Mon, 04 May 2015

Package sglasso updated to version 1.2 with previous version 1.1-1 dated 2015-04-02

Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

Diff between sglasso versions 1.1-1 dated 2015-04-02 and 1.2 dated 2015-05-04

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More information about sglasso at CRAN
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Package samplesize4surveys updated to version 2.4.0.900 with previous version 2.2.0 dated 2015-04-29

Title: Sample Size Calculations for Complex Surveys
Description: Computes the required sample size for estimation of totals, means and proportions under complex sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas <hugogutierrez@usantotomas.edu.co>

Diff between samplesize4surveys versions 2.2.0 dated 2015-04-29 and 2.4.0.900 dated 2015-05-04

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Package rgr updated to version 1.1.11 with previous version 1.1.10 dated 2015-01-03

Title: Applied Geochemistry EDA
Description: Geological Survey of Canada (GSC) functions for exploratory data analysis with applied geochemical data, with special application to the estimation of background ranges and identification of outliers, 'anomalies', to support mineral exploration and environmental studies. Additional functions are provided to support analytical data QA/QC, ANOVA for investigations of field sampling and analytical variability, and utility tasks. NOTE: function caplot() for concentration-area plots employs package 'akima', however, 'akima' is only licensed for not-for-profit use. Therefore, not-for-profit users of 'rgr' will have to independently make package 'akima' available through library(....); and use of function caplot() by for-profit users will fail.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett <garrett@NRCan.gc.ca>

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Package PopGenome updated to version 2.1.6 with previous version 2.1.5 dated 2015-05-01

Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.
Author: Bastian Pfeifer [aut, cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Bastian Pfeifer <Bastian.Pfeifer@uni-duesseldorf.de>

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Package numDeriv updated to version 2014.2-1 with previous version 2012.9-1 dated 2012-10-14

Title: Accurate Numerical Derivatives
Description: Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using Richardson's extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than Richardson's extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.
Author: Paul Gilbert and Ravi Varadhan
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

Diff between numDeriv versions 2012.9-1 dated 2012-10-14 and 2014.2-1 dated 2015-05-04

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Package ncvreg updated to version 3.4-0 with previous version 3.3-0 dated 2015-03-18

Title: Regularization Paths for SCAD and MCP Penalized Regression Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

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Package labdsv updated to version 1.7-0 with previous version 1.6-1 dated 2013-09-13

Title: Ordination and Multivariate Analysis for Ecology
Description: A variety of ordination and community analyses useful in analysis of data sets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>

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Package InvariantCausalPrediction updated to version 0.3-2 with previous version 0.3-1 dated 2015-04-14

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

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Package DVHmetrics updated to version 0.3 with previous version 0.2 dated 2015-04-08

Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics, gEUD, BED, EQD2, NTCP, TCP, show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre], Heiko Karle [aut], Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>

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Package wgaim updated to version 1.4-7 with previous version 1.4-6 dated 2015-02-03

Title: Whole Genome Average Interval Mapping for QTL Detection using Mixed Models
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>

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Package stabledist updated to version 0.7-0 with previous version 0.6-6 dated 2013-06-12

Title: Stable Distribution Functions
Description: Density, Probability and Quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.
Author: Diethelm Wuertz, Martin Maechler and Rmetrics core team members.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package sdcMicro updated to version 4.5.0 with previous version 4.4.0 dated 2014-07-18

Title: Statistical Disclosure Control Methods for Anonymization of Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly confidential. This package can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. In addition, various risk estimation methods are included. Note that the package 'sdcMicroGUI' includes a graphical user interface for various methods in this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>

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Package fishmove updated to version 0.3-2 with previous version 0.3-1 dated 2015-03-24

Title: Prediction of Fish Movement Parameters
Description: Functions to predict fish movement parameters plotting leptokurtic fish dispersal kernels (see Radinger and Wolter, 2014: Patterns and predictors of fish dispersal in rivers. Fish and Fisheries. 15:456-473.)
Author: Johannes Radinger
Maintainer: Johannes Radinger <jradinger@igb-berlin.de>

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Package beeswarm updated to version 0.2.0 with previous version 0.1.6 dated 2013-09-20

