Fri, 30 Sep 2016

Package LANDD updated to version 1.1.0 with previous version 1.0.0 dated 2015-10-06

Title: Liquid Association for Network Dynamics Detection
Description: Using Liquid Association for Network Dynamics Detection.
Author: Shangzhao Qiu, Yan Yan, Tianwei Yu
Maintainer: Shangzhao Qiu <qsz1328@gmail.com>

Diff between LANDD versions 1.0.0 dated 2015-10-06 and 1.1.0 dated 2016-09-30

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Permanent link

Package seleniumPipes updated to version 0.3.7 with previous version 0.3.0 dated 2016-08-24

Title: R Client Implementing the W3C WebDriver Specification
Description: The W3C WebDriver specification defines a way for out-of-process programs to remotely instruct the behaviour of web browsers. It is detailed at <https://w3c.github.io/webdriver/webdriver-spec.html>. This package provides an R client implementing the W3C specification.
Author: John Harrison [aut, cre]
Maintainer: John Harrison <johndharrison0@gmail.com>

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Package joint.Cox updated to version 2.8 with previous version 2.7 dated 2016-09-21

Title: Penalized Likelihood Estimation and Dynamic Prediction under the Joint Frailty-Copula Models Between Tumour Progression and Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction under the joint frailty-copula model between tumour progression and death for meta-analysis. The method is applicable for meta-analytic data combining several studies. The data should have information on both terminal event time (time-to-death) and non-terminal event time (time-to-tumour progression).
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

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Package downscale updated to version 1.2-3 with previous version 1.2-2 dated 2016-08-19

Title: Downscaling Species Occupancy
Description: A set of functions that downscales species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>

Diff between downscale versions 1.2-2 dated 2016-08-19 and 1.2-3 dated 2016-09-30

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Package bio3d updated to version 2.3-0 with previous version 2.2-4 dated 2015-12-12

Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@umich.edu>

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Package MendelianRandomization updated to version 0.2.0 with previous version 0.1.0 dated 2016-08-31

Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <yavorsko@tcd.ie>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>

Diff between MendelianRandomization versions 0.1.0 dated 2016-08-31 and 0.2.0 dated 2016-09-30

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Package FamEvent updated to version 1.2 with previous version 1.1 dated 2016-03-09

Title: Family Age-at-Onset Data Simulation and Penetrance Estimation
Description: Simulates age-at-onset traits associated with a segregating major gene in family data obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment correction is utilized to estimate age-dependent penetrance functions either parametrically from the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm can infer missing genotypes and carrier probabilities estimated from family's genotype and phenotype information or from a fitted model. Plot functions include pedigrees of simulated families and predicted penetrance curves based on specified parameter values.
Author: Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Maintainer: Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>

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Package braQCA updated to version 0.9.9.3 with previous version 0.9.9.1 dated 2016-05-17

Title: Bootstrapped Robustness Assessment for Qualitative Comparative Analysis
Description: Test the robustness of a user's Qualitative Comparative Analysis solutions to randomness, using the bootstrapped assessment: baQCA(). This package also includes a function that provides recommendations for improving solutions to reach typical significance levels: brQCA().
Author: C. Ben Gibson [aut, cre], Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>

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Package FrF2 updated to version 1.7-2 with previous version 1.7-1 dated 2014-07-31

Title: Fractional Factorial Designs with 2-Level Factors
Description: Regular and non-regular Fractional Factorial 2-level designs can be created. Furthermore, analysis tools for Fractional Factorial designs with 2-level factors are offered (main effects and interaction plots for all factors simultaneously, cube plot for looking at the simultaneous effects of three factors, full or half normal plot, alias structure in a more readable format than with the built-in function alias).
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>

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Package dMod updated to version 0.3.2 with previous version 0.3.1 dated 2016-05-18

Title: Dynamic Modeling and Parameter Estimation in ODE Models
Description: The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>

Diff between dMod versions 0.3.1 dated 2016-05-18 and 0.3.2 dated 2016-09-30

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Package propr updated to version 2.0.1 with previous version 2.0.0 dated 2016-08-27

Title: Calculating Proportionality Between Vectors of Compositional Data
Description: The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, this approach lacks statistical validity when applied to relative data, including those biological count data produced by microarray assays or high-throughput RNA-sequencing. Two metrics of proportionality, phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived from compositional data analysis, a branch of math dealing specifically with relative data, represent novel alternatives to correlation. This package introduces a programmatic framework for the calculation of feature dependence through proportionality, as discussed in the cited publications.
Author: Thomas Quinn [aut, cre], David Lovell [aut]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>

Diff between propr versions 2.0.0 dated 2016-08-27 and 2.0.1 dated 2016-09-30

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Package hBayesDM updated to version 0.2.3.1 with previous version 0.2.3 dated 2016-07-17

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut]
Maintainer: Woo-Young Ahn <ahn.280@osu.edu>

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Package cowplot updated to version 0.6.3 with previous version 0.6.2 dated 2016-04-20

Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2' package. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot package.
Author: Claus O. Wilke [aut, cre], Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>

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Thu, 29 Sep 2016

Package oasis updated to version 2.1 with previous version 0.99.5 dated 2015-12-26

Title: Multiple Sclerosis Lesion Segmentation using Magnetic Resonance Imaging (MRI)
Description: Trains and makes predictions from the OASIS method, described in detail in the paper "OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI" <doi:10.1016/j.nicl.2013.03.002>. OASIS is a method for multiple sclerosis (MS) lesion segmentation on structural magnetic resonance image (MRI) studies. OASIS creates probability maps of lesion presence using the FLAIR, T2, T1, and PD structural MRI volumes. This packages allows for training of the OASIS model and prediction of OASIS probability maps from a trained model with user supplied studies that have a gold standard lesion segmentation masks. The package will also create OASIS probability maps for MRI studies using the OASIS model from the OASIS paper if no gold standard lesion segmentation masks are available.
Author: Elizabeth M. Sweeney [aut, cre], John Muschelli [aut], R. Taki Shinohara [aut]
Maintainer: Elizabeth M. Sweeney <emsweene@jhsph.edu>

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Package treescape updated to version 1.10.17 with previous version 1.9.17 dated 2016-06-13

Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treescapeServer()'.
Author: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>

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Package paleomorph updated to version 0.1.3 with previous version 0.1.2 dated 2016-08-08

Title: Geometric Morphometric Tools for Paleobiology
Description: Fill missing symmetrical data with mirroring, calculate Procrustes alignments with or without scaling, and compute standard or vector correlation and covariance matrices (congruence coefficients) of 3D landmarks. Tolerates missing data for all analyses.
Author: Tim Lucas, Anjali Goswami
Maintainer: Tim Lucas <timcdlucas@gmail.com>

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Package spcadjust updated to version 1.1 with previous version 1.0 dated 2015-11-21

Title: Functions for Calibrating Control Charts
Description: Calibration of thresholds of control charts such as CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy <a.gandy@imperial.ac.uk> and Jan Terje Kvaloy <jan.t.kvaloy@uis.no>.
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>

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Package npsp updated to version 0.5-3 with previous version 0.3-6 dated 2014-10-20

Title: Nonparametric Spatial Statistics
Description: Multidimensional nonparametric spatio-temporal (geo)statistics. S3 classes and methods for multidimensional: linear binning, local polynomial kernel regression, density and variogram estimation. Nonparametric methods for trend and variogram inference.
Author: Ruben Fernandez-Casal
Maintainer: Ruben Fernandez-Casal <rubenfcasal@gmail.com>

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Package NNS updated to version 0.2.2 with previous version 0.2.1 dated 2016-09-13

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>

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Package MetaIntegrator updated to version 1.0.3 with previous version 1.0.1 dated 2016-08-30

Title: Meta-Analysis of Gene Expression Data
Description: A pipeline for the meta-analysis of gene expression data. We have assembled several analysis and plot functions to perform integrated multi-cohort analysis of gene expression data (meta- analysis). Methodology described in: <http://biorxiv.org/content/early/2016/08/25/071514>.
Author: Winston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney, Erika Bongen, Purvesh Khatri
Maintainer: Winston A. Haynes <hayneswa@stanford.edu>

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Package bfa updated to version 0.4 with previous version 0.3.1 dated 2014-02-11

Title: Bayesian Factor Analysis
Description: Provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models under a range of priors.
Author: Jared Murray
Maintainer: Jared Murray <jsmurray@stat.cmu.edu>

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Wed, 28 Sep 2016

Package addinslist updated to version 0.2 with previous version 0.1 dated 2016-05-04

Title: Discover and Install Useful RStudio Addins
Description: Browse through a continuously updated list of existing RStudio addins and install/uninstall their corresponding packages.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

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Package VWPre updated to version 0.9.0 with previous version 0.7.0 dated 2016-06-19

Title: Tools for Preprocessing Visual World Data
Description: Gaze data from the Visual World Paradigm requires significant preprocessing prior to plotting and analyzing the data. This package provides functions for preparing visual world eye-tracking data for statistical analysis and plotting. It can prepare data for linear analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM). Additionally, it contains various plotting functions for creating grand average and conditional average plots. See the vignette for samples of the functionality. Currently, the functions in this package are designed for handling data collected with SR Research Eyelink eye trackers using Sample Reports created in SR Research Data Viewer; however, in subsequent releases we would like to add functionality for data collected with other systems.
Author: Vincent Porretta [aut, cre], Aki-Juhani Kyröläinen [aut], Jacolien van Rij [ctb], Juhani Järvikivi [ctb]
Maintainer: Vincent Porretta <vincentporretta@gmail.com>

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Package pmml updated to version 1.5.1 with previous version 1.5.0 dated 2015-08-05

