguez [ctb], Edzer Pebesma [ctb], Jon Skoien [ctb]
Maintainer: Alessandro Samuel-Rosa

Diff between pedometrics versions 0.1-9 dated 2014-08-08 and 0.3-0 dated 2014-11-19

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Package PopED updated to version 0.1.2 with previous version 0.1.1 dated 2014-05-27

Title: Population (and individual) optimal Experimental Design
Description: PopED computes optimal experimental designs for both population studies and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix (FIM).
Author: Andrew C. Hooker [aut, cre, trl, cph], Sebastian Ueckert [aut] (MATLAB version), Marco Foracchia [aut] (O-Matrix version), Joakim Nyberg [aut] (MATLAB version), Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker

Diff between PopED versions 0.1.1 dated 2014-05-27 and 0.1.2 dated 2014-11-19

 PopED-0.1.1/PopED/inst/examples/ex.2.d.warfarin.ODE.R                                   |only
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 PopED-0.1.2/PopED/DESCRIPTION                                                           |   47 -
 PopED-0.1.2/PopED/MD5                                                                   |  269 +++++----
 PopED-0.1.2/PopED/NAMESPACE                                                             |    2 
 PopED-0.1.2/PopED/NEWS                                                                  |   37 +
 PopED-0.1.2/PopED/R/Doptim.R                                                            |   18 
 PopED-0.1.2/PopED/R/RS_opt_gen.R                                                        |    4 
 PopED-0.1.2/PopED/R/build_sfg.R                                                         |only
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 PopED-0.1.2/PopED/R/ed_laplace_ofv.R                                                    |   28 -
 PopED-0.1.2/PopED/R/evaluate.e.ofv.fim.R                                                |    2 
 PopED-0.1.2/PopED/R/evaluate.fim.R                                                      |   19 
 PopED-0.1.2/PopED/R/feval.R                                                             |    6 
 PopED-0.1.2/PopED/R/get_all_params.R                                                    |   42 -
 PopED-0.1.2/PopED/R/get_fim_size.R                                                      |   24 
 PopED-0.1.2/PopED/R/getfulld.R                                                          |   26 
 PopED-0.1.2/PopED/R/log_prior_pdf.R                                                     |    2 
 PopED-0.1.2/PopED/R/m1.R                                                                |   29 -
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 PopED-0.1.2/PopED/R/ofv_criterion.R                                                     |    1 
 PopED-0.1.2/PopED/R/plot_efficiency_of_windows.R                                        |   70 ++
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 PopED-0.1.2/PopED/inst/examples/ex.4.PKPD.1.comp.emax.R                                 |   26 
 PopED-0.1.2/PopED/inst/examples/ex.5.PD.emax.hill.R                                     |   25 
 PopED-0.1.2/PopED/inst/examples/ex.6.PK.1.comp.oral.sd.R                                |   65 +-
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 PopED-0.1.2/PopED/inst/shinyapp/ui.R                                                    |    8 
 PopED-0.1.2/PopED/man/Doptim.Rd                                                         |   54 +
 PopED-0.1.2/PopED/man/Dtrace.Rd                                                         |   12 
 PopED-0.1.2/PopED/man/LEDoptim.Rd                                                       |   70 +-
 PopED-0.1.2/PopED/man/LinMatrixH.Rd                                                     |   14 
 PopED-0.1.2/PopED/man/LinMatrixL.Rd                                                     |   18 
 PopED-0.1.2/PopED/man/LinMatrixLH.Rd                                                    |   14 
 PopED-0.1.2/PopED/man/LinMatrixL_occ.Rd                                                 |   14 
 PopED-0.1.2/PopED/man/PopED-internal.Rd                                                 |    1 
 PopED-0.1.2/PopED/man/PopED-package.Rd                                                  |    2 
 PopED-0.1.2/PopED/man/RS_opt.Rd                                                         |   60 +-
 PopED-0.1.2/PopED/man/RS_opt_gen.Rd                                                     |   80 +-
 PopED-0.1.2/PopED/man/a_line_search.Rd                                                  |   14 
 PopED-0.1.2/PopED/man/bfgsb_min.Rd                                                      |    2 
 PopED-0.1.2/PopED/man/blockexp.Rd                                                       |    6 
 PopED-0.1.2/PopED/man/blockfinal.Rd                                                     |   42 -
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 PopED-0.1.2/PopED/man/blockopt.Rd                                                       |    6 
 PopED-0.1.2/PopED/man/calc_autofocus.Rd                                                 |   22 
 PopED-0.1.2/PopED/man/calc_ofv_and_fim.Rd                                               |   62 +-
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 PopED-0.1.2/PopED/man/cell.Rd                                                           |    2 
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 PopED-0.1.2/PopED/man/ed_mftot.Rd                                                       |   16 
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 PopED-0.1.2/PopED/man/evaluate.fim.Rd                                                   |    2 
 PopED-0.1.2/PopED/man/feps.add.Rd                                                       |    8 
 PopED-0.1.2/PopED/man/feps.add.prop.Rd                                                  |    8 
 PopED-0.1.2/PopED/man/feps.prop.Rd                                                      |    8 
 PopED-0.1.2/PopED/man/feval.Rd                                                          |    4 
 PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.md.CL.Rd                                        |    2 
 PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.md.KE.Rd                                        |    2 
 PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd                                        |    2 
 PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd                                        |    2 
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 PopED-0.1.2/PopED/man/fileparts.Rd                                                      |    2 
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 PopED-0.1.2/PopED/man/get_all_params.Rd                                                 |    2 
 PopED-0.1.2/PopED/man/get_rse.Rd                                                        |   38 -
 PopED-0.1.2/PopED/man/getfulld.Rd                                                       |    4 
 PopED-0.1.2/PopED/man/gradf_eps.Rd                                                      |   14 
 PopED-0.1.2/PopED/man/isempty.Rd                                                        |    2 
 PopED-0.1.2/PopED/man/isfield.Rd                                                        |    2 
 PopED-0.1.2/PopED/man/log_prior_pdf.Rd                                                  |    6 
 PopED-0.1.2/PopED/man/mf.Rd                                                             |    6 
 PopED-0.1.2/PopED/man/mf3.Rd                                                            |    6 
 PopED-0.1.2/PopED/man/mf5.Rd                                                            |    2 
 PopED-0.1.2/PopED/man/mf6.Rd                                                            |    2 
 PopED-0.1.2/PopED/man/mf7.Rd                                                            |    2 
 PopED-0.1.2/PopED/man/mf8.Rd                                                            |    2 
 PopED-0.1.2/PopED/man/mfea.Rd                                                           |   10 
 PopED-0.1.2/PopED/man/mftot.Rd                                                          |   24 
 PopED-0.1.2/PopED/man/mftot0.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot1.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot2.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot3.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot4.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot5.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot6.Rd                                                         |    2 
 PopED-0.1.2/PopED/man/mftot7.Rd                                                         |    2 
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 PopED-0.1.2/PopED/man/ofv_criterion.Rd                                                  |    2 
 PopED-0.1.2/PopED/man/ofv_fim.Rd                                                        |    6 
 PopED-0.1.2/PopED/man/ones.Rd                                                           |    2 
 PopED-0.1.2/PopED/man/pargen.Rd                                                         |    2 
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 PopED-0.1.2/PopED/man/poped.choose.Rd                                                   |    4 
 PopED-0.1.2/PopED/man/poped_optimize.Rd                                                 |   46 -
 PopED-0.1.2/PopED/man/rand.Rd                                                           |    2 
 PopED-0.1.2/PopED/man/randn.Rd                                                          |    2 
 PopED-0.1.2/PopED/man/randperm.Rd                                                       |    2 
 PopED-0.1.2/PopED/man/size.Rd                                                           |    2 
 PopED-0.1.2/PopED/man/test_for_max.Rd                                                   |    2 
 PopED-0.1.2/PopED/man/test_for_min.Rd                                                   |    2 
 PopED-0.1.2/PopED/man/test_for_zeros.Rd                                                 |    2 
 PopED-0.1.2/PopED/man/test_mat_size.Rd                                                  |    2 
 PopED-0.1.2/PopED/man/tic.Rd                                                            |    2 
 PopED-0.1.2/PopED/man/toc.Rd                                                            |    2 
 PopED-0.1.2/PopED/man/zeros.Rd                                                          |    2 
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Package DataCombine updated to version 0.2.7 with previous version 0.2.2 dated 2014-08-13

