Wed, 05 Nov 2014

New package poplite with initial version 0.99.5
Package: poplite
Version: 0.99.5
Date: 2014-6-17
Title: Tools for simplifying the population and querying of SQLite databases
Author: Daniel Bottomly
Maintainer: Daniel Bottomly
Depends: R (>= 3.1), methods, dplyr (>= 0.3.0.2)
Imports: DBI, igraph, lazyeval, RSQLite (>= 1.0.0)
Suggests: testthat, Lahman, VariantAnnotation
Description: Provides objects and accompanying methods which facilitates populating and querying SQLite databases.
License: GPL-3
Collate: tableSchemaList.R Database.R external_funcs.R
Packaged: 2014-11-05 22:58:20 UTC; bottomly
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-06 01:25:06

More information about poplite at CRAN
Permanent link

New package CpGFilter with initial version 1.0
Package: CpGFilter
Type: Package
Title: CpG Filtering Method Based on Intra-class Correlation Coefficients
Version: 1.0
Date: 2014-10-31
Author: Jun Chen
Maintainer: Jun Chen
Description: Filter CpGs based on Intra-class Correlation Coefficients (ICCs) when replicates are available. ICCs are calculated by fitting linear mixed effects models to all samples including the un-replicated samples. Including the large number of un-replicated samples improves ICC estimates dramatically. The method accommodates any replicate design.
License: GPL-2
Packaged: 2014-11-05 22:37:14 UTC; m123485
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-06 01:21:42

More information about CpGFilter at CRAN
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New package xtal with initial version 1.0
Package: xtal
Type: Package
Title: Crystallization Toolset
Version: 1.0
Date: 2014-10-31
Author: Qingan Sun, Xiaojun Li
Maintainer: Qingan Sun
Description: Tool set for crystallographer to design and analyze crystallization experiments of ribosome from Mycobacterium tuberculosis
License: GPL-2 | GPL-3
Depends: methods,graphics, grDevices, stats, utils
LazyLoad: yes
Packaged: 2014-11-05 22:05:33 UTC; Home
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-06 00:42:08

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Package VGAM updated to version 0.9-5 with previous version 0.9-4 dated 2014-05-28

Title: Vector Generalized Linear and Additive Models
Description: This package fits many (150+) models and distributions by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. This is done via the vector generalized linear and additive model (VGLM/VGAM) classes and associated models (reduced-rank VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, row-column interaction models). These are abbreviated RR-VGLMs, QRR-VGLMs, RR-VGAMs and RCIMs. These include constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology as well as constrained additive ordination (CAO). Note that these functions are subject to change, especially before version 1.0.0 is released; see the NEWS file for latest changes.
Author: Thomas W. Yee
Maintainer: Thomas Yee

Diff between VGAM versions 0.9-4 dated 2014-05-28 and 0.9-5 dated 2014-11-05

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 VGAM-0.9-5/VGAM/R/family.actuary.R               |  516 ++---
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 VGAM-0.9-5/VGAM/R/family.univariate.R            | 2172 +++++++++++++++--------
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Package msgl updated to version 2.0.125.1 with previous version 2.0.125.0 dated 2014-03-26

Title: High Dimensional Multiclass Classification Using Sparse Group Lasso
Description: Sparse group lasso multiclass classification, suitable for high dimensional problems with many classes. Fast algorithm for solving the multinomial sparse group lasso convex optimization problem. This package apply template metaprogramming techniques, therefore -- when compiling the package from source -- a high level of optimization is needed to gain full speed (e.g. for the GCC compiler use -O3). Use of multiple processors for cross validation and subsampling is supported through OpenMP. The Armadillo C++ library is used as the primary linear algebra engine.
Author: Martin Vincent
Maintainer: Martin Vincent

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Package lsgl updated to version 1.0.123.1 with previous version 1.0.123.0 dated 2014-03-25

Title: Linear Sparse Group Lasso
Description: Linear multiple output using sparse group lasso
Author: Martin Vincent
Maintainer: Martin Vincent

Diff between lsgl versions 1.0.123.0 dated 2014-03-25 and 1.0.123.1 dated 2014-11-05