Title: Generate PMML for Various Models
Description: The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define statistical and data mining models and to share models between PMML compliant applications. More information about PMML and the Data Mining Group can be found at http:// www.dmg.org. The generated PMML can be imported into any PMML consuming application, such as the Zementis ADAPA and UPPI scoring engines which allow for predictive models built in R to be deployed and executed on site, in the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza, Pivotal, Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler (arules), Zementis Inc, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha, Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@zementis.net>

Diff between pmml versions 1.5.0 dated 2015-08-05 and 1.5.1 dated 2016-09-28

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Package DoE.base updated to version 0.29 with previous version 0.28 dated 2016-03-10

Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE Packages
Description: Package DoE.base creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre], Boyko Amarov [ctb], Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>

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Package astsa updated to version 1.6 with previous version 1.5 dated 2016-07-31

Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples by Shumway and Stoffer, fourth edition.
Author: David Stoffer
Maintainer: David Stoffer <stoffer@pitt.edu>

Diff between astsa versions 1.5 dated 2016-07-31 and 1.6 dated 2016-09-28

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Package msgl updated to version 2.3.0 with previous version 2.2.1 dated 2016-09-10

Title: High Dimensional Multiclass Classification Using Sparse Group Lasso
Description: Multinomial logistic regression with sparse group lasso penalty. Simultaneous feature selection and parameter estimation for classification. Suitable for high dimensional multiclass classification with many classes. The algorithm computes the sparse group lasso penalized maximum likelihood estimate. Use of parallel computing for cross validation and subsampling is supported through the 'foreach' and 'doParallel' packages. Development version is on GitHub, please report package issues on GitHub.
Author: Martin Vincent
Maintainer: Martin Vincent <martin.vincent.dk@gmail.com>

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Package fslr updated to version 2.0 with previous version 1.9.2.1 dated 2016-09-06

Title: Wrapper Functions for FSL ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')
Description: Wrapper functions that interface with 'FSL' (http:// fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package freesurfer updated to version 1.0 with previous version 0.9.8 dated 2016-09-07

Title: Wrapper Functions for 'Freesurfer'
Description: Wrapper functions that interface with 'Freesurfer' (https:// surfer.nmr.mgh.harvard.edu/), a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package cartogram updated to version 0.0.2 with previous version 0.0.1 dated 2016-08-30

Title: Create Cartograms with R
Description: Construct continuous and non-contiguous area cartograms.
Author: Sebastian Jeworutzki [aut, cre], Timothee Giraud [ctb], Nicolas Lambert [ctb], Roger Bivand [cph], Edzer Pebesma [cph]
Maintainer: Sebastian Jeworutzki <sebastian.jeworutzki@ruhr-uni-bochum.de>

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Package BEDMatrix updated to version 1.3.0 with previous version 1.2.0 dated 2016-03-04

Title: Matrices Backed by Binary PED Files (PLINK)
Description: A matrix-like data structure that allows for efficient, convenient, and scalable subsetting of binary genotype/phenotype files generated by PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), the whole genome association analysis toolset, without loading the entire file into memory.
Author: Alexander Grueneberg [aut, cre], Lian Lian [ctb], Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>

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Package AncestryMapper updated to version 2.0 with previous version 1.2 dated 2015-02-03

Title: Assigning Ancestry Based on Population References
Description: Assigns genetic ancestry to an individual and studies relationships between local and global populations.
Author: Tiago R Magalhaes, Eoghan T O'Halloran
Maintainer: Eoghan T O'Halloran <eoghan.ohalloran2@mail.dcu.ie>

Diff between AncestryMapper versions 1.2 dated 2015-02-03 and 2.0 dated 2016-09-28

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Package spm12r updated to version 2.0 with previous version 1.1.1 dated 2015-11-03

Title: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'
Description: Installs 'SPM12' to the R library directory and has associated functions for 'fMRI' and general imaging utilities, called through 'MATLAB'.
Author: John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>

Diff between spm12r versions 1.1.1 dated 2015-11-03 and 2.0 dated 2016-09-28

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Package sglOptim updated to version 1.3.0 with previous version 1.2.2 dated 2016-09-10

Title: Generic Sparse Group Lasso Solver
Description: Fast generic solver for sparse group lasso optimization problems. The loss (objective) function must be defined in a C++ module. The optimization problem is solved using a coordinate gradient descent algorithm. The algorithm is applicable to a broad class of convex loss functions. Convergence of the algorithm is established (see reference). Use of parallel computing for cross validation and subsampling is supported through the 'foreach' and 'doParallel' packages. Development version is on github, please report package issues on github. Development version is on github, please report package issues on github.
Author: Martin Vincent
Maintainer: Martin Vincent <martin.vincent.dk@gmail.com>

Diff between sglOptim versions 1.2.2 dated 2016-09-10 and 1.3.0 dated 2016-09-28

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Package red updated to version 0.1.1 with previous version 0.1.0 dated 2016-08-23

Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <http://www.iucn.org> for more information) red list criteria.
Author: Pedro Cardoso
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>

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Package QGglmm updated to version 0.5 with previous version 0.4 dated 2016-07-13