Title: R tools for making it easier to combine and clean data sets.
Description: R tools for combining and cleaning data sets, including filling in missing observations with data from another data frame and creating lag/lead variables.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud

Diff between DataCombine versions 0.2.2 dated 2014-08-13 and 0.2.7 dated 2014-11-19

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Package basicspace updated to version 0.15 with previous version 0.13 dated 2014-11-09

Title: Recovering a Basic Space from Issue Scales
Description: Conducts Aldrich-McKelvey and Blackbox Scaling to Recover Latent Dimensions of Judgment
Author: Keith Poole , Howard Rosenthal , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: James Lo

Diff between basicspace versions 0.13 dated 2014-11-09 and 0.15 dated 2014-11-19

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Package climdex.pcic updated to version 1.1-4 with previous version 1.1-1 dated 2014-04-03

Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of extreme climate indices.
Author: David Bronaugh for the Pacific Climate Impacts Consortium
Maintainer: James Hiebert

Diff between climdex.pcic versions 1.1-1 dated 2014-04-03 and 1.1-4 dated 2014-11-19

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Tue, 18 Nov 2014

Package waterData updated to version 1.0.4 with previous version 1.0.3 dated 2013-12-14

Title: An R Package for Retrieval, Analysis, and Anomaly Calculation of Daily Hydrologic Time Series Data
Description: This package imports U.S. Geological Survey (USGS) daily hydrologic data from USGS web services, plots the data, addresses some common data problems, and calculates and plots anomalies.
Author: Karen R. Ryberg and Aldo V. Vecchia
Maintainer: Karen R. Ryberg

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Package Peptides updated to version 1.0.2 with previous version 1.0.1 dated 2014-10-16

Title: Calculate Indices and Theoretical Properties of Protein Sequences
Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot XVG output files from GROMACS molecular dynamics package.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio

