Planet R

November 21, 2014

CRANberries

New package rfUtilities with initial version 1.0

Package: rfUtilities
Title: Random Forests model selection and performance evaluation
Version: 1.0
Date: 2014-11-09
Authors@R: as.person(c(person(family="Evans", given="Jeffrey S.", email="jeffrey_evans@tnc.org", role = c("aut", "cre")), person(family="Murphy", given="Melanie A.", role = c("aut"))))
Description: Utilities for Random Forest model selection, class balance correction, significance test, cross validation and probability partial plots.
Depends: R (>= 3.1.2), randomForest (>= 4.6-10), e1071 (>= 1.6-4)
Maintainer: Jeffrey S. Evans
License: GPL-3
URL: http://evansmurphy.wix.com/evansspatial
NeedsCompilation: no
Repository: CRAN
LazyData: true
Packaged: 2014-11-21 00:40:47 UTC; jevans
Author: Jeffrey S. Evans [aut, cre], Melanie A. Murphy [aut]
Date/Publication: 2014-11-21 07:56:12

More information about rfUtilities at CRAN

November 21, 2014 07:13 AM

New package Ramd with initial version 0.2

Package: Ramd
Title: Tools For Managing File/function Dependencies In R
Description: A "define" function is provided that allows for inclusion of external scripts without polluting the global namespace and makes it easier to write modular R code.
Version: 0.2
Author: Robert Krzyzanowski
Maintainer: Robert Krzyzanowski
Depends: R (>= 3.0.0)
Suggests: testthat, testthatsomemore
License: GPL (>= 2)
LazyData: true
Packaged: 2014-11-21 00:25:59 UTC; robertk
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-21 07:56:08

More information about Ramd at CRAN

November 21, 2014 07:12 AM

New package interpretR with initial version 0.1.0

Package: interpretR
Type: Package
Title: Binary Classifier Interpretation functions: Partial Dependence Plots
Version: 0.1.0
Date: 2014-11-21
Depends: randomForest
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings
Description: Create partial dependence plots for binary (cross-validated) classification models. Currently only binary classification models estimated with the packages randomForest and ada are supported.
License: GPL (>= 2)
Packaged: 2014-11-21 06:40:26 UTC; michelballings
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-21 07:56:10

More information about interpretR at CRAN

November 21, 2014 07:12 AM

New package db.r with initial version 0.1.0

Package: db.r
Type: Package
Version: 0.1.0
Date: 2014-11-17
Title: A Database Exploration Tool with Assisted Querying and Schema Exploration
Author: Greg Lamp
Maintainer: Greg Lamp
Depends: R (>= 2.12), methods
Imports: DBI, rjson (>= 0.2.14), stringr
Suggests: testthat (>= 0.2), RPostgreSQL (>= 0.2.14), RMySQL (>= 0.2.14), RSQLite (>= 1.0.0)
Description: db.r uses OOP style objects (with an API akin to C++, Python, Ruby, Javascript, etc.) to help make visualizing the tables, columns, and available operations on your database easier. db.r dynamically loads database schemas, execute queries, and manage credentials.
License: FreeBSD
URL: https://github.com/yhat/db.r
BugReports: https://github.com/yhat/db.r/issues
Packaged: 2014-11-20 23:05:21.040 UTC; glamp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-21 01:25:02

More information about db.r at CRAN

November 21, 2014 01:14 AM

November 20, 2014

CRANberries

New package treethresh with initial version 0.1-8

Package: treethresh
Version: 0.1-8
Date: 2014-11-20
Title: Methods for Tree-based Local Adaptive Thresholding
Author: Ludger Evers and Tim Heaton
Maintainer: Ludger Evers
Depends: R (>= 2.10), EbayesThresh, wavethresh
Description: This package implements TreeThresh, a locally adaptive version of EbayesThresh.
License: GPL (>= 3)
Repository: CRAN
Packaged: 2014-11-20 13:25:37 UTC; levers
NeedsCompilation: yes
Date/Publication: 2014-11-20 17:38:02

More information about treethresh at CRAN

November 20, 2014 05:13 PM

New package sprinter with initial version 1.0.0

Package: sprinter
Type: Package
Title: Framework for Screening Prognostic Interactions
Version: 1.0.0
Date: 2014-04-11
Author: Isabell Hoffmann
Maintainer: Isabell Hoffmann
VignetteBuilder: knitr
Suggests: parallel, knitr
Depends: R (>= 3.0.0), randomForestSRC, CoxBoost, survival, LogicReg
Description: The main function of this package builds prognostic models for time-to-event settings that consider interactions by combining available statistical components. Furthermore, it provides a function for evaluating the relevance of the selected interactions by resampling techniques.
License: GPL-2
Packaged: 2014-11-20 16:07:06 UTC; hoffm005
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 17:29:53

More information about sprinter at CRAN

November 20, 2014 05:13 PM

New package bglm with initial version 1.0

Package: bglm
Type: Package
Title: Bayesian Estimation in Generalized Linear Models
Version: 1.0
Date: 2014-10-29
Author: Nicolas Molano-Gonzalez, Edilberto Cepeda-Cuervo
Maintainer: Nicolas Molano-Gonzalez
Description: Implementation of Bayesian estimation in generalized linear models following Gamerman (1997).
License: GPL-2
Depends: R (>= 3.0.2), mvtnorm, methods
Suggests: car, coda, faraway
Packaged: 2014-11-20 17:02:59 UTC; A80873475
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 18:16:40

More information about bglm at CRAN

November 20, 2014 05:12 PM

New package statcheck with initial version 1.0.0

Package: statcheck
Type: Package
Title: Extract statistics from articles and recompute p values
Version: 1.0.0
Date: 2014-11-15
Author: Sacha Epskamp & Michele B. Nuijten
Maintainer: Michele B. Nuijten
Depends: R (>= 2.14.2), plyr
Description: Extract statistics from articles and recompute p values.
License: GPL-2
LazyLoad: yes
ByteCompile: yes
Packaged: 2014-11-18 12:25:05 UTC; mnuijten
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 10:44:36