Title: Estimate Quantitative Genetics Parameters from Generalised Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil <bonamy@horus.ens.fr>
Maintainer: Pierre de Villemereuil <bonamy@horus.ens.fr>

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Package pcalg updated to version 2.4-3 with previous version 2.4-2 dated 2016-09-26

Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC) are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb], Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>

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Package papayar updated to version 1.0 with previous version 0.0.3 dated 2016-05-12

Title: View Medical Research Images using the Papaya JavaScript Library
Description: Users pass images and objects of class 'nifti' from the 'oro.nifti' package to a Papaya, an interactive lightweight JavaScript viewer. Although many packages can view individual slices or projections of image and matrix data, this package allows for quick and easy interactive browsing of images. The viewer is based off of the Mango software, which is a lightweight medical image viewer.
Author: John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package jiebaR updated to version 0.9.1 with previous version 0.8.1 dated 2016-04-18

Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of CppJieba
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>

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Permanent link

Package histmdl updated to version 0.6-1 with previous version 0.5-1 dated 2016-01-26

Title: A Most Informative Histogram-Like Model
Description: Using the MDL principle, it is possible to estimate parameters for a histogram-like model. The package contains the implementation of such an estimation method.
Author: Jouke Witteveen
Maintainer: Jouke Witteveen <j.witteveen@gmail.com>

Diff between histmdl versions 0.5-1 dated 2016-01-26 and 0.6-1 dated 2016-09-28

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 R/histmdl.R |   35 +++++++++++++++++++++--------------
 3 files changed, 27 insertions(+), 20 deletions(-)

More information about histmdl at CRAN
Permanent link

Package rcmdcheck updated to version 1.2.1 with previous version 1.1.0 dated 2016-04-16

Title: Run 'R CMD check' from 'R' and Capture Results
Description: Run 'R CMD check' from 'R' programmatically, and capture the results of the individual checks.
Author: Gabor Csardi
Maintainer: Gabor Csardi <gcsardi@mango-solutions.com>

Diff between rcmdcheck versions 1.1.0 dated 2016-04-16 and 1.2.1 dated 2016-09-28

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Package RCircos updated to version 1.2.0 with previous version 1.1.3 dated 2015-12-14

Title: Circos 2D Track Plot
Description: A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
Author: Hongen Zhang
Maintainer: Hongen Zhang <hzhang.henry@gmail.com>

Diff between RCircos versions 1.1.3 dated 2015-12-14 and 1.2.0 dated 2016-09-28

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More information about RCircos at CRAN
Permanent link

Package lsgl updated to version 1.3.0 with previous version 1.2.1 dated 2016-09-10

Title: Linear Sparse Group Lasso
Description: Linear multiple output using sparse group lasso. The algorithm finds the sparse group lasso penalized maximum likelihood estimator. This result in feature and parameter selection, and parameter estimation. Use of parallel computing for cross validation and subsampling is supported through the 'foreach' and 'doParallel' packages. Development version is on github, please report package issues on github.
Author: Martin Vincent
Maintainer: Martin Vincent <martin.vincent.dk@gmail.com>

Diff between lsgl versions 1.2.1 dated 2016-09-10 and 1.3.0 dated 2016-09-28

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More information about lsgl at CRAN
Permanent link

Package gcbd updated to version 0.2.6 with previous version 0.2.5 dated 2013-12-12

Title: 'GPU'/CPU Benchmarking in Debian-Based Systems
Description: 'GPU'/CPU Benchmarking on Debian-package based systems This package benchmarks performance of a few standard linear algebra operations (such as a matrix product and QR, SVD and LU decompositions) across a number of different 'BLAS' libraries as well as a 'GPU' implementation. To do so, it takes advantage of the ability to 'plug and play' different 'BLAS' implementations easily on a Debian and/or Ubuntu system. The current version supports - 'Reference BLAS' ('refblas') which are un-accelerated as a baseline - Atlas which are tuned but typically configure single-threaded - Atlas39 which are tuned and configured for multi-threaded mode - 'Goto Blas' which are accelerated and multi-threaded - 'Intel MKL' which is a commercial accelerated and multithreaded version. As for 'GPU' computing, we use the CRAN package - 'gputools' For 'Goto Blas', the 'gotoblas2-helper' script from the ISM in Tokyo can be used. For 'Intel MKL' we use the Revolution R packages from Ubuntu 9.10.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between gcbd versions 0.2.5 dated 2013-12-12 and 0.2.6 dated 2016-09-28

 ChangeLog          |   23 +++++++++++++++++++++++
 DESCRIPTION        |   39 +++++++++++++++++++--------------------
 MD5                |   14 +++++++-------
 NAMESPACE          |   11 ++++++++++-
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 8 files changed, 70 insertions(+), 39 deletions(-)

More information about gcbd at CRAN
Permanent link

Package easyVerification updated to version 0.3.0 with previous version 0.2.0 dated 2016-01-25