Diff between Peptides versions 1.0.1 dated 2014-10-16 and 1.0.2 dated 2014-11-18

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Package analogue updated to version 0.16-0 with previous version 0.14-0 dated 2014-08-29

Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre], Jari Oksanen [aut]
Maintainer: Gavin L. Simpson

Diff between analogue versions 0.14-0 dated 2014-08-29 and 0.16-0 dated 2014-11-18

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Package TSclust updated to version 1.2.3 with previous version 1.2.2 dated 2014-10-28

Title: Time Series Clustering Utilities
Description: This package contains a set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.
Author: Pablo Montero Manso, José Antonio Vilar
Maintainer: Pablo Montero

Diff between TSclust versions 1.2.2 dated 2014-10-28 and 1.2.3 dated 2014-11-18

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Package secr updated to version 2.9.1 with previous version 2.9.0 dated 2014-09-22

Title: Spatially explicit capture-recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford

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More information about secr at CRAN
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Package nodiv updated to version 0.9.2 with previous version 0.9.1 dated 2014-11-13

Title: Compares the distribution of sister clades through a phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution). DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard

Diff between nodiv versions 0.9.1 dated 2014-11-13 and 0.9.2 dated 2014-11-18

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More information about nodiv at CRAN
Permanent link

Package smacpod updated to version 1.1.1 with previous version 1.0.0 dated 2014-11-01

Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Various statistical methods for analyzing case-control point data. The methods available closely follow those in chapter 6 of Applied Spatial Statistics for Public Health Data by Waller and Gotway (2004).
Author: Joshua French
Maintainer: Joshua French

Diff between smacpod versions 1.0.0 dated 2014-11-01 and 1.1.1 dated 2014-11-18

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Package robustbase updated to version 0.92-1 with previous version 0.91-1 dated 2014-05-01

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably Peter Rousseeuw and Christophe Croux, see file 'Copyrights'; Valentin Todorov , Andreas Ruckstuhl , Matias Salibian-Barrera , Tobias Verbeke , Manuel Koller , Martin Maechler
Maintainer: Martin Maechler

Diff between robustbase versions 0.91-1 dated 2014-05-01 and 0.92-1 dated 2014-11-18

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More information about robustbase at CRAN
Permanent link

Package sidier updated to version 3.0 with previous version 2.3 dated 2013-08-09

Title: Substitution and Indel Distances to Infer Evolutionary Relationships
Description: sidier is a library and R package for evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares

Diff between sidier versions 2.3 dated 2013-08-09 and 3.0 dated 2014-11-18

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Package rPref updated to version 0.3 with previous version 0.2 dated 2014-10-14

Title: rPref
Description: Routines to select and visualize the maxima for a given strict partial order. This especially includes the computation of the Pareto frontier, also known as (Top-k) Skyline operator, and some generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks

Diff between rPref versions 0.2 dated 2014-10-14 and 0.3 dated 2014-11-18

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Package phylolm updated to version 2.2 with previous version 2.1 dated 2014-06-05

Title: Phylogenetic Linear Regression
Description: the phylolm package provides functions for fitting phylogenetic linear regression models and phylogenetic logistic regression. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree.
Author: Lam Si Tung Ho [aut, cre], Cecile Ane [aut], Robert Lachlan [ctb], Kelsey Tarpinian [ctb]
Maintainer: Lam Si Tung Ho

Diff between phylolm versions 2.1 dated 2014-06-05 and 2.2 dated 2014-11-18

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Package ExtremeBounds updated to version 0.1.4.2 with previous version 0.1.4.1 dated 2014-05-23

Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac
Maintainer: Marek Hlavac

Diff between ExtremeBounds versions 0.1.4.1 dated 2014-05-23 and 0.1.4.2 dated 2014-11-18

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Package CCAGFA updated to version 1.0.4 with previous version 1.0.3 dated 2013-05-06

Title: Bayesian canonical correlation analysis and group factor analysis
Description: Variational Bayesian algorithm for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA)
Author: Seppo Virtanen, Eemeli Leppaaho and Arto Klami
Maintainer: Seppo Virtanen

Diff between CCAGFA versions 1.0.3 dated 2013-05-06 and 1.0.4 dated 2014-11-18

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Package C50 updated to version 0.1.0-21 with previous version 0.1.0-19 dated 2014-06-07

Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition
Author: Max Kuhn, Steve Weston, Nathan Coulter. C code for C5.0 by R. Quinlan
Maintainer: Max Kuhn

Diff between C50 versions 0.1.0-19 dated 2014-06-07 and 0.1.0-21 dated 2014-11-18

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Package XBRL updated to version 0.99.13 with previous version 0.99.12 dated 2014-08-11