More information about statcheck at CRAN

November 20, 2014 09:13 AM

New package frmhet with initial version 1.0

Package: frmhet
Type: Package
Title: Regression Analysis of Fractional Responses Under Unobserved Heterogeneity
Version: 1.0
Date: 2014-11-18
Author: Joaquim J.S. Ramalho
Maintainer: Joaquim J.S. Ramalho
Description: Estimation and specification analysis of fractional regression models with neglected heterogeneity and/or endogenous covariates.
License: GPL-2
Packaged: 2014-11-20 08:27:53 UTC; Joaquim
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 10:32:36

More information about frmhet at CRAN

November 20, 2014 09:12 AM

New package dfmta with initial version 1.0-3

Package: dfmta
Type: Package
Title: Phase I/II Adaptive Dose-Finding Design For MTA
Version: 1.0-3
Date: 2014-11-19
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
Copyright: All files in src/CppBugs are copyright Whit Armstrong. All other files are copyright Institut de Recherches Internationales Servier and Institut national de la sante et de la recherche medicale.
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization", Statistics in Medicine, 2014.
License: GPL-3
Depends: R (>= 3.1.0)
LinkingTo: RcppArmadillo (>= 0.3.910), BH (>= 1.54), RcppProgress (>= 0.1), Rcpp
Packaged: 2014-11-19 10:24:40 UTC; jjourdan
NeedsCompilation: yes
X-CRAN-Comment: Archived on 2014-11-18 as attempts to use a non-portable mix of C++11 and Fortran.
Repository: CRAN
Date/Publication: 2014-11-20 11:03:17

More information about dfmta at CRAN

November 20, 2014 09:12 AM

New package curl with initial version 0.2

Package: curl
Type: Package
Title: A Connection Interface to Libcurl.
Version: 0.2
Date: 2014-11-19
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: The curl() function provides a drop-in replacement for base url() with better performance and support for http 2.0, ssl (https, ftps), gzip, deflate and other libcurl goodies. This interface is implemented using the RConnection API in order to support incremental processing of both binary and text streams. If you are looking for a more user friendly http client, try the RCurl or httr packages instead.
License: MIT + file LICENSE
SystemRequirements: libcurl, OpenSSL (e.g: libcurl4-openssl-dev)
URL: http://github.com/jeroenooms/curl
BugReports: http://github.com/jeroenooms/curl/issues
Packaged: 2014-11-20 07:59:04 UTC; jeroen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-20 10:54:22

More information about curl at CRAN

November 20, 2014 09:12 AM

New package oaxaca with initial version 0.1

Package: oaxaca
Type: Package
Title: Blinder-Oaxaca decomposition
Version: 0.1
Date: 2014-11-19
Author: Marek Hlavac
Maintainer: Marek Hlavac
Description: An implementation of the Blinder-Oaxaca decomposition for linear regression models.
License: GPL (>= 2)
Imports: Formula, ggplot2, reshape2
LazyData: yes
Collate: 'oaxaca-internal.R' 'oaxaca.R'
Packaged: 2014-11-20 03:13:39 UTC; Marek Hlavac
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 08:13:35

More information about oaxaca at CRAN

November 20, 2014 07:15 AM

New package EGRET with initial version 2.0.0

Package: EGRET
Type: Package
Title: Exploration and Graphics for RivEr Trends (EGRET)
Version: 2.0.0
Date: 2014-10-13
Authors@R: c( person("Robert", "Hirsch", role = c("aut"), email = "rhirsch@usgs.gov"), person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov"))
Description: EGRET includes statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm Weighted Regressions on Time, Discharge, and Season (WRTDS).
License: CC0
Depends: R (>= 3.0)
Imports: dataRetrieval, survival, fields, stats, lubridate, methods
Suggests: xtable, knitr, extrafont
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
URL: http://pubs.usgs.gov/tm/04/a10/
Packaged: 2014-11-20 04:21:11 UTC; ldecicco
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 08:05:16

More information about EGRET at CRAN

November 20, 2014 07:13 AM

November 19, 2014

CRANberries

New package ilc with initial version 1.0

Package: ilc
Type: Package
Title: Lee-Carter Mortality Models using Iterative Fitting Algorithms
Version: 1.0
Date: 2014-11-19
Depends: R (>= 3.0.3), demography, rainbow, forecast, date
Imports: survival
Author: Zoltan Butt, Steven Haberman and Han Lin Shang
Maintainer: Zoltan Butt
Description: Fitting a class of Lee-Carter mortality models using iterative fitting algorithm.
License: GPL (>= 2)
LazyData: yes
LazyLoad: yes
LazyDataCompression: xz
Packaged: 2014-11-19 19:29:14 UTC; cbeit
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-20 00:45:16

More information about ilc at CRAN

November 19, 2014 11:12 PM

Bioconductor Project Working Papers

CRANberries

New package PGICA with initial version 1.0

Package: PGICA
Type: Package
Title: Parallel Group ICA Algorithm
Version: 1.0
Date: 2014-11-12
Author: Shaojie Chen; Lei Huang; Huitong Qiu; Ani Eloyan; Brian Caffo; Ciprian Crainiceanu
Maintainer: Shaojie Chen
Description: A Group ICA Algorithm that can run in parallel on an SGE platform or multi-core PCs
License: GPL-2
Imports: parallel, fastICA
Packaged: 2014-11-19 16:15:49 UTC; Jason
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-19 17:33:48

More information about PGICA at CRAN

November 19, 2014 05:13 PM

New package SEAsic with initial version 0.1

Package: SEAsic
Title: Score Equity Assessment- summary index computation
Version: 0.1
Authors@R: c(person("Anne Corinne", "Huggins-Manley", role = c("aut", "cre"), email = "ahuggins@coe.ufl.edu"), person("Douglas", "Whitaker", role = "aut"))
Author: Anne Corinne Huggins-Manley [aut, cre], Douglas Whitaker [aut]
Maintainer: Anne Corinne Huggins-Manley
Description: This package conducts Score Equity Assessment (SEA; Dorans, 2004) by calculating and plotting multiple SEA indices as introduced by a variety of authors and summarized by Huggins and Penfield (2012).
Depends: R (>= 3.1.1)
License: GPL-3
LazyData: true
Packaged: 2014-11-19 01:32:05 UTC; Doug
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-19 16:46:34