Title: The Bee Swarm Plot, an Alternative to Stripchart
Description: The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.
Author: Aron Eklund
Maintainer: Aron Eklund <eklund+beeswarm@cbs.dtu.dk>

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Package vdg updated to version 1.1 with previous version 1.0.1 dated 2015-02-13

Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots and similar graphics for exploring the properties of experimental designs. The design region is explored via random sampling, which allows for more flexibility than traditional variance dispersion graphs. A formula interface is leveraged to provide access to complex model formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or multiple model formulae. Instead of using pointwise optimization to find the minimum and maximum scaled prediction variance curves, which can be inaccurate and time consuming, this package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph]
Maintainer: Pieter Schoonees

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Package simPH updated to version 1.3.1 with previous version 1.3 dated 2015-02-11

Title: Tools for Simulating and Plotting Quantities of Interest Estimated from Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud

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Package s20x updated to version 3.1-16 with previous version 3.1-15 dated 2015-03-27

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

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 s20x-3.1-16/s20x/man/boxqq.Rd                                                       |   60 
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 s20x-3.1-16/s20x/man/camplake.df.Rd                                                 |   36 
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 s20x-3.1-16/s20x/man/mening.df.Rd                                                   |   26 
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 s20x-3.1-16/s20x/man/skewness.Rd                                                    |   40 
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Permanent link

New package RANN.L1 with initial version 2.5
Encoding: UTF-8
Package: RANN.L1
Title: Fast Nearest Neighbour Search (Wraps ANN Library) Using L1 Metric
Version: 2.5
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis, Kirill Müller
Copyright: ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details.
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L1 (Manhattan, taxicab) metric. Please see package 'RANN' for the same functionality using the L2 (Euclidean) metric.
Maintainer: Kirill Müller
License: GPL (>= 3)
URL: https://github.com/jefferis/RANN/tree/master-L1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2015-05-04 08:20:21 UTC; muelleki
Repository: CRAN
Date/Publication: 2015-05-04 11:54:30

More information about RANN.L1 at CRAN
Permanent link

Package docopt updated to version 0.4.3.3 with previous version 0.4.2 dated 2015-01-05

Title: Command-Line Interface Specification Language
Description: Define a command-line interface by just giving it a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge

Diff between docopt versions 0.4.2 dated 2015-01-05 and 0.4.3.3 dated 2015-05-04

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Package ASMap updated to version 0.4-1 with previous version 0.4 dated 2015-04-13

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor , David Butler .
Maintainer: Julian Taylor

Diff between ASMap versions 0.4 dated 2015-04-13 and 0.4-1 dated 2015-05-04

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Permanent link

Package JMbayes updated to version 0.7-2 with previous version 0.7-0 dated 2015-03-13

Title: Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos

Diff between JMbayes versions 0.7-0 dated 2015-03-13 and 0.7-2 dated 2015-05-04

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Permanent link

New package clustering.sc.dp with initial version 1.0
Package: clustering.sc.dp
Type: Package
Title: Optimal Distance-Based Clustering for Multidimensional Data with Sequential Constraint
Version: 1.0
Date: 2015-04-28
Authors@R: c(person("Tibor", "Szkaliczki", role = c("aut", "cre"), email = "szkaliczki.tibor@sztaki.mta.hu"), person("J.", "Song", role = "ctb", email = "joemsong@cs.nmsu.edu"))
Author: Tibor Szkaliczki [aut, cre], J. Song [ctb]
Maintainer: Tibor Szkaliczki
Depends: R (>= 2.10.0)
Description: A dynamic programming algorithm for optimal clustering multidimensional data with sequential constraint. The algorithm minimizes the sum of squares of within-cluster distances. The sequential constraint allows only subsequent items of the input data to form a cluster. The sequential constraint is typically required in clustering data streams or items with time stamps such as video frames, GPS signals of a vehicle, movement data of a person, e-pen data, etc. The algorithm represents an extension of Ckmeans.1d.dp to multiple dimensional spaces. Similarly to the one-dimensional case, the algorithm guarantees optimality and repeatability of clustering. Method clustering.sc.dp can find the optimal clustering if the number of clusters is known. Otherwise, methods findwithinss.sc.dp and backtracking.sc.dp can be used.
License: LGPL (>= 3)
NeedsCompilation: yes
Packaged: 2015-05-04 06:24:46 UTC; Asus
Repository: CRAN
Date/Publication: 2015-05-04 09:27:25