Title: Extraction of Business Financial Information from XBRL Documents
Description: XBRL is a package suited to extract business financial information from an Extensible Business Reporting Language (XBRL) instance file and the associated collection of files that defines its Discoverable Taxonomy Set (DTS). These files are usually disseminated across different remote locations. XBRL documents employ many technologies defined by XML standards, such as XML Schema, Namespaces, XLink, and XPath, which make the extraction of information involved. The functions provided by this package address this complexity, returning data frames containing the enclosed information readily available to perform analyses. XBRL has been successfully tested in analyzing 10-K and 10-Q submissions from USA filing companies that are publicly available at the EDGAR system of the Securities and Exchange Commission (SEC). As published taxonomy files (such as "http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd") are immutable and are used by most filers, XBRL offers the option of downloading them only the first time they are referred, keeping a local cache copy that can be used from then on. This speeds-up the process, specially on slow connections. XBRL is not and does not aim to be (at least yet) a validating XBRL processor. XBRL is still a work in progress. As such, functions and produced data frames may change structure in future versions until stabilization.
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso

Diff between XBRL versions 0.99.12 dated 2014-08-11 and 0.99.13 dated 2014-11-18

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Package spatialTailDep updated to version 1.0.2 with previous version 1.0.1 dated 2014-08-14

Title: Estimation of spatial tail dependence models
Description: Provides functions implementing the pairwise M-estimator for parametric models for stable tail dependence functions described in "An M-estimator of spatial tail dependence" (Einmahl, J.H.J., Kiriliouk, A., Krajina, A. and Segers, J., 2014). See http://arxiv.org/abs/1403.1975.
Author: Anna Kiriliouk, Johan Segers
Maintainer: Anna Kiriliouk

Diff between spatialTailDep versions 1.0.1 dated 2014-08-14 and 1.0.2 dated 2014-11-18

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Package paleofire updated to version 1.1.4 with previous version 1.1.3 dated 2014-05-22

Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez

Diff between paleofire versions 1.1.3 dated 2014-05-22 and 1.1.4 dated 2014-11-18

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Package mets updated to version 1.0 with previous version 0.2.8 dated 2014-05-13

Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate event history data. Including multivariate cumulative incidence models, and bivariate random effects probit models (Liability models). Also contains two-stage binomial modelling that can do pairwise odds-ratio dependence modelling based marginal logistic regression models. This is an alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst

Diff between mets versions 0.2.8 dated 2014-05-13 and 1.0 dated 2014-11-18

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 man/casewise.Rd               |    4 
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 man/fast.pattern.Rd           |   16 
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 man/internal.Rd               |    4 
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 man/lifetable.matrix.Rd       |    6 
 man/mena.Rd                   |    2 
 man/mets-package.Rd           |    2 
 man/migr.Rd                   |    2 
 man/multcif.Rd                |    2 
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 src/biprobit.cpp              |  222 ++++++++---
 src/claytonoakes.cpp          |   91 ++++
 src/cor.cpp                   |    2 
 src/fastcox.cpp               |  113 +++---
 src/fastcox.h                 |    5 
 src/plackettMLE.cpp           |   78 +++-
 src/tools.cpp                 |    9 
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 109 files changed, 2399 insertions(+), 1221 deletions(-)

More information about mets at CRAN
Permanent link

Package lokern updated to version 1.1-6 with previous version 1.1-5 dated 2013-11-19

Title: Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
Description: Kernel regression smoothing with adaptive local or global plug-in bandwidth selection.
Author: Eva Herrmann (F77 & S original); Packaged for R and enhanced by Martin Maechler
Maintainer: Martin Maechler

Diff between lokern versions 1.1-5 dated 2013-11-19 and 1.1-6 dated 2014-11-18

 lokern-1.1-5/lokern/data/xSim.rda        |only
 lokern-1.1-6/lokern/ChangeLog            |    5 ++++
 lokern-1.1-6/lokern/DESCRIPTION          |    9 ++++----
 lokern-1.1-6/lokern/MD5                  |   30 +++++++++++++--------------
 lokern-1.1-6/lokern/NAMESPACE            |    1 
 lokern-1.1-6/lokern/R/glkerns.R          |    4 +--
 lokern-1.1-6/lokern/R/lokerns.R          |    3 ++
 lokern-1.1-6/lokern/TODO                 |   16 +++++++++-----
 lokern-1.1-6/lokern/data/xSim.R          |only
 lokern-1.1-6/lokern/man/KernS-methods.Rd |   24 +++++++++++++--------
 lokern-1.1-6/lokern/man/glkerns.Rd       |    7 ++++--
 lokern-1.1-6/lokern/man/lokerns.Rd       |    9 +++++---
 lokern-1.1-6/lokern/src/auxkerns.f       |    6 ++---
 lokern-1.1-6/lokern/src/glkerns.f        |   11 ++++------
 lokern-1.1-6/lokern/src/lokerns.f        |   12 +++++-----
 lokern-1.1-6/lokern/tests/lok1.R         |    2 +
 lokern-1.1-6/lokern/tests/lok1.Rout.save |   34 ++++++++++++++++++++++++++++---
 17 files changed, 114 insertions(+), 59 deletions(-)

More information about lokern at CRAN
Permanent link

Package lava updated to version 1.3 with previous version 1.2.6 dated 2014-05-07

Title: Latent Variable Models
Description: Estimation and simulation of latent variable models
Author: Klaus K. Holst
Maintainer: Klaus K. Holst