More information about SEAsic at CRAN

November 19, 2014 03:13 PM

New package QuACN with initial version 1.8.0

Package: QuACN
Type: Package
Title: QuACN: Quantitative Analysis of Complex Networks
Version: 1.8.0
Date: 2014-11-18
Author: Karl G. Kugler, Matthias Wieser, Matthias Dehmer, Michael Schutte, Laurin A.J. Mueller
Maintainer: Karl G. Kugler
Description: Quantitative Analysis of Complex Networks. This package offers a set of topological network measures to analyze complex Networks structurally.
License: LGPL
LazyLoad: yes
Depends: graph, RBGL, combinat
Suggests: Rmpfr
Imports: igraph
Packaged: 2014-11-19 13:47:45 UTC; karl.kugler
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-19 16:45:22

More information about QuACN at CRAN

November 19, 2014 03:13 PM

New package acnr with initial version 0.2.4

Package: acnr
Type: Package
Title: Annotated Copy-Number Regions
Version: 0.2.4
Date: 2014-10-27
Author: Morgane Pierre-Jean and Pierre Neuvial
Maintainer: Morgane Pierre-Jean
Description: This data package contains SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.
License: LGPL (>= 2.1)
Depends: R (>= 2.10), R.utils, xtable
Repository: CRAN
Repository/R-Forge/Project: jointseg
Repository/R-Forge/Revision: 142
Repository/R-Forge/DateTimeStamp: 2014-11-17 15:27:15
Date/Publication: 2014-11-19 11:43:31
Packaged: 2014-11-17 15:45:28 UTC; rforge
NeedsCompilation: no

More information about acnr at CRAN

November 19, 2014 11:12 AM

New package analogueExtra with initial version 0.1-0

Package: analogueExtra
Type: Package
Title: Additional functions for use with the analogue package
Version: 0.1-0
Date: 18 Nov 2014
Depends: vegan3d (>= 0.65-0), analogue (>= 0.16-0)
Imports: rgl
Suggests: testthat
Authors@R: c(person(given = c("Gavin", "L."), family = "Simpson", role = c("aut", "cre"), email = "ucfagls@gmail.com"))
Maintainer: Gavin L. Simpson
BugReports: https://github.com/gavinsimpson/analogueExtra/issues
NeedsCompilation: yes
Description: Provides additional functionality for the analogue package that is not required by all users of the main package.
License: GPL-2
ByteCompile: true
URL: https://github.com/gavinsimpson/analogueExtra
Packaged: 2014-11-18 23:01:34.400 UTC; gavin
Author: Gavin L. Simpson [aut, cre]
Repository: CRAN
Date/Publication: 2014-11-19 02:11:54

More information about analogueExtra at CRAN

November 19, 2014 01:12 AM

Dirk Eddelbuettel

R / Finance 2015 Call for Papers

Earlier today, Josh send the text below to the R-SIG-Finance list, and I updated the R/Finance website, including its Call for Papers page, accordingly.

We are once again very excited about our conference, thrilled about the four confirmed keynotes, and hope that many R / Finance users will not only join us in Chicago in May 2015 -- but also submit an exciting proposal.

So read on below, and see you in Chicago in May!

Call for Papers:

R/Finance 2015: Applied Finance with R
May 29 and 30, 2015
University of Illinois at Chicago, IL, USA

The seventh annual R/Finance conference for applied finance using R will be held on May 29 and 30, 2015 in Chicago, IL, USA at the University of Illinois at Chicago. The conference will cover topics including portfolio management, time series analysis, advanced risk tools, high-performance computing, market microstructure, and econometrics. All will be discussed within the context of using R as a primary tool for financial risk management, portfolio construction, and trading.

Over the past six years, R/Finance has included attendees from around the world. It has featured presentations from prominent academics and practitioners, and we anticipate another exciting line-up for 2015. This year will include invited keynote presentations by Emanuel Derman, Louis Marascio, Alexander McNeil, and Rishi Narang.

We invite you to submit complete papers in pdf format for consideration. We will also consider one-page abstracts (in txt or pdf format) although more complete papers are preferred. We welcome submissions for both full talks and abbreviated "lightning talks." Both academic and practitioner proposals related to R are encouraged.

All slides will be made publicly available at conference time. Presenters are strongly encouraged to provide working R code to accompany the slides. Data sets should also be made public for the purposes of reproducibility (though we realize this may be limited due to contracts with data vendors). Preference may be given to presenters who have released R packages.

The conference will award two (or more) $1000 prizes for best papers. A submission must be a full paper to be eligible for a best paper award. Extended abstracts, even if a full paper is provided by conference time, are not eligible for a best paper award. Financial assistance for travel and accommodation may be available to presenters, however requests must be made at the time of submission. Assistance will be granted at the discretion of the conference committee.

Please make your submission online at this link. The submission deadline is January 31, 2015. Submitters will be notified via email by February 28, 2015 of acceptance, presentation length, and financial assistance (if requested).

Additional details will be announced via the R/Finance conference website as they become available. Information on previous years' presenters and their presentations are also at the conference website.