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New package lpme with initial version 1.0.0
Package: lpme
Type: Package
Title: Local Polynomial Estimator in Measurement Error Models
Version: 1.0.0
Date: 2014-11-4
Author: Haiming Zhou and Xianzheng Huang
Maintainer: Haiming Zhou
Description: Two local polynomial estimators for solving the errors-in-variables problem: one is in Delaigle, Fan, and Carroll (2009), and one is in Huang and Zhou (2014+). The SIMEX bandwidth selection method is also provided for both estimators.
License: GPL (>= 2)
Depends: R (>= 3.0.2)
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp, RcppArmadillo (>= 0.4.300.0)
Packaged: 2014-11-05 01:14:57 UTC; Haiming
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-06 01:03:45

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Package GetoptLong updated to version 0.0.8 with previous version 0.0.7 dated 2014-10-11

Title: Parsing Command-line Arguments and Variable Interpolation
Description: Parsing command-line arguments by Perl module Getopt::Long. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GetoptLong versions 0.0.7 dated 2014-10-11 and 0.0.8 dated 2014-11-05

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Package elliptic updated to version 1.3-5 with previous version 1.3-3 dated 2013-12-05

Title: elliptic functions
Description: A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin

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New package anim.plots with initial version 0.1
Package: anim.plots
Type: Package
Title: Simple Animated Plots For R
Version: 0.1
Date: 2014-10-27
Author: David Hugh-Jones
Maintainer: David Hugh-Jones
Description: Simple animated versions of basic R plots, using the 'animation' package. Includes animated versions of plot, barplot, persp, contour, filled.contour, hist, curve, points, lines, text, symbols, segments, and arrows.
License: GPL-2
LazyData: TRUE
VignetteBuilder: knitr
Imports: animation
Suggests: maps, knitr
Packaged: 2014-11-05 18:25:43 UTC; david
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-06 00:46:21

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New package Watersheds with initial version 1.0
Package: Watersheds
Type: Package
Title: Spatial Watershed Aggregation and Spatial Drainage Network Analysis
Version: 1.0
Date: 2013-08-10
Author: J.A. Torres
Maintainer: J. A. Torres
Description: Methods for watersheds aggregation and spatial drainage network analysis.
License: GPL (>= 2)
Depends: R (>= 2.10), methods, sp, maptools, rgeos, lattice, splancs
Packaged: 2014-11-05 14:03:40 UTC; j_mata01
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-05 20:25:43

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Package strap updated to version 1.4 with previous version 1.3 dated 2014-08-08

Title: Stratigraphic Tree Analysis for Palaeontology
Description: Functions for the stratigraphic analysis of phylogenetic trees.
Author: Mark A. Bell Graeme T. Lloyd .
Maintainer: Mark A. Bell

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Package TRSbook updated to version 1.0.1 with previous version 1.0 dated 2014-11-03

Title: Functions and Datasets to Accompany the Book "The R Software: Fundamentals of Programming and Statistical Analysis"
Description: Functions and datasets for the reader of the book "The R Software: Fundamentals of Programming and Statistical Analysis".
Author: Lafaye de Micheaux Pierre, Drouilhet Remy, Liquet Benoit
Maintainer: P Lafaye de Micheaux

Diff between TRSbook versions 1.0 dated 2014-11-03 and 1.0.1 dated 2014-11-05

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Package MPAgenomics updated to version 1.1.2 with previous version 1.1.0 dated 2014-07-23

Title: Multi-Patient Analysis of Genomic Markers
Description: Preprocess and analysis of genomic data. MPAgenomics provides wrappers from commonly used packages to streamline their repeated manipulation, offering an easy-to-use pipeline. The segmentation of successive multiple profiles is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given outcome.
Author: Quentin Grimonprez with contributions from Guillemette Marot and Samuel Blanck. Some functions use code created by Sjoerd Vosse, Mark van de Wiel, Pierre Neuvial, Henrik Bengtsson.
Maintainer: Samuel Blanck

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New package ionflows with initial version 1.0
Package: ionflows
Type: Package
Title: Calculate the Number of Required Flows for Semiconductor Sequencing
Version: 1.0
Date: 2014-10-21
Author: Michael Bockmayr and Jan Budczies
Depends: Biostrings, BSgenome.Hsapiens.UCSC.hg19
Maintainer: Michael Bockmayr
Description: Two methods for calculation of the number of required flows for semiconductor sequencing: 1. Using a simulation, the number of flows can be calculated for a concrete list of amplicons. 2. An exact combinatorial model is evaluated to calculate the number of flows for a random ensemble of sequences.
License: GPL-3
Encoding: UTF-8
Packaged: 2014-11-05 14:10:54 UTC; mlb47
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-05 20:32:17