More information about clustering.sc.dp at CRAN
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Package apsimr updated to version 1.0 with previous version 0.1 dated 2014-06-12

Title: Edit, Run and Evaluate APSIM Simulations Easily Using R
Description: The Agricultural Production Systems sIMulator (APSIM) is a widely used simulator of agricultural systems. This package includes functions to create, edit and run APSIM simulations from R. It also includes functions to visualize the results of an APSIM simulation and perform sensitivity/uncertainty analysis of APSIM either via functions in the sensitivity package or by novel emulator-based functions. For more on APSIM including download instructions go to \url{www.apsim.info}.
Author: Bryan Stanfill
Maintainer: Bryan Stanfill

Diff between apsimr versions 0.1 dated 2014-06-12 and 1.0 dated 2015-05-04

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Permanent link

New package Rlinkedin with initial version 0.1
Package: Rlinkedin
Version: 0.1
Title: Access to the LinkedIn API via R
Description: A series of functions that allow users to access the LinkedIn API to get information about connections, search for people and jobs, share updates with their network, and create group discussions. For more information about using the API please visit https://developer.linkedin.com/.
Author: Michael Piccirilli
Maintainer: Michael Piccirilli
Depends: R (>= 2.12.0), httr, XML, httpuv
License: GPL-2
LazyData: true
URL: https://github.com/mpiccirilli/Rlinkedin
Packaged: 2015-05-04 04:10:10 UTC; mikepicc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-04 07:41:06

More information about Rlinkedin at CRAN
Permanent link

Package emdatr updated to version 0.3 with previous version 0.2 dated 2014-05-12

Title: Global Disaster Losses from the EMDAT Database Using R
Description: The 'EMDAT' database provides information on human and financial losses from more than 21,000 major natural global disasters from 1900 to the present. This package provides the entire data available from 'EMDAT' and also additional relevant information such as historical national GDP and population. Moreover, this package also provides functionality to extract desired subsets of the 'EMDAT' data. The examples provided in the vignette demonstrate the functionality provided by 'emdatr'. The goal of 'emdatr' is to promote the use of 'EMDAT' data, bring transparency to the data, shed light on the limitations of the data, and make the analysis of the data easier using R.
Author: Gopi Goteti
Maintainer: Gopi Goteti

Diff between emdatr versions 0.2 dated 2014-05-12 and 0.3 dated 2015-05-04

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 emdatr-0.3/emdatr/DESCRIPTION               |   40 +++++------
 emdatr-0.3/emdatr/LICENSE                   |only
 emdatr-0.3/emdatr/MD5                       |   33 ++++-----
 emdatr-0.3/emdatr/NAMESPACE                 |    2 
 emdatr-0.3/emdatr/NEWS                      |   16 ++++
 emdatr-0.3/emdatr/R/data.r                  |   74 ++++++++++----------
 emdatr-0.3/emdatr/R/extract_emdat.r         |   13 +--
 emdatr-0.3/emdatr/build/vignette.rds        |binary
 emdatr-0.3/emdatr/data/emdat_sample.rda     |binary
 emdatr-0.3/emdatr/data/usa_cpi.rda          |binary
 emdatr-0.3/emdatr/inst/doc/emdatr_demo.R    |only
 emdatr-0.3/emdatr/inst/doc/emdatr_demo.Rmd  |only
 emdatr-0.3/emdatr/inst/doc/emdatr_demo.html |only
 emdatr-0.3/emdatr/man/emdat_sample.Rd       |  100 +++++++++++++---------------
 emdatr-0.3/emdatr/man/emdatr.Rd             |   23 ++----
 emdatr-0.3/emdatr/man/extract_emdat.Rd      |   29 +++-----
 emdatr-0.3/emdatr/man/usa_cpi.Rd            |   22 +++---
 emdatr-0.3/emdatr/vignettes/emdatr_demo.Rmd |only
 22 files changed, 182 insertions(+), 170 deletions(-)

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