For the program committee:

Gib Bassett, Peter Carl, Dirk Eddelbuettel, Brian Peterson, Dale Rosenthal,
Jeffrey Ryan, Joshua Ulrich

November 19, 2014 12:59 AM

November 18, 2014

CRANberries

New package attribrisk with initial version 0.1

Package: attribrisk
Type: Package
Title: Population Attributable Risk
Version: 0.1
Date: 2014-03-06
Author: Louis Schenck, Elizabeth Atkinson, Cynthia Crowson, Terry Therneau
Maintainer: Louis Schenck
VignetteBuilder: knitr
Suggests: knitr,xtable,testthat
Depends: survival,boot
LazyData: Yes
LazyLoad: Yes
Description: Estimates population (etiological) attributable risk for unmatched, pair-matched or set-matched case-control designs and returns a list containing the estimated attributable risk, estimates of coefficients, and their standard errors, from the (conditional, If necessary) logistic regression used for estimating the relative risk.
License: LGPL (>= 2)
Packaged: 2014-11-18 19:57:43 UTC; m110631
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-18 21:15:06

More information about attribrisk at CRAN

November 18, 2014 09:12 PM

Removed CRANberries

Package ssd (with last version 0.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-11-18 0.2

November 18, 2014 07:14 PM

Bioconductor Project Working Papers

Testing Gene-Environment Interactions in the Presence of Measurement Error

Complex diseases result from an interplay between genetic and environmental risk factors, and it is of great interest to study the gene-environment interaction (GxE) to understand the etiology of complex diseases. Recent developments in genetics field allows one to study GxE systematically. However, one difficulty with GxE arises from the fact that environmental exposures are often measured with error. In this paper, we focus on testing GxE when the environmental exposure E is subject to measurement error. Surprisingly, contrast to the well-established results that the naive test ignoring measurement error is valid in testing the main effects, we find that the naive test for GxE leads to inflated type I error under the null hypothesis of no interaction. The naive test also leads to biased estimates of the GxE effect. The analytic form of the bias term for general linear models is obtained, which is shown to be closely related to regression calibration. We then propose a regression calibration based approach to correct measurement error for testing GxE when either validation data or replicates are available. Extensive simulation studies are conducted to illustrate the performance of various tests with moderate sample sizes. Based on both theoretical and empirical results, we recommend the proposed test, as its type I error is properly controlled and it has at least comparable power to the naive test even when naive test is valid. The proposed methods are applied to study the gene–blood pressure interaction for cardiovascular diseases in an ancillary study of the Women’s Health Initiative.

by Chongzhi Di et al. at November 18, 2014 05:18 PM

CRANberries

New package ssd with initial version 0.2

Package: ssd
Type: Package
Title: Sample Size Determination (SSD) for Unordered Categorical Data
Version: 0.2
Date: 2014-11-10
Author: Junheng Ma and Jiayang Sun
Maintainer: Junheng Ma
Description: ssd calculates the sample size needed to detect the differences between two sets of unordered categorical data.
License: GPL-2
Packaged: 2014-11-18 14:05:32 UTC; Junheng Ma
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-18 15:55:21

More information about ssd at CRAN

November 18, 2014 03:21 PM

Removed CRANberries

Package dfmta (with last version 1.0-1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-11-06 1.0-1
2014-11-04 1.0

November 18, 2014 03:21 PM

CRANberries

New package selectspm with initial version 0.1

Package: selectspm
Type: Package
Title: Select point patterns models based on minimum contrast and AIC
Version: 0.1
Date: 2014-11-18
Author: Marcelino de la Cruz
Depends: spatstat, ecespa
Maintainer: Marcelino de la Cruz
Description: Package to fit and select point patterns models based on minimum contrast and AIC
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-11-18 13:19:51 UTC; marcelino
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-18 15:28:45

More information about selectspm at CRAN

November 18, 2014 03:20 PM

New package MCS with initial version 0.1.0

Package: MCS
Type: Package
Title: Model Confidence Set Procedure
Version: 0.1.0
Date: 2014-10-20
Author: Leopoldo Catania & Mauro Bernardi
Maintainer: Leopoldo Catania
Depends: R(>= 3.0.1)
Description: Perform the model confidence set procedure of Hansen et al (2011).
License: GPL-2
Imports: methods
Packaged: 2014-11-18 11:00:54 UTC; Leopoldo Catania
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-18 13:49:53

More information about MCS at CRAN

November 18, 2014 01:13 PM

New package ensurer with initial version 1.0

Package: ensurer
Type: Package
Title: Ensure values at runtime
Version: 1.0
Date: 2014-11-17
Author: Stefan Holst Milton Bache
Maintainer: Stefan Holst Milton Bache
Description: Add simple runtime contracts to R values. These ensure that values fulfil certain conditions and will raise appropriate errors if they do not.
License: MIT + file LICENSE
Suggests: magrittr, testthat, knitr
VignetteBuilder: knitr
ByteCompile: Yes
URL: https://github.com/smbache/ensurer
Packaged: 2014-11-17 21:48:45 UTC; shb
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-18 13:27:13

More information about ensurer at CRAN

November 18, 2014 01:13 PM

Dirk Eddelbuettel

RcppAnnoy 0.0.3

Hours after the initial blog post announcing the first release of the new package RcppAnnoy, Qiang Kou sent us a very nice pull request adding mmap support in Windows.

So a new release with Windows support is on now CRAN, and Windows binaries should be available by this evening as usual.

To recap, RcppAnnoy wraps the small, fast, and lightweight C++ template header library Annoy written by Erik Bernhardsson for use at Spotify. RcppAnnoy uses Rcpp Modules to offer the exact same functionality as the Python module wrapped around Annoy.