Diff between lava versions 1.2.6 dated 2014-05-07 and 1.3 dated 2014-11-18

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 lava-1.3/lava/INDEX                           |   14 -
 lava-1.3/lava/MD5                             |  353 +++++++++++++-------------
 lava-1.3/lava/NAMESPACE                       |   29 +-
 lava-1.3/lava/NEWS                            |   28 +-
 lava-1.3/lava/R/Missing.R                     |   72 ++++-
 lava-1.3/lava/R/addattr.R                     |    4 
 lava-1.3/lava/R/addhook.R                     |    1 
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 lava-1.3/lava/R/baptize.R                     |    2 
 lava-1.3/lava/R/bootstrap.R                   |   10 
 lava-1.3/lava/R/cancel.R                      |    4 
 lava-1.3/lava/R/categorical.R                 |   41 ++-
 lava-1.3/lava/R/children.R                    |    8 
 lava-1.3/lava/R/coef.R                        |    8 
 lava-1.3/lava/R/compare.R                     |   38 +-
 lava-1.3/lava/R/confint.R                     |    4 
 lava-1.3/lava/R/constrain.R                   |    6 
 lava-1.3/lava/R/correlation.R                 |    2 
 lava-1.3/lava/R/covariance.R                  |    8 
 lava-1.3/lava/R/curereg.R                     |   38 +-
 lava-1.3/lava/R/deriv.R                       |    6 
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 lava-1.3/lava/R/equivalence.R                 |    2 
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 lava-1.3/lava/R/fix.R                         |   22 -
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 lava-1.3/lava/R/functional.R                  |    4 
 lava-1.3/lava/R/glmest.R                      |   66 ++--
 lava-1.3/lava/R/gof.R                         |   15 -
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 lava-1.3/lava/R/heavytail.R                   |    4 
 lava-1.3/lava/R/iid.R                         |   13 
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 lava-1.3/lava/R/information.R                 |   10 
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 lava-1.3/lava/tests/testthat/test-constrain.R |   19 -
 183 files changed, 2637 insertions(+), 1933 deletions(-)

More information about lava at CRAN
Permanent link

Package fishmethods updated to version 1.7-0 with previous version 1.6-0 dated 2014-03-10

Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from literature and colleague contributions
Author: Gary A. Nelson
Maintainer: Gary A. Nelson

Diff between fishmethods versions 1.6-0 dated 2014-03-10 and 1.7-0 dated 2014-11-18

 DESCRIPTION          |    8 ++++----
 MD5                  |   32 ++++++++++++++++++--------------
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 19 files changed, 92 insertions(+), 64 deletions(-)

More information about fishmethods at CRAN
Permanent link

Package car updated to version 2.0-22 with previous version 2.0-21 dated 2014-08-16

Title: Companion to Applied Regression
Description: This package accompanies J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Daniel Adler [ctb], Douglas Bates [ctb], Gabriel Baud-Bovy [ctb], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], Gregor Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Rafael Laboissiere [ctb], Georges Monette [ctb], Duncan Murdoch [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian Ripley [ctb], William Venables [ctb], Achim Zeileis [ctb], R-Core [ctb]
Maintainer: John Fox

Diff between car versions 2.0-21 dated 2014-08-16 and 2.0-22 dated 2014-11-18

 car-2.0-21/car/data/Blackmoor.rda          |only
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 car-2.0-22/car/R/compareCoefs.R            |  130 +-
 car-2.0-22/car/R/densityPlot.R             |    7 
 car-2.0-22/car/R/linearHypothesis.R        | 1405 ++++++++++++++---------------
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 car-2.0-22/car/R/scatterplot.R             |   11 
 car-2.0-22/car/R/scatterplotMatrix.R       |  383 ++++---
 car-2.0-22/car/R/scatterplotSmoothers.R    |   31 
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 31 files changed, 1765 insertions(+), 1511 deletions(-)

More information about car at CRAN
Permanent link

Package sda updated to version 1.3.5 with previous version 1.3.4 dated 2014-07-28

Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: This package provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with variable selection. The classifier is trained using James-Stein-type shrinkage estimators and predictor variables are ranked using correlation-adjusted t-scores (CAT scores). Variable selection error is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer

Diff between sda versions 1.3.4 dated 2014-07-28 and 1.3.5 dated 2014-11-18

 DESCRIPTION               |   14 +-
 MD5                       |   12 +-
 NEWS                      |    7 +
 R/sda.ranking.R           |   14 +-
 inst/doc/index.html       |    2 
 inst/doc/sda-khan-data.R  |  232 +++++++++++++++++++++++++++++-----------------
 inst/doc/sda-singh-data.R |  120 +++++++++++++++--------
 7 files changed, 255 insertions(+), 146 deletions(-)

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Package RRreg updated to version 0.2.0 with previous version 0.1.3 dated 2014-09-20

Title: Correlation and Regression Analyses for Randomized Response Data
Description: RRreg provides univariate and multivariate methods to analyze randomized response (RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A survey technique for eliminating evasive answer bias. Journal of the American Statistical Association, 60, 63–69). Besides univariate estimates of true proportions, RR variables can be used for correlations, as dependent variable in a logistic regression and as predictors in a linear regression. For simulation and bootstrap purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck

Diff between RRreg versions 0.1.3 dated 2014-09-20 and 0.2.0 dated 2014-11-18

 DESCRIPTION              |   34 ++--
 MD5                      |   72 +++++----
 NAMESPACE                |    3 
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 R/RRcor.models.R         |   82 +++++-----
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 R/RRlog.CDM.R            |    2 
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Permanent link