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New package geocodeHERE with initial version 0.1
Package: geocodeHERE
Title: Wrapper for Nokia's HERE Geocoding API
Version: 0.1
Author: "Cory Nissen [aut, cre]"
Maintainer: Cory Nissen
Description: Wrapper for Nokia's HERE geocoding API. See http://here.com/ for more information on HERE and https://developer.here.com/geocoder for more information on the HERE geocoding API.
Depends: R (>= 3.1.1)
License: MIT + file LICENSE
LazyData: true
Imports: httr
URL: https://github.com/corynissen/geocodeHERE
Packaged: 2014-11-05 14:19:01 UTC; c
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-05 20:32:15

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Package trip updated to version 1.1-19 with previous version 1.1-18 dated 2014-09-23

Title: Spatial Analysis of Animal Track Data
Description: Functions for accessing and manipulating spatial data for animal tracking. Filter for speed and create time spent plots from animal track data.
Author: Michael D. Sumner [aut, cre], Sebastian Luque [ctb]
Maintainer: Michael D. Sumner

Diff between trip versions 1.1-18 dated 2014-09-23 and 1.1-19 dated 2014-11-05

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Package shape updated to version 1.4.2 with previous version 1.4.1 dated 2014-01-08

Title: Functions for plotting graphical shapes, colors
Description: Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...
Author: Karline Soetaert
Maintainer: Karline Soetaert

Diff between shape versions 1.4.1 dated 2014-01-08 and 1.4.2 dated 2014-11-05

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Package NMOF updated to version 0.34-0 with previous version 0.28-2 dated 2013-09-06

Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book 'Numerical Methods and Optimization in Finance' by M. Gilli, D. Maringer and E. Schumann. The package provides implementations of several optimisation heuristics, such as Differential Evolution, Genetic Algorithms and Threshold Accepting. There are also functions for the valuation of financial instruments, such as bonds and options, and functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann

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 58 files changed, 2298 insertions(+), 1621 deletions(-)

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Package MGL updated to version 1.1 with previous version 1.0 dated 2014-11-03

Title: Module Graphical Lasso
Description: An aggressive dimensionality reduction and network estimation technique for a high-dimensional Gaussian graphical model (GGM). Please refer to: Efficient Dimensionality Reduction for High-Dimensional Network Estimation, Safiye Celik, Benjamin A. Logsdon, Su-In Lee, Proceedings of The 31st International Conference on Machine Learning, 2014, p. 1953--1961.
Author: Safiye Celik
Maintainer: Safiye Celik

Diff between MGL versions 1.0 dated 2014-11-03 and 1.1 dated 2014-11-05

 MGL-1.0/MGL/src/Makefile |only
 MGL-1.1/MGL/DESCRIPTION  |    6 +++---
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 MGL-1.1/MGL/src/MGL.c    |   18 +++++++++---------
 4 files changed, 14 insertions(+), 15 deletions(-)

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Package MAT updated to version 2.2 with previous version 2.0 dated 2014-09-26

Title: Multidimensional Adaptive Testing
Description: Simulate Multidimensional Adaptive Testing
Author: Seung W. Choi and David R. King
Maintainer: Seung W. Choi

Diff between MAT versions 2.0 dated 2014-09-26 and 2.2 dated 2014-11-05

 DESCRIPTION        |    6 ++---
 MD5                |    8 +++---
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 man/MAT-package.Rd |    5 +---
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Package label.switching updated to version 1.3 with previous version 1.2 dated 2013-12-04

Title: Relabelling MCMC outputs of mixture models
Description: The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis

Diff between label.switching versions 1.2 dated 2013-12-04 and 1.3 dated 2014-11-05

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New package hcp with initial version 0.1
Package: hcp
Type: Package
Title: Change Point Estimation for Regression with Heteroscedastic Data
Description: Estimation of parameters in 3-segment (i.e. 2 change-point) regression models with heteroscedastic variances is provided based on both likelihood and hybrid Bayesian approaches, with and without continuity constraints at the change points.
Version: 0.1
Author: Stephen J.Ganocy, Jiayang Sun, and Yulei Wang
Maintainer: Yulei Wang
License: GPL-2 | GPL-3
LazyData: true
Packaged: 2014-11-05 01:46:40 UTC; Yulei
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-05 14:14:28

More information about hcp at CRAN
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