Courtesy of CRANberries, there is also a diffstat report for this release. More detailed information is on the RcppAnnoy page page.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

November 18, 2014 11:48 AM

Removed CRANberries

Package wrassp (with last version 0.1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-11-17 0.1.2

November 18, 2014 11:14 AM

CRANberries

New package simPop with initial version 0.2.6

Package: simPop
Type: Package
Title: Simulation of Synthetic Populations for Survey Data Considering Auxiliary Information
Version: 0.2.6
Date: 2014-09-17
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ
Depends: R(>= 3.0.0), lattice, vcd, data.table
Imports: laeken, MASS, Rcpp (>= 0.11.0), e1071, parallel, nnet, doParallel, foreach, colorspace, methods
LinkingTo: Rcpp
Description: Simulate populations for surveys based on auxiliary data including model-based methods, calibration and combinatorial optimization tools. Developed with support of the International Household Survey Network, DFID Trust Fund TF011722
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-11-17 12:53:32 UTC; templ
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-18 11:19:59

More information about simPop at CRAN

November 18, 2014 11:13 AM

November 17, 2014

CRANberries

New package wrassp with initial version 0.1.2

Package: wrassp
Version: 0.1.2
Title: Interface to the ASSP Library
Authors@R: as.person(c( "Raphael Winkelmann [aut, cre]", "Lasse Bombien [aut]", "Michel Scheffers [aut]"))
Description: wrassp is a wrapper around Michel Scheffers's libassp (Advanced Speech Signal Processor). The libassp library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner.
Depends: R (>= 3.1.1)
VignetteBuilder: knitr
Suggests: compare(>= 0.2.4), knitr(>= 1.7), testthat(>= 0.7.1.99)
License: GPL (>= 3)
URL: https://github.com/IPS-LMU/wrassp
BugReports: https://github.com/IPS-LMU/wrassp/issues
Packaged: 2014-11-17 10:59:15 UTC; ripley
Author: Raphael Winkelmann [aut, cre], Lasse Bombien [aut], Michel Scheffers [aut]
Maintainer: Raphael Winkelmann
SystemRequirements: GNU make
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-17 11:59:34

More information about wrassp at CRAN

November 17, 2014 11:13 AM

New package spThin with initial version 0.1.0

Package: spThin
Type: Package
Title: Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models
Version: 0.1.0
Date: 2014-11-16
Author: Matthew E. Aiello-Lammens, Robert A. Boria, Aleksandar Radosavljevic, Bruno Vilela, and Robert P. Anderson
Maintainer: Matthew E. Aiello-Lammens
Description: spThin is a set of functions that can be used to spatially thin species occurrence data. The resulting thinned data can be used in ecological modeling, such as ecological niche modeling.
Depends: spam, grid, fields, knitr
LazyData: TRUE
License: GPL-3
VignetteBuilder: knitr
Packaged: 2014-11-17 02:17:13 UTC; mlammens
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-17 08:57:55

More information about spThin at CRAN

November 17, 2014 07:12 AM

November 16, 2014

CRANberries

New package sla with initial version 0.1

Package: sla
Type: Package
Title: Two-Group Straight Line ANCOVA
Description: Provides directly interpretable estimated coefficients for four models in connection with the two-group straight line ANCOVA problem: (A) the full model, which requires the fitting of two intercepts and two slopes; (B) a reduced model, which requires the fitting of a single intercept and single slope; (C) a reduced model, which requires the fitting of two separate intercepts and a single, common slope; and (D) a reduced model, which requires the fitting of a single, common intercept and two separate slopes. The summary function provides tests of fit for the (null) hypotheses of: (1) equivalent data sets, (2) equivalent slopes, and (3) equivalent intercepts.
Version: 0.1
License: GPL-2
Authors@R: as.person(c( "W. Gregory Alvord [aut, cre]", "Nick Carchedi [aut]" ))
Depends: R (>= 3.0.2)
Suggests: MASS, car, ISwR, knitr
VignetteBuilder: knitr
Packaged: 2014-11-16 21:31:22 UTC; nicholasacarchedi
Author: W. Gregory Alvord [aut, cre], Nick Carchedi [aut]
Maintainer: W. Gregory Alvord
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-17 00:54:34

More information about sla at CRAN

November 16, 2014 11:12 PM

New package ISOpureR with initial version 1.0.4

Package: ISOpureR
Version: 1.0.4
Date: 2013-08-25
Title: Deconvolution of Tumour Profiles
Authors@R: c(person("Gerald Quon", role = "aut", email = "gquon@mit.edu"), person("Catalina V Anghel", role = c("aut", "trl"), email="Catalina Anghel@oicr.on.ca"), person("Syed Haider", role = "aut", email="Syed.Haider@oicr.on.ca"), person("Francis Nguyen", role = "aut"), person("Amit G Deshwar", role = "aut"), person("Quaid D Morris", role = "aut", email = "Quaid.Morris@utoronto.ca"), person("Paul C Boutros", role = c("aut", "cre"), email = "Paul.Boutros@oicr.on.ca"))
Author: Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D Morris [aut], Paul C Boutros [aut, cre]
Maintainer: Paul C Boutros
Depends: R (>= 3.1.1)
Suggests: knitr
VignetteBuilder: knitr
Description: Deconvolution of mixed tumour profiles into normal and cancer for each patient, using the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires mixed tumour profiles and a set of unmatched "basis" normal profiles.
License: GPL-2
Packaged: 2014-11-16 18:20:24 UTC; canghel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-16 22:15:14

More information about ISOpureR at CRAN

November 16, 2014 09:13 PM

Dirk Eddelbuettel

Introducing RcppAnnoy

A new package RcppAnnoy is now on CRAN.

It wraps the small, fast, and lightweight C++ template header library Annoy written by Erik Bernhardsson for use at Spotify.

While Annoy is setup for use by Python, RcppAnnoy offers the exact same functionality from R via Rcpp.