Title: Ensemble Forecast Verification for Large Data Sets
Description: Set of tools to simplify application of atomic forecast verification metrics for (comparative) verification of ensemble forecasts to large data sets. The forecast metrics are imported from the 'SpecsVerification' package, and additional forecast metrics are provided with this package. Alternatively, new user-defined forecast scores can be implemented using the example scores provided and applied using the functionality of this package.
Author: MeteoSwiss [aut, cph], Jonas Bhend [cre], Jacopo Ripoldi [ctb], Claudia Mignani [ctb], Irina Mahlstein [ctb], Rebecca Hiller [ctb], Christoph Spirig [ctb], Mark Liniger [ctb], Andreas Weigel [ctb], Joaqu'in Bedia Jimenez [ctb], Matteo De Felice [ctb]
Maintainer: Jonas Bhend <jonas.bhend@meteoswiss.ch>

Diff between easyVerification versions 0.2.0 dated 2016-01-25 and 0.3.0 dated 2016-09-28

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Package DJL updated to version 2.6 with previous version 2.5 dated 2016-08-18

Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development. Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>

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Package comf updated to version 0.1.6 with previous version 0.1.5 dated 2016-09-13

Title: Functions for Thermal Comfort Research
Description: Functions to calculate various common and less common thermal comfort indices, convert physical variables, and evaluate the performance of thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>

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Tue, 27 Sep 2016

Package sbtools updated to version 1.1.6 with previous version 1.1.3 dated 2016-08-19

Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
Author: Tim Kern [cre], Luke Winslow [aut], Scott Chamberlain [aut], Alison Appling [aut], Jordan Read [aut]
Maintainer: Tim Kern <kernt@usgs.gov>

Diff between sbtools versions 1.1.3 dated 2016-08-19 and 1.1.6 dated 2016-09-27

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Package PCGSE updated to version 0.3 with previous version 0.2 dated 2014-05-07

Title: Principal Component Gene Set Enrichment
Description: Contains logic for computing the statistical association of variable groups, i.e., gene sets, with respect to the principal components of genomic data.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>

Diff between PCGSE versions 0.2 dated 2014-05-07 and 0.3 dated 2016-09-27

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Package DynNom updated to version 3.0.1 with previous version 3.0 dated 2016-09-20

Title: Dynamic Nomograms for Linear, Generalized Linear and Proportional Hazard Models
Description: Demonstrate the results of a statistical model object as a dynamic nomogram in an 'RStudio' panel or web browser. DynNom supports a variety of model objects; 'lm', 'glm', 'coxph' and also 'Ols', 'Glm', 'lrm', 'cph' models.
Author: Amirhossein Jalali, Davood Roshan, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>

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Package blavaan updated to version 0.2-2 with previous version 0.2-1 dated 2016-09-20

Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre], Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>

Diff between blavaan versions 0.2-1 dated 2016-09-20 and 0.2-2 dated 2016-09-27

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Package berryFunctions updated to version 1.12.3 with previous version 1.12.2 dated 2016-09-21

Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>

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Package GameTheory updated to version 2.4 with previous version 2.0 dated 2015-08-10

Title: Cooperative Game Theory
Description: Implementation of a common set of punctual solutions for Cooperative Game Theory.
Author: Sebastian Cano-Berlanga
Maintainer: Sebastian Cano-Berlanga <cano.berlanga@gmail.com>

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Package sjPlot updated to version 2.1.0 with previous version 2.0.2 dated 2016-07-31

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package SIDES updated to version 1.6 with previous version 1.5 dated 2016-09-15

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

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Package qwraps2 updated to version 0.2.2 with previous version 0.2.1 dated 2016-05-30

Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into '.Rnw' or '.Rmd' files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at <https://github.com/dewittpe/qwraps/>. The implementation and limited scope of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre], Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>

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Package nontarget updated to version 1.9 with previous version 1.8 dated 2016-03-14

Title: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos <mloos@looscomputing.ch>

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Package funrar updated to version 1.0.1 with previous version 1.0.0 dated 2016-07-15

Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al (accepted). Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity.
Author: Matthias Grenié [aut, cre], Pierre Denelle [aut], Caroline Tucker [aut]
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>

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Package nproc updated to version 2.0.1 with previous version 1.2 dated 2016-08-11

Title: Neyman-Pearson Receiver Operating Characteristics
Description: Given a sample of class 0 and class 1 and a classification method, the package generates the corresponding Neyman-Pearson classifier with a pre-specified type-I error control and Neyman-Pearson Receiver Operating Characteristics.
Author: Yang Feng, Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>

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Package NHMM updated to version 3.6 with previous version 3.5 dated 2014-11-26

Title: Bayesian Non-Homogenous Markov and Mixture Models (Multiple Time Series)
Description: Bayesian HMM and NHMM modeling for multiple time series. The emission distribution can be mixtures of Gammas, Poissons, Normals and zero inflation is possible.
Author: Tracy Holsclaw
Maintainer: Tracy Holsclaw <iamrandom@iamrandom.com>

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Package ecp updated to version 3.0.0 with previous version 2.0.0 dated 2015-05-20