Package seacarb updated to version 3.0.2 with previous version 3.0 dated 2014-04-05

Title: seawater carbonate chemistry with R
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph], Jean-Marie Epitalon [aut], Heloise Lavigne [aut], James Orr [ctb], Bernard Gentili [ctb], Andreas Hofmann [ctb], Aurélien Proye [ctb], Karline Soetaert [ctb], James Rae [ctb]
Maintainer: Jean-Pierre Gattuso

Diff between seacarb versions 3.0 dated 2014-04-05 and 3.0.2 dated 2014-11-18

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Permanent link

Package scrm updated to version 1.3-3 with previous version 1.3-2 dated 2014-10-22

Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution.
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cph, ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab

Diff between scrm versions 1.3-2 dated 2014-10-22 and 1.3-3 dated 2014-11-18

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Permanent link

Package rtkpp updated to version 0.8.4 with previous version 0.8.3 dated 2014-10-23

Title: STK++ Integration To R Using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff

Diff between rtkpp versions 0.8.3 dated 2014-10-23 and 0.8.4 dated 2014-11-18

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 rtkpp-0.8.4/rtkpp/.Rinstignore                                                                    |   18 
 rtkpp-0.8.4/rtkpp/DESCRIPTION                                                                     |   15 
 rtkpp-0.8.4/rtkpp/MD5                                                                             |  246 ++---
 rtkpp-0.8.4/rtkpp/NAMESPACE                                                                       |   22 
 rtkpp-0.8.4/rtkpp/R/ClusterAlgo.R                                                                 |   42 
 rtkpp-0.8.4/rtkpp/R/ClusterCategorical.R                                                          |  304 ++++--
 rtkpp-0.8.4/rtkpp/R/ClusterDiagGaussian.R                                                         |  278 +++--
 rtkpp-0.8.4/rtkpp/R/ClusterGamma.R                                                                |  233 +++--
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 rtkpp-0.8.4/rtkpp/R/ClusterInit.R                                                                 |    2 
 rtkpp-0.8.4/rtkpp/R/ClusterModelNames.R                                                           |   96 +-
 rtkpp-0.8.4/rtkpp/R/ClusterPlot.R                                                                 |   24 
 rtkpp-0.8.4/rtkpp/R/ClusterStrategy.R                                                             |   38 
 rtkpp-0.8.4/rtkpp/R/IClusterModel.R                                                               |  301 +++---
 rtkpp-0.8.4/rtkpp/R/global.R                                                                      |   27 
 rtkpp-0.8.4/rtkpp/R/rtkpp.R                                                                       |  170 +++
 rtkpp-0.8.4/rtkpp/R/rtkppFlags.R                                                                  |   11 
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 rtkpp-0.8.4/rtkpp/data/birds.rda                                                                  |binary
 rtkpp-0.8.4/rtkpp/data/car.rda                                                                    |binary
 rtkpp-0.8.4/rtkpp/data/geyser.rda                                                                 |binary
 rtkpp-0.8.4/rtkpp/data/titanic.rda                                                                |binary
 rtkpp-0.8.4/rtkpp/inst/NEWS.Rd                                                                    |    9 
 rtkpp-0.8.4/rtkpp/inst/makefile                                                                   |  466 +++++-----
 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_Givens.h                                      |   40 
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 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_Qr.h                                          |   19 
 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_SymEigen.h                                    |   29 
 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_lapack_Qr.h                                   |   19 
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 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_Qr.cpp                                            |   37 
 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_SymEigen.cpp                                      |   31 
 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_lapack_Qr.cpp                                     |   31 
 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_lapack_SymEigen.cpp                               |   21 
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 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_Clust_Util.cpp                                 |   43 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IDataManager.cpp                               |   12 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IMixture.cpp                                   |   40 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IMixtureComposer.cpp                           |   29 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IMixtureManager.cpp                            |   14 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureAlgo.cpp                                |   50 +
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureComposer.cpp                            |   32 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureFacade.cpp                              |   27 
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureInit.cpp                                |   61 -
 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureStrategy.cpp                            |  150 +--
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 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_BSplineCoefficients.h                         |   45 
 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_BSplineRegression.h                           |    4 
 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_Regress_Util.h                                |   22 
 rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineRegressionPage.cpp                 |    6 
 rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_BSplineCoefficients.cpp                           |   59 -
 rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_Regress_Util.cpp                                  |   24 
 rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_ClusterFacade.h                                 |   13 
 rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_ClusterLauncher.h                               |   53 -
 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/include/STK_Integer.h                                    |   24 
 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/include/STK_Range.h                                      |   11 
 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/include/STK_String.h                                     |    4 
 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/src/STK_Integer.cpp                                      |   28 
 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/src/STK_Range.cpp                                        |   10 
 rtkpp-0.8.4/rtkpp/inst/projects/Sdk/include/STK_IRunner.h                                         |    2 
 rtkpp-0.8.4/rtkpp/man/ClusterAlgo-class.Rd                                                        |    2 
 rtkpp-0.8.4/rtkpp/man/ClusterCategorical-class.Rd                                                 |    9 
 rtkpp-0.8.4/rtkpp/man/ClusterDiagGaussian-class.Rd                                                |    9 
 rtkpp-0.8.4/rtkpp/man/ClusterGamma-class.Rd                                                       |    9 
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 rtkpp-0.8.4/rtkpp/man/ClusterModels-class.Rd                                                      |   22 
 rtkpp-0.8.4/rtkpp/man/ClusterStrategy-class.Rd                                                    |    6 
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 rtkpp-0.8.4/rtkpp/man/IClusterComponent-class.Rd                                                  |only
 rtkpp-0.8.4/rtkpp/man/car.Rd                                                                      |   14 
 rtkpp-0.8.4/rtkpp/man/clusterAlgo.Rd                                                              |    3 
 rtkpp-0.8.4/rtkpp/man/clusterCategorical.Rd                                                       |    4 
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 rtkpp-0.8.4/rtkpp/man/clusterDiagGaussian.Rd                                                      |    9 
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 rtkpp-0.8.4/rtkpp/man/clusterGamma.Rd                                                             |    8 
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 rtkpp-0.8.4/rtkpp/man/clusterInit.Rd                                                              |    2 
 rtkpp-0.8.4/rtkpp/man/clusterStrategy.Rd                                                          |   21 
 rtkpp-0.8.4/rtkpp/man/extract-methods.Rd                                                          |   12 
 rtkpp-0.8.4/rtkpp/man/initialize-methods.Rd                                                       |   52 -
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 rtkpp-0.8.4/rtkpp/man/plot-ClusterGamma-method.Rd                                                 |    2 
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 rtkpp-0.8.4/rtkpp/man/print-methods.Rd                                                            |   21 
 rtkpp-0.8.4/rtkpp/man/show-methods.Rd                                                             |   24 
 rtkpp-0.8.4/rtkpp/man/summary-methods.Rd                                                          |   12 
 rtkpp-0.8.4/rtkpp/src/Makevars                                                                    |   17 
 rtkpp-0.8.4/rtkpp/src/STK_ClusterFacade.cpp                                                       |   16 
 rtkpp-0.8.4/rtkpp/src/STK_ClusterLauncher.cpp                                                     |  260 +++--
 rtkpp-0.8.4/rtkpp/src/clusterMixture.cpp                                                          |   18 
 rtkpp-0.8.4/rtkpp/tests/clusterDiagGaussianLikelihood.R                                           |    8 
 rtkpp-0.8.4/rtkpp/tests/clusterGammaLikelihood.R                                                  |    8 
 138 files changed, 3057 insertions(+), 2055 deletions(-)