A new page for RcppAnnoy provides some more detail, example code and further links. See a recent blog post by Erik for a performance comparison of different approximate nearest neighbours libraries for Python.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

November 16, 2014 02:36 PM

CRANberries

New package RcppAnnoy with initial version 0.0.2

Package: RcppAnnoy
Type: Package
Title: Rcpp Bindings for Annoy, a Library for Approximate Nearest Neighbors
Version: 0.0.2
Date: 2014-11-13
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Description: Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the Rcpp and BH packages, exposing the same interface as the original Python wrapper to Annoy. See https://github.com/spotify/annoy for more on Annoy. Annoy is released under Version 2.0 of the Apache License.
License: GPL (>= 2)
Imports: methods, Rcpp (>= 0.11.3)
LinkingTo: Rcpp, BH
Suggests: RUnit
OS_type: unix
Packaged: 2014-11-13 17:33:28.744301 UTC; edd
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-16 12:19:15

More information about RcppAnnoy at CRAN

November 16, 2014 11:12 AM

New package vudc with initial version 1.0

Package: vudc
Type: Package
Title: Visualization of Univariate Data for Comparison
Version: 1.0
Date: 2014-11-15
Author: Csaba Farago
Maintainer: Csaba Farago
Description: Contains 2 new functions for visualization of univariate data: ccdplot and qddplot, along with input data.
License: GPL (>= 2)
Packaged: 2014-11-15 22:12:23 UTC; U521684
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-16 08:49:31

More information about vudc at CRAN

November 16, 2014 07:13 AM

November 15, 2014

CRANberries

New package GUIProfiler with initial version 0.1.2

Package: GUIProfiler
Type: Package
Title: Profiler Graphical User Interface
Version: 0.1.2
Date: 2014-11-14
Author: Fernando de Villar and Angel Rubio
Depends: Nozzle.R1, MASS
Maintainer: Fernando de Villar
Description: GUIProfiler shows graphically the results of profiling R programs by tracking their execution time.
License: GPL
Packaged: 2014-11-14 23:31:50 UTC; Gonzalo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-15 08:15:18

More information about GUIProfiler at CRAN

November 15, 2014 07:12 AM

New package EMDomics with initial version 0.99.0

Package: EMDomics
Title: Earth Mover's Distance for Differential Analysis of Genomics Data
Description: The EMDomics algorithm is used to perform a supervised two-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between two groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the two distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into the other, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores.
Version: 0.99.0
Authors@R: c( person("Daniel", "Schmolze", email="emd@schmolze.com", role=c("aut", "cre")), person("Andrew", "Beck", email="abeck2@bidmc.harvard.edu", role="aut"), person("Sheida", "Nabavi", email="sheida_nabavi@hms.harvard.edu", role="aut"))
Maintainer: Daniel Schmolze
Depends: R (>= 2.14.0)
Imports: emdist, BiocParallel, matrixStats, ggplot2
Suggests: knitr
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Packaged: 2014-11-14 21:41:39 UTC; Daniel
Author: Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi [aut]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-15 08:16:29

More information about EMDomics at CRAN

November 15, 2014 07:12 AM

November 14, 2014

Journal of Statistical Software

Fitting Accelerated Failure Time Models in Routine Survival Analysis with R Package aftgee

Vol. 61, Issue 11, Nov 2014

Abstract:

Accelerated failure time (AFT) models are alternatives to relative risk models which are used extensively to examine the covariate effects on event times in censored data regression. Nevertheless, AFT models have been much less utilized in practice due to lack of reliable computing methods and software. This paper describes an R package aftgee that implements recently developed inference procedures for AFT models with both the rank-based approach and the least squares approach. For the rank-based approach, the package allows various weight choices and uses an induced smoothing procedure that leads to much more efficient computation than the linear programming method. With the rank-based estimator as an initial value, the generalized estimating equation approach is used as an extension of the least squares approach to the multivariate case. Additional sampling weights are incorporated to handle missing data needed as in case-cohort studies or general sampling schemes. A simulated dataset and two real life examples from biomedical research are employed to illustrate the usage of the package.

November 14, 2014 08:00 AM

November 13, 2014

Bioconductor Project Working Papers

Personalized Evaluation of Biomarker Value: A Cost-benefit Perspective

For a patient who is facing a treatment decision, the added value of information provided by a biomarker depends on the individual patient’s expected response to treatment with and without the biomarker, as well as his/her tolerance of disease and treatment harm. However, individualized estimators of the value of a biomarker are lacking. We propose a new graphical tool named the subject-specific expected benefit curve for quantifying the personalized value of a biomarker in aiding a treatment decision. We develop semiparametric estimators for two general settings: i) when biomarker data are available from a randomized trial; and ii) when biomarker data are available from a cohort or a cross-sectional study, together with external information about a multiplicative treatment effect. We also develop adaptive bootstrap confidence intervals for consistent inference in the presence of non-regularity. The proposed method is used to evaluate the individualized value of the serum creatinine marker in informing treatment decisions for the prevention of renal artery stenosis.

by Ying Huang et al. at November 13, 2014 11:05 PM

CRANberries

New package toxtestD with initial version 2.0

Package: toxtestD
Type: Package
Title: Experimental design for binary toxicity tests
Version: 2.0
Date: 2014-11-12
Author: Nadia Keddig and Werner Wosniok
Maintainer: Nadia Keddig
Description: Calculates sample size and dose allocation for binary toxicity tests, using the Fish Embryo Toxicity Test as example. An optimal test design is obtained by running (i) spoD (calculate the number of individuals to test under control conditions), (ii) setD (estimate the minimal sample size per treatment given the users precision requirements) and (iii) doseD (construct an individual dose scheme).
License: GPL-2
Packaged: 2014-11-13 13:46:15 UTC; wwosniok
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-13 17:22:05

More information about toxtestD at CRAN

November 13, 2014 05:12 PM

New package plotROC with initial version 1.2

Package: plotROC
Type: Package
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Version: 1.2
Date: 2014-11-12
Author: Michael C Sachs
Maintainer: Michael C Sachs
Description: Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.
License: MIT + file LICENSE
URL: http://sachsmc.github.io/plotROC
Depends: R (>= 3.0.0)
Imports: grid, ggplot2, gridSVG, shiny
Suggests: ggthemes, knitr
VignetteBuilder: knitr
Packaged: 2014-11-13 14:30:53 UTC; sachsmc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-13 17:20:59

