Wed, 20 Nov 2013

New package sensitivitymv with initial version 1.2
Package: sensitivitymv
Type: Package
Title: Sensitivity Analysis in Observational Studies
Version: 1.2
Date: 2013-11-20
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum
Description: Sensitivity analysis in observational studies, including evidence factors and amplification, using the permutation distribution of Huber-Maritz M-statistics, including the permutational t-test.
License: GPL-2
LazyLoad: yes
Packaged: 2013-11-20 18:30:58 UTC; rosenbap
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-11-20 21:27:05

More information about sensitivitymv at CRAN
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Package polspline updated to version 1.1.9 with previous version 1.1.8 dated 2013-04-24

Title: Polynomial spline routines
Description: Routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars, by C. Kooperberg and co-authors
Author: Charles Kooperberg
Maintainer: Charles Kooperberg

Diff between polspline versions 1.1.8 dated 2013-04-24 and 1.1.9 dated 2013-11-20

 polspline-1.1.8/polspline/INDEX          |only
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 polspline-1.1.9/polspline/R/polspline.R  |    2 +-
 polspline-1.1.9/polspline/src/polymars.c |    3 ++-
 5 files changed, 13 insertions(+), 13 deletions(-)

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Package MsatAllele updated to version 1.05 with previous version 1.04 dated 2013-08-02

Title: Visualizes the scoring and binning of microsatellite fragment sizes
Description: The package contains functions to: 1) load ah files from Strand software and build a R data base; 2) plot different graphical displays of the fragment sizes obtained for each locus and their bins; 3) interact with graphs to sort the data base for a given locus and range, allowing to easily trace back a particular group of samples to its original Strand file; bin fragment size data into population genetics files. 4) From version 1.04 on, the user can set manually bin limits and write files combining the manual and automatic methods to bin alleles.
Author: Filipe Alberto
Maintainer: Filipe Alberto

Diff between MsatAllele versions 1.04 dated 2013-08-02 and 1.05 dated 2013-11-20

 DESCRIPTION               |    8 ++--
 MD5                       |    8 ++--
 R/read.frag.sizes.R       |   85 ++++++++++++++++++++++++++--------------------
 man/MsatAllele-package.Rd |    4 +-
 man/read.frag.sizes.Rd    |    3 +
 5 files changed, 61 insertions(+), 47 deletions(-)

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Package rtop updated to version 0.3-43 with previous version 0.3-42 dated 2013-08-21

Title: Interpolation of data with variable spatial support
Description: Package for geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.
Author: Jon Olav Skoien
Maintainer: Jon Olav Skoien

Diff between rtop versions 0.3-42 dated 2013-08-21 and 0.3-43 dated 2013-11-20

 DESCRIPTION      |   10 ++--
 MD5              |   16 +++----
 R/findOverlap.R  |  113 +++++++++++++++++++++++++++++++++++--------------------
 R/fitVariogram.R |    8 +++
 R/gDist.r        |    8 +--
 R/rtop.R         |   29 ++++----------
 R/sceua.R        |   35 ++++++++++-------
 R/varMat.R       |   16 ++++---
 demo/rtopCandG.r |    2 
 9 files changed, 137 insertions(+), 100 deletions(-)

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New package ggHorizon with initial version 0.1
Package: ggHorizon
Title: An implementation of Horizon Graph
Description: Implements horizon graphs based on ggplot2.
Version: 0.1
Author: Thomas Kern
Maintainer: Thomas Kern
Depends: R (>= 3.0.2), ggplot2 (>= 0.9.3), plyr (>= 1.8), RColorBrewer (>= 1.0.5), proto
License: GPL (>= 2)
LazyData: true
Collate: 'plot_horizon.r' 'smooth.r' 'theme.r'
Packaged: 2013-11-17 14:30:04 UTC; thomaskern
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-11-20 17:51:28

More information about ggHorizon at CRAN
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Package frailtypack updated to version 2.5 with previous version 2.4.1 dated 2013-04-26

Title: General Frailty models: shared, joint and nested frailty models with prediction
Description: Frailtypack now fits several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation. 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. Prediction values are available. Left truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata (max=2) are allowed. In each model, the random effects have a gamma distribution, but you can switch to a log-normal in shared and joint models. Now, you can also consider time-varying covariates effects in Cox, shared and joint models. The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau

Diff between frailtypack versions 2.4.1 dated 2013-04-26 and 2.5 dated 2013-11-20

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More information about frailtypack at CRAN
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Package witness updated to version 1.2 with previous version 1.1 dated 2013-09-20

Title: This package fits eyewitness data using Clark's (2003) WITNESS model
Description: WITNESS is a computational model intended to understand the psychological processes underlying eyewitness identification. This package contains the WITNESS computational model as well as two methods of fitting the model to data.
Author: Dustin Fife
Maintainer: Dustin Fife