More information about rtkpp at CRAN
Permanent link

Package rsml updated to version 1.2 with previous version 1.0 dated 2014-10-23

Title: Plant Root System Markup Language (RSML) File Processing
Description: Read and analyse Root System Markup Language (RSML) files, used to store plant root system architecture data. More information can be found here: http://rootsystemml.github.io/
Author: Guillaume Lobet
Maintainer: Guillaume Lobet

Diff between rsml versions 1.0 dated 2014-10-23 and 1.2 dated 2014-11-18

 DESCRIPTION                    |   12 +
 MD5                            |   94 ++++++-------
 NAMESPACE                      |   36 +++++
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 data/anagallis.rda             |binary
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Package RcppAnnoy updated to version 0.0.3 with previous version 0.0.2 dated 2014-11-16

Title: Rcpp Bindings for Annoy, a Library for Approximate Nearest Neighbors
Description: Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the Rcpp and BH packages, exposing the same interface as the original Python wrapper to Annoy. See https://github.com/spotify/annoy for more on Annoy. Annoy is released under Version 2.0 of the Apache License. Also included is a small Windows port of mmap which is release under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between RcppAnnoy versions 0.0.2 dated 2014-11-16 and 0.0.3 dated 2014-11-18

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Package LMest updated to version 2.0 with previous version 1.0 dated 2012-11-28

Title: Fit Latent Markov models in basic versions
Description: Fit certain versions of the Latent Markov model for longitudinal categorical data.
Author: Francesco Bartolucci, Silvia Pandolfi - University of Perugia (IT) -, and Fulvia Pennoni - University of Milano Bicocca
Maintainer: Francesco Bartolucci

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Package cooccur updated to version 1.2 with previous version 1.1 dated 2014-05-06

Title: Probabilistic Species Co-occurrence Analysis in R
Description: This R package applies the probabilistic model of species co-occurrence (Veech 2013) to a set of species distributed among a set of survey or sampling sites. The algorithm calculates the observed and expected frequencies of co-occurrence between each pair of species. The expected frequency is based on the distribution of each species being random and independent of the other species. The analysis returns the probabilities that a more extreme (either low or high) value of co-occurrence could have been obtained by chance. The package also includes functions for visualizing species co-occurrence results and preparing data for downstream analyses.
Author: Daniel M. Griffith, Joseph A. Veech, and Charles J. Marsh
Maintainer: Daniel M. Griffith

Diff between cooccur versions 1.1 dated 2014-05-06 and 1.2 dated 2014-11-18

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More information about cooccur at CRAN
Permanent link