More information about plotROC at CRAN

November 13, 2014 05:12 PM

New package DetR with initial version 0.0.1

Package: DetR
Type: Package
Title: Suite of Deterministic and Robust Algorithms for Linear Regression
Version: 0.0.1
Date: 2013-01-13
Suggests: mvtnorm
Imports: matrixStats, robustbase
Depends: R (>= 3.1.1),
LinkingTo: Rcpp (>= 0.10.5), RcppEigen (>= 0.3.2.2)
SystemRequirements: C++11
Description: DetLTS, DetMM (and DetS) Algorithms for Deterministic, Robust Linear Regression.
License: GPL (>= 2)
LazyLoad: yes
Authors@R: c(person( "Kaveh","Vakili" , role = c("aut", "cre"), email = "vakili.kaveh.email@gmail.com"), person("Mia", "Hubert", role = "ths", email = "mia.hubert@wis.kuleuven.be"), person("Peter", "Rousseeuw", role = "ths", email = "peter.rousseeuw@wis.kuleuven.be"))
Maintainer: Kaveh Vakili
Author: Kaveh Vakili [aut, cre], Mia Hubert [ths], Peter Rousseeuw [ths]
Packaged: 2014-11-13 13:26:20 UTC; kaveh
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-13 17:19:53

More information about DetR at CRAN

November 13, 2014 05:12 PM

New package nodiv with initial version 0.9.1

Package: nodiv
Type: Package
Title: Compares the distribution of sister clades through a phylogeny
Version: 0.9.1
Date: 2014-11-09
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution). DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Depends: R (>= 3.0), picante, raster, ape, sp, vegan
License: GPL-2
Packaged: 2014-11-13 09:50:41 UTC; michael
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-13 14:24:58

More information about nodiv at CRAN

November 13, 2014 01:12 PM

Journal of Statistical Software

rFerns: An Implementation of the Random Ferns Method for General-Purpose Machine Learning

Vol. 61, Issue 10, Nov 2014

Abstract:

Random ferns is a very simple yet powerful classification method originally introduced for specific computer vision tasks. In this paper, I show that this algorithm may be considered as a constrained decision tree ensemble and use this interpretation to introduce a series of modifications which enable the use of random ferns in general machine learning problems. Moreover, I extend the method with an internal error approximation and an attribute importance measure based on corresponding features of the random forest algorithm. I also present the R package rFerns containing an efficient implementation of this modified version of random ferns.

November 13, 2014 08:00 AM

NPCirc: An R Package for Nonparametric Circular Methods

Vol. 61, Issue 9, Nov 2014

Abstract:

Nonparametric density and regression estimation methods for circular data are included in the R package NPCirc. Specifically, a circular kernel density estimation procedure is provided, jointly with different alternatives for choosing the smoothing parameter. In the regression setting, nonparametric estimation for circular-linear, circular-circular and linear-circular data is also possible via the adaptation of the classical Nadaraya-Watson and local linear estimators. In order to assess the significance of the features observed in the smooth curves, both for density and regression with a circular covariate and a linear response, a SiZer technique is developed for circular data, namely CircSiZer. Some data examples are also included in the package, jointly with a routine that allows generating mixtures of different circular distributions.

November 13, 2014 08:00 AM

OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests

Vol. 61, Issue 8, Nov 2014

Abstract:

Continuous diagnostic tests are often used for discriminating between healthy and diseased populations. For the clinical application of such tests, it is useful to select a cutpoint or discrimination value c that defines positive and negative test results. In general, individuals with a diagnostic test value of c or higher are classified as diseased. Several search strategies have been proposed for choosing optimal cutpoints in diagnostic tests, depending on the underlying reason for this choice. This paper introduces an R package, known as OptimalCutpoints, for selecting optimal cutpoints in diagnostic tests. It incorporates criteria that take the costs of the different diagnostic decisions into account, as well as the prevalence of the target disease and several methods based on measures of diagnostic test accuracy. Moreover, it enables optimal levels to be calculated according to levels of given (categorical) covariates. While the numerical output includes the optimal cutpoint values and associated accuracy measures with their confidence intervals, the graphical output includes the receiver operating characteristic (ROC) and predictive ROC curves. An illustration of the use of OptimalCutpoints is provided, using a real biomedical dataset.

November 13, 2014 08:00 AM

CRANberries

New package megaptera with initial version 1.0-0

Package: megaptera
Type: Package
Title: MEGAPhylogeny Techniques in R
Version: 1.0-0
Date: 2014-10-30
Author: Christoph Heibl
Maintainer: Christoph Heibl
Depends: R (>= 2.10), snowfall, ips
Imports: ape, seqinr, methods, RPostgreSQL, XML
Suggests: knitr
Description: Given a set of taxa and marker, the goal is build a complete and correct sequence alignment for phylogenetic analysis.
License: GPL (>= 2)
VignetteBuilder: knitr
Packaged: 2014-11-13 06:55:15 UTC; stoffi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-13 08:44:56

More information about megaptera at CRAN

November 13, 2014 07:13 AM

New package ega with initial version 1.0.0

Package: ega
Title: Error Grid Analysis
Version: 1.0.0
Authors@R: c( person("Daniel", "Schmolze", email="ega@schmolze.com", role=c("aut", "cre")) )
Maintainer: Daniel Schmolze
Description: Functions for assigning Clarke or Parkes (Consensus) error grid zones to blood glucose values, and for plotting both types of error grids.
Depends: R (>= 2.14.0)
Imports: ggplot2
Suggests: knitr
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Packaged: 2014-11-13 03:06:49 UTC; daniel
Author: Daniel Schmolze [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-13 07:43:13

More information about ega at CRAN

November 13, 2014 07:13 AM

New package bde with initial version 1.0

Package: bde
Type: Package
Title: Bounded Density Estimation
Version: 1.0
Date: 2013-06-19
Author: Guzman Santafe, Borja Calvo, Aritz Perez and Jose A. Lozano
Maintainer: Guzman Santafe
Depends: R (>= 2.0)
Imports: methods,shiny,ggplot2
Description: This package includes S4 classes to deal with different estimators for densities in bounded domains. That is, a collection of different approaches to estimate densities defined within the interval [lower.limit, upper.limit], where lower.limit and upper.limit are values that can be set by the user.
License: GPL-2
LazyData: TRUE
Collate: BoundedDensity.R KernelDensity.R Chen99Kernel.R MicroBetaChen99Kernel.R MacroBetaChen99Kernel.R BoundaryKernel.R NoBoundaryKernel.R NormalizedBoundaryKernel.R Muller91BoundaryKernel.R JonesCorrectionMuller91BoundaryKernel.R Muller94BoundaryKernel.R JonesCorrectionMuller94BoundaryKernel.R BernsteinPolynomials.R Vitale.R BrVitale.R KakizawaB1.R KakizawaB2.R KakizawaB3.R HirukawaJLNKernel.R HirukawaTSKernel.R MacroBetaHirukawaJLNKernel.R MacroBetaHirukawaTSKernel.R utils.R bde.R
Packaged: 2014-11-12 17:42:43 UTC; gsantafe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-13 07:38:50