Title: Non-Parametric Multiple Change-Point Analysis of Multivariate Data
Description: Implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and probabilistic pruning, with no distributional assumptions other than the existence of certain absolute moments in one method. Hierarchical and exact search methods are included. All methods return the set of estimated change- points as well as other summary information.
Author: Nicholas A. James, Wenyu Zhang and David S. Matteson
Maintainer: Nicholas A. James <nj89@cornell.edu>

Diff between ecp versions 2.0.0 dated 2015-05-20 and 3.0.0 dated 2016-09-27

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Package corHMM updated to version 1.20 with previous version 1.19 dated 2016-06-13

Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>

Diff between corHMM versions 1.19 dated 2016-06-13 and 1.20 dated 2016-09-27

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Mon, 26 Sep 2016

Package GetoptLong updated to version 0.1.5 with previous version 0.1.4 dated 2016-08-14

Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

Diff between GetoptLong versions 0.1.4 dated 2016-08-14 and 0.1.5 dated 2016-09-26

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Package circlize updated to version 0.3.9 with previous version 0.3.8 dated 2016-08-14

Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

Diff between circlize versions 0.3.8 dated 2016-08-14 and 0.3.9 dated 2016-09-26

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Package BioFTF updated to version 1.2-0 with previous version 1.1-0 dated 2016-09-05

Title: Biodiversity Assessment Using Functional Tools
Description: The main drawback of the most common biodiversity indices is that different measures may lead to different rankings among communities. This instrument overcomes this limit using some functional tools with the diversity profiles. In particular, the derivatives, the curvature, the radius of curvature, the arc length, and the surface area are proposed. The goal of this method is to interpret in detail the diversity profiles and obtain an ordering between different ecological communities on the basis of diversity. In contrast to the typical indices of diversity, the proposed method is able to capture the multidimensional aspect of biodiversity, because it takes into account both the evenness and the richness of the species present in an ecological community.
Author: Fabrizio Maturo [aut, cre], Francesca Fortuna [aut], Tonio Di Battista [aut]
Maintainer: Fabrizio Maturo <f.maturo@unich.it>

Diff between BioFTF versions 1.1-0 dated 2016-09-05 and 1.2-0 dated 2016-09-26

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Package arulesCBA updated to version 1.0.1 with previous version 1.0 dated 2016-08-28

Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson
Maintainer: Ian Johnson <ianjjohnson@icloud.com>

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Package svgPanZoom updated to version 0.3.3 with previous version 0.3.2 dated 2016-03-09

Title: R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Description: This 'htmlwidget' provides pan and zoom interactivity to R graphics, including 'base', 'lattice', and 'ggplot2'. The interactivity is provided through the 'svg-pan-zoom.js' library. Various options to the widget can tailor the pan and zoom experience to nearly any user desire.
Author: Anders Riutta et. al. [aut, cph] (svg-pan-zoom.js BSD-licensed library in htmlwidgets/lib, https://github.com/ariutta/svg-pan-zoom), Jorik Tangelder [aut, cph] (hammer.js MIT-licensed touch library in htmlwidgets/lib, https://github.com/hammerjs/hammer), Kent Russell [aut, cre] (R interface to svg-pan-zoom.js)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between svgPanZoom versions 0.3.2 dated 2016-03-09 and 0.3.3 dated 2016-09-26

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Package rtweet updated to version 0.3.0 with previous version 0.2.0 dated 2016-08-14

Title: Collecting Twitter Data
Description: An implementation of calls designed to extract and organize Twitter data via Twitter's REST and stream APIs. Functions formulate GET and POST requests and convert response objects to more user friendly structures, e.g., data frames or lists. Specific consideration is given to functions designed to return tweets, friends, and followers.
Author: Michael W. Kearney
Maintainer: Michael W. Kearney <mkearney@ku.edu>

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Package rpostgis updated to version 1.0.2 with previous version 1.0.0 dated 2016-08-20

Title: R Interface to a 'PostGIS' Database
Description: Provides additional functions to the 'RPostgreSQL' package to interface R with a 'PostGIS'-enabled database, as well as convenient wrappers to common 'PostgreSQL' queries.
Author: Mathieu Basille [aut], David Bucklin [aut, cre]
Maintainer: David Bucklin <dbucklin@ufl.edu>

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Package rpart.plot updated to version 2.1.0 with previous version 2.0.1 dated 2016-06-22

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 <milbo@sonic.net>

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Package ITGM updated to version 0.3 with previous version 0.2 dated 2016-09-09

Title: Individual Tree Growth Modeling
Description: Individual tree model is an instrument to support the decision with regard to forest management. This package provides functions that let you work with data for this model. Also other support functions and extension related to this model are available.
Author: Clayton Vieira Fraga Filho, Miqueias Fernandes
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>

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Package GUILDS updated to version 1.3 with previous version 1.2.1 dated 2015-04-21