Diff between witness versions 1.1 dated 2013-09-20 and 1.2 dated 2013-11-20

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 7 files changed, 26 insertions(+), 22 deletions(-)

More information about witness at CRAN
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Package ecp updated to version 1.5.5 with previous version 1.5.4 dated 2013-06-08

Title: Nonparametric Multiple Change Point Analysis of Multivariate Data
Description: This package performs hierarchical change point analysis through the use of U-statistics. Both agglomerative and divisive procedures return the set of change points estimates, and other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James

Diff between ecp versions 1.5.4 dated 2013-06-08 and 1.5.5 dated 2013-11-20

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More information about ecp at CRAN
Permanent link

Package devtools updated to version 1.4 with previous version 1.3 dated 2013-07-04

Title: Tools to make developing R code easier
Description: Collection of package development tools
Author: Hadley Wickham [aut, cre], Winston Chang [aut], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Hadley Wickham

Diff between devtools versions 1.3 dated 2013-07-04 and 1.4 dated 2013-11-20

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Package ade4 updated to version 1.6-2 with previous version 1.5-2 dated 2013-04-11

Title: Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray , Anne-Béatrice Dufour , and Jean Thioulouse , with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Simon Penel

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Package truncSP updated to version 1.2.1 with previous version 1.2 dated 2013-05-13

Title: Semi-parametric estimators of truncated regression models
Description: Semi-parametric estimation of truncated linear regression models
Author: Anita Lindmark and Maria Karlsson, Department of Statistics, Umea University
Maintainer: Anita Lindmark

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Package PearsonDS updated to version 0.97 with previous version 0.96 dated 2013-10-02

Title: Pearson Distribution System
Description: Implementation of the Pearson distribution system, including full support for the (d,p,q,r)-family of functions for probability distributions and fitting via method of moments and maximum likelihood method.
Author: Martin Becker and Stefan Klner
Maintainer: Martin Becker

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Package hypred updated to version 0.4 with previous version 0.2 dated 2012-08-01

Title: Simulation of genomic data in applied genetics
Description: The package is intended for simulating high density genomic data. The meiosis is simulated under a count-location model, the genetic structure can include additive and dominance effects. The low level nature of the package provides great flexibility in creating all kinds of populations.
Author: Frank Technow
Maintainer: Frank Technow

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Package epiR updated to version 0.9-51 with previous version 0.9-48 dated 2013-04-08

Title: An R package for the analysis of epidemiological data
Description: An R package for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani and Peter Solymos.
Maintainer: Mark Stevenson

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Package seqminer updated to version 2.0 with previous version 1.9.1 dated 2013-11-15

Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL format) into R
Description: Integrate sequencing data (VCF) or meta-analysis results in R
Author: Xiaowei Zhan and Dajiang Liu , with contributions of Jean-loup Gailly and Mark Adler (they wrote zlib and provide license so we include zlib source code), Julian Seward (this author wrote bzip2 and with BSD license we include bzip2 source codes) and Heng Li (this author wrote tabix and with MIT license we include tabix source codes).
Maintainer: Xiaowei Zhan

Diff between seqminer versions 1.9.1 dated 2013-11-15 and 2.0 dated 2013-11-20

 seqminer-1.9.1/seqminer/src/VCFRecord_flymake.h |only
 seqminer-2.0/seqminer/ChangeLog                 |    8 ++++++++
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 seqminer-2.0/seqminer/src/rvMetaLoader.cpp      |    1 +
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 15 files changed, 43 insertions(+), 26 deletions(-)

More information about seqminer at CRAN
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Package rgbif updated to version 0.4.0 with previous version 0.3.0 dated 2013-07-19

Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut], Vijay Barve [aut], Dan Mcglinn [aut]
Maintainer: Scott Chamberlain

Diff between rgbif versions 0.3.0 dated 2013-07-19 and 0.4.0 dated 2013-11-20

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Package RcppArmadillo updated to version 0.3.920.3 with previous version 0.3.920.1 dated 2013-09-29

Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library (currently version 3.920.1). Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.3.920.1 dated 2013-09-29 and 0.3.920.3 dated 2013-11-20

 ChangeLog                                    |   13 +++++++++++++
 DESCRIPTION                                  |    8 ++++----
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 inst/examples/fastLm.r                       |   24 +++++++++++++++++++++++-
 inst/examples/varSimulation.r                |    4 ++--
 inst/include/armadillo_bits/Mat_meat.hpp     |   11 +++++++----
 inst/include/armadillo_bits/arma_version.hpp |    2 +-
 12 files changed, 70 insertions(+), 21 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link


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