Package boolean3 updated to version 3.1.6 with previous version 3.1.5 dated 2014-06-25

Title: Boolean Binary Response Models
Description: This package implements a partial-observability procedure for testing Boolean hypotheses that generalizes the binary response GLM as outlined in Braumoeller (2003).
Author: Jason W. Morgan
Maintainer: Jason W. Morgan

Diff between boolean3 versions 3.1.5 dated 2014-06-25 and 3.1.6 dated 2014-11-18

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Mon, 17 Nov 2014

Package vegan updated to version 2.2-0 with previous version 2.0-10 dated 2013-12-12

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen

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Package sparkTable updated to version 0.12.0 with previous version 0.11.0 dated 2014-07-01

Title: Sparklines and graphical tables for tex and html
Description: Create Sparklines and graphical tables for documents and websites
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik

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Package rcicr updated to version 0.2.5 with previous version 0.2.4 dated 2014-09-30

Title: Reverse correlation image classification toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch

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Package BDgraph updated to version 2.13 with previous version 2.12 dated 2014-09-24

Title: Graph estimation based on birth-death MCMC approach
Description: This package provides a Bayesian methodology for structure learning in undirected graphical models. Our Bayesian methodology is based on birth-death Markov chain Monte Carlo (BDMCMC) algorithm which is the main function with the name 'bdgraph'. The main target of this package is high-dimensional data analysis wherein usually p >> n. The computation is memory-optimized using the sparse matrix output.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

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Package cvAUC updated to version 1.0.2 with previous version 1.0.1 dated 2014-11-04

Title: Cross-Validated Area Under the ROC Curve Confidence Intervals
Description: This package contains various tools for working with and evaluating cross-validated area under the ROC curve (AUC) estimators. The primary functions of the package are ci.cvAUC and ci.pooled.cvAUC, which report cross-validated AUC and compute confidence intervals for cross-validated AUC estimates based on influence curves for i.i.d. and pooled repeated measures data, respectively. One benefit to using influence curve based confidence intervals is that they require much less computation time than bootstrapping methods. The utility functions, AUC and cvAUC, are simple wrappers for functions from the ROCR package.
Author: Erin LeDell, Maya Petersen, Mark van der Laan
Maintainer: Erin LeDell

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Package randomLCA updated to version 1.0-1 with previous version 1.0-0 dated 2014-10-14

Title: Random Effects Latent Class Analysis
Description: Fits random effects latent class models, as well as standard latent class models.
Author: Ken Beath
Maintainer: Ken Beath

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Sun, 16 Nov 2014

Package randtests updated to version 1.0 with previous version 0.3 dated 2014-03-19

Title: Testing randomness in R
Description: Several non parametric randomness tests for numeric sequences
Author: Frederico Caeiro and Ayana Mateus
Maintainer: Frederico Caeiro

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Package mcprofile updated to version 0.2-1 with previous version 0.2-0 dated 2014-05-30

Title: Multiple Contrast Profiles
Description: Calculation of signed root deviance profiles for linear combinations of parameters in a generalized linear model. Multiple tests and simultaneous confidence intervals are provided.
Author: Daniel Gerhard
Maintainer: Daniel Gerhard <00gerhard@gmail.com>

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Package goric updated to version 0.0-8 with previous version 0.0-7 dated 2012-11-28

Title: Generalized Order-Restricted Information Criterion
Description: Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate regression models
Author: Daniel Gerhard [aut, cre], Rebecca M. Kuiper [aut]
Maintainer: Daniel Gerhard <00gerhard@gmail.com>

Diff between goric versions 0.0-7 dated 2012-11-28 and 0.0-8 dated 2014-11-16

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Package care updated to version 1.1.6 with previous version 1.1.5 dated 2014-07-28

Title: High-Dimensional Regression and CAR Score Variable Selection
Description: The "care" package implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between care versions 1.1.5 dated 2014-07-28 and 1.1.6 dated 2014-11-16

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Package glpkAPI updated to version 1.2.11 with previous version 1.2.10 dated 2014-01-08

Title: R Interface to C API of GLPK
Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

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Package coneproj updated to version 1.5 with previous version 1.4 dated 2014-04-26

Title: Primal or Dual Cone Projections with Routines for Constrained Regression
Description: This package contains routines for cone projection and quadratic programming, as well as routines to do estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao

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Package GeneNet updated to version 1.2.11 with previous version 1.2.10 dated 2014-07-28

Title: Modeling and Inferring Gene Networks
Description: GeneNet is a package for analyzing gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between GeneNet versions 1.2.10 dated 2014-07-28 and 1.2.11 dated 2014-11-16

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Package MVN updated to version 3.7 with previous version 3.6 dated 2014-11-14

Title: Multivariate Normality Tests
Description: Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as discriminant analysis, principal component analysis, MANOVA, etc. Here, we present an R package to asses multivariate normality. The MVN package contains three widely used multivariate normality tests, including Mardia's, Henze-Zirkler's, Royston's, graphical approaches, including chi-square Q-Q plot, perspective plot and contour plot and two outlier detection methods based on Mahalanobis distance. We have also developed web-tool version of the package which is available at http://www.biosoft.hacettepe.edu.tr/MVN/.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz

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