Title: Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure
Description: A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
Author: Thijs Janzen [aut, cre], Bart Haegeman [ctb], Franck Jabot [ctb], Jerome Chave [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>

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Package Fgmutils updated to version 0.9.3 with previous version 0.9 dated 2016-09-09

Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
Author: Clayton Vieira Fraga Filho, Ana Paula Simiqueli, Gilson Fernandes da Silva, Miqueias Fernandes, Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>

Diff between Fgmutils versions 0.9 dated 2016-09-09 and 0.9.3 dated 2016-09-26

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Package FedData updated to version 2.2.0 with previous version 2.0.10 dated 2016-09-08

Title: Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package allows for retrieval of five datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; and the International Tree Ring Data Bank. Additional data sources are in the works, including global DEM resources (ETOPO1, ETOPO5, ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>

Diff between FedData versions 2.0.10 dated 2016-09-08 and 2.2.0 dated 2016-09-26

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Package seqMeta updated to version 1.6.6 with previous version 1.6.5 dated 2016-01-26

Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley, Brian Davis
Maintainer: Brian Davis <Brian.Davis281@gmail.com>

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Package Rlabkey updated to version 2.1.131 with previous version 2.1.130 dated 2016-05-25

Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

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Package plotly updated to version 4.5.2 with previous version 3.6.0 dated 2016-05-17

Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre], Chris Parmer [aut, cph], Toby Hocking [aut], Scott Chamberlain [aut], Karthik Ram [aut], Marianne Corvellec [aut], Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>

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Package pcalg updated to version 2.4-2 with previous version 2.2-4 dated 2015-07-23

Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC) are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb], Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>

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Package ecospat updated to version 2.1.0 with previous version 2.0 dated 2016-05-26

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

Diff between ecospat versions 2.0 dated 2016-05-26 and 2.1.0 dated 2016-09-26

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Permanent link

Package dequer updated to version 2.0-0 with previous version 1.0 dated 2015-07-05

Title: Stacks, Queues, and 'Deques' for R
Description: Queues, stacks, and 'deques' are list-like, abstract data types. These are meant to be very cheap to "grow", or insert new objects into. A typical use case involves storing data in a list in a streaming fashion, when you do not necessarily know how may elements need to be stored. Unlike R's lists, the new data structures provided here are not necessarily stored contiguously, making insertions and deletions at the front/end of the structure much faster. The underlying implementation is new and uses a head/tail doubly linked list; thus, we do not rely on R's environments or hashing. To avoid unnecessary data copying, most operations on these data structures are performed via side-effects.
Author: Drew Schmidt [aut, cre]
Maintainer: Drew Schmidt <wrathematics@gmail.com>

Diff between dequer versions 1.0 dated 2015-07-05 and 2.0-0 dated 2016-09-26

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Permanent link

Package VineCopula updated to version 2.0.5 with previous version 2.0.4 dated 2016-08-08

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Thomas Nagler [aut, cre], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthias Killiches [ctb], Harry Joe [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

Diff between VineCopula versions 2.0.4 dated 2016-08-08 and 2.0.5 dated 2016-09-26

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More information about VineCopula at CRAN
Permanent link

Package svgViewR updated to version 1.2 with previous version 1.0.1 dated 2015-06-17

Title: 3D Animated Interactive Visualizations Using SVG
Description: Creates 3D animated, interactive visualizations in Scalable Vector Graphics (SVG) format that can be viewed in a web browser.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between svgViewR versions 1.0.1 dated 2015-06-17 and 1.2 dated 2016-09-26

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Package srvyr updated to version 0.2.0 with previous version 0.1.2 dated 2016-06-28

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

Diff between srvyr versions 0.1.2 dated 2016-06-28 and 0.2.0 dated 2016-09-26

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Package sjstats updated to version 0.5.0 with previous version 0.4.0 dated 2016-08-26

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

Diff between sjstats versions 0.4.0 dated 2016-08-26 and 0.5.0 dated 2016-09-26

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Package SimDesign updated to version 1.3 with previous version 1.2 dated 2016-09-09

Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R. The package controls the structure and back-end of Monte Carlo simulations by utilizing a general generate-analyse-summarise strategy. The functions provided control common simulation issues such as re-simulating non-convergent results, support parallel back-end and MPI distributed computations, save and restore temporary files, aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between SimDesign versions 1.2 dated 2016-09-09 and 1.3 dated 2016-09-26

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Package RODBC updated to version 1.3-14 with previous version 1.3-13 dated 2016-04-14

Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre], Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between RODBC versions 1.3-13 dated 2016-04-14 and 1.3-14 dated 2016-09-26

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Package rgho updated to version 0.2.2 with previous version 0.2.1 dated 2016-09-08

Title: Access WHO Global Health Observatory Data from R
Description: Access WHO Global Health Observatory data from R via the Athena web service, an application program interface providing a simple query interface to the World Health Organization's data and statistics content.
Author: Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>

Diff between rgho versions 0.2.1 dated 2016-09-08 and 0.2.2 dated 2016-09-26

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Package RcppCNPy updated to version 0.2.6 with previous version 0.2.5 dated 2016-08-26

Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write facilities for files created with (or for) the 'NumPy' extension for 'Python'. Vectors and matrices of numeric types can be read or written to and from files as well as compressed files. Support for integer files is available if the package has been built with -std=c++11 which is the default starting with release 0.2.3 following the release of R 3.1.0, and available on all platforms following the release of R 3.3.0 with the updated 'Rtools'.
Author: Dirk Eddelbuettel and Wush Wu
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppCNPy versions 0.2.5 dated 2016-08-26 and 0.2.6 dated 2016-09-26

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Package pbapply updated to version 1.3-0 with previous version 1.2-2 dated 2016-08-26

Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options. Functions can exploit parallel processing resources.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>

Diff between pbapply versions 1.2-2 dated 2016-08-26 and 1.3-0 dated 2016-09-26

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Package mongolite updated to version 0.9 with previous version 0.8.1 dated 2016-03-21

Title: Fast and Simple MongoDB Client for R
Description: High-performance MongoDB client based on 'libmongoc' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, SSL encryption and SASL authentication. The vignette gives a brief overview of the available methods in the package.
Author: Jeroen Ooms [aut, cre], MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between mongolite versions 0.8.1 dated 2016-03-21 and 0.9 dated 2016-09-26

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Package momentchi2 updated to version 0.1.5 with previous version 0.1.0 dated 2015-02-25

Title: Moment-Matching Methods for Weighted Sums of Chi-Squared Random Variables
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.
Author: Dean Bodenham
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>

Diff between momentchi2 versions 0.1.0 dated 2015-02-25 and 0.1.5 dated 2016-09-26

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Package etl updated to version 0.3.3.1 with previous version 0.3.3 dated 2016-07-27

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

Diff between etl versions 0.3.3 dated 2016-07-27 and 0.3.3.1 dated 2016-09-26

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Package clusrank updated to version 0.4-4 with previous version 0.4-3 dated 2016-09-05

Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre], Mei-Ling Ting Lee [ctb], Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>

Diff between clusrank versions 0.4-3 dated 2016-09-05 and 0.4-4 dated 2016-09-26

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Package clogitLasso updated to version 1.0.1 with previous version 1.0 dated 2016-08-01

Title: Lasso Estimation of Conditional Logistic Regression Models for Matched Case-Control Studies
Description: Fit a sequence of conditional logistic regression models with lasso, for small to large sized samples.
Author: Marius Kwemou <marius.kwemou@gmail.com> and Marta Avalos
Maintainer: Marius Kwemou <marius.kwemou@gmail.com>

Diff between clogitLasso versions 1.0 dated 2016-08-01 and 1.0.1 dated 2016-09-26

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Package CAMAN updated to version 0.74 with previous version 0.73 dated 2015-09-01

Title: Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN
Description: Tools for the analysis of finite semiparametric mixtures. These are useful when data is heterogeneous, e.g. in pharmacokinetics or meta-analysis. The NPMLE and VEM algorithms (flexible support size) and EM algorithms (fixed support size) are provided for univariate and bivariate data.
Author: Peter Schlattmann <peter.schlattmann@mti.uni-jena.de>, Johannes Hoehne, Maryna Verba
Maintainer: Philipp Doebler <philipp.doebler@googlemail.com>

Diff between CAMAN versions 0.73 dated 2015-09-01 and 0.74 dated 2016-09-26

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Package boral updated to version 1.1 with previous version 1.0.1 dated 2016-07-25

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

Diff between boral versions 1.0.1 dated 2016-07-25 and 1.1 dated 2016-09-26

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Package activity updated to version 1.1 with previous version 1.0 dated 2014-09-29

Title: Animal Activity Statistics
Description: Provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear variables with time (or other circular variables).
Author: Marcus Rowcliffe <marcus.rowcliffe@ioz.ac.uk>
Maintainer: Marcus Rowcliffe <marcus.rowcliffe@ioz.ac.uk>

Diff between activity versions 1.0 dated 2014-09-29 and 1.1 dated 2016-09-26

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Sun, 25 Sep 2016

Package dfphase1 updated to version 1.0.1 with previous version 1.0 dated 2016-09-22

Title: Phase I Control Charts (with Emphasis on Distribution-Free Methods)
Description: Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution.
Author: Giovanna Capizzi and Guido Masarotto
Maintainer: Giovanna Capizzi <giovanna.capizzi@unipd.it>

Diff between dfphase1 versions 1.0 dated 2016-09-22 and 1.0.1 dated 2016-09-25

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Package dataframes2xls updated to version 0.4.7 with previous version 0.4.6 dated 2014-11-25

Title: Write Data Frames to Xls Files
Description: Writes data frames to xls files. It supports multiple sheets and basic formatting.
Author: Guido van Steen
Maintainer: Guido van Steen <vansteen@users.sourceforge.net>

Diff between dataframes2xls versions 0.4.6 dated 2014-11-25 and 0.4.7 dated 2016-09-25

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