More information about bde at CRAN

November 13, 2014 07:12 AM

November 12, 2014

CRANberries

New package tufterhandout with initial version 1.2

Package: tufterhandout
Type: Package
Title: Tufte-style html document format for rmarkdown
Version: 1.2
Date: 2014-11-07
Author: Michael Sachs
Maintainer: Michael Sachs
Description: Custom template and output formats for use with rmarkdown. Produce Edward Tufte-style handouts in html formats with full support for rmarkdown features
License: MIT + file LICENSE
URL: http://sachsmc.github.io/tufterhandout
Depends: rmarkdown, knitr
Suggests: ggplot2
VignetteBuilder: knitr
Packaged: 2014-11-12 16:04:09 UTC; sachsmc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-12 18:28:26

More information about tufterhandout at CRAN

November 12, 2014 05:12 PM

November 11, 2014

CRANberries

New package GLDreg with initial version 1.0

Package: GLDreg
Type: Package
Title: Fit GLD Regression Model and GLD Quantile Regression Model to Empirical Data
Version: 1.0
Date: 2014-11-11
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su
Depends: GLDEX (>= 2.0.0.1)
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
License: GPL (>= 3)
Packaged: 2014-11-10 21:54:01 UTC; Steve
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-11 12:23:43

More information about GLDreg at CRAN

November 11, 2014 11:12 AM

November 10, 2014

CRANberries

New package tumblR with initial version 1.0

Package: tumblR
Type: Package
Title: Tumblr API
Version: 1.0
Date: 2014-09-27
Author: Andrea Capozio
Maintainer: Andrea Capozio
Description: This package provides an R-interface to the Tumblr web API (see Tumblr v2 API on https://www.tumblr.com/docs/en/api/v2). Tumblr is a microblogging platform and social networking website (https://www.tumblr.com).
Depends: R (>= 3.0.0), httr (>= 0.4), RCurl (>= 1.95-4.3), ROAuth (>= 0.9.3), stringr (>= 0.6.2), RJSONIO (>= 1.3-0)
License: Artistic-2.0
Collate: 'avatar.R' 'dashboard.R' 'def.postParams.R' 'follow.R' 'followers.R' 'http.connection.R' 'info.blog.R' 'like.post.R' 'likes.R' 'post.R' 'post.delete.R' 'post.edit.R' 'post.reblog.R' 'posts.R' 'posts.draft.R' 'posts.queue.R' 'posts.submission.R' 'tagged.R' 'unfollow.R' 'unlike.post.R' 'user.following.R' 'user.info.R' 'user.likes.R' 'compact.R' 'nonce.R' 'oauth.encode.R' 'oauth.encode1.R' 'sort.names.R'
Packaged: 2014-11-10 20:43:21 UTC; Andrea
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-10 22:46:49

More information about tumblR at CRAN

November 10, 2014 09:12 PM

New package episplineDensity with initial version 0.0-1

Package: episplineDensity
Version: 0.0-1
Date: 2014-11-08
Title: Density Estimation with Soft Information by Exponential Epi-splines
Author: Sam Buttrey, Johannes Royset, and Roger Wets, based on the Matlab code of Royset and Wets
Maintainer: Sam Buttrey
Depends: nloptr, pracma
Description: Produce one-dimensional density estimates using exponential epi-splines. The user may incorporate soft information, by imposing constraints that (i) require unimodality; (ii) require that the density be monotone non-increase or non-decreasing; (iii) put upper bounds on first or second moments; (iv) bound the density's values at mesh points; (v) require that the estimate be continuous or continuously differentiable; and more.
License: GPL-2
Packaged: 2014-11-10 15:51:07 UTC; sebuttre
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-10 18:33:30

More information about episplineDensity at CRAN

November 10, 2014 05:13 PM

New package D2C with initial version 1.0

Package: D2C
Type: Package
Title: Predicting Causal Direction from Dependency Features
Version: 1.0
Date: 2014-06-10
Author: Gianluca Bontempi, Catharina Olsen, Maxime Flauder
Maintainer: Catharina Olsen
Description: The relationship between statistical dependency and causality lies at the heart of all statistical approaches to causal inference. The D2C package implements a supervised machine learning approach to infer the existence of a directed causal link between two variables in multivariate settings with n>2 variables. The approach relies on the asymmetry of some conditional (in)dependence relations between the members of the Markov blankets of two variables causally connected. The D2C algorithm predicts the existence of a direct causal link between two variables in a multivariate setting by (i) creating a set of of features of the relationship based on asymmetric descriptors of the multivariate dependency and (ii) using a classifier to learn a mapping between the features and the presence of a causal link
License: Artistic-2.0
Depends: randomForest
Imports: gRbase, lazy, RBGL, MASS, corpcor, infotheo, methods, Rgraphviz
LazyData: true
Packaged: 2014-11-10 14:36:35 UTC; cat
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-10 18:07:50

More information about D2C at CRAN

November 10, 2014 05:13 PM

Dirk Eddelbuettel

BH release 1.54.0-5

A new release of BH, our package providing Boost headers for use by R is now on CRAN. This release was triggered via a request by Ben Goodrich as noted below who asked for Boost Circular Buffer which RStan uses.

No other changes were made.

Changes in version 1.54.0-5 (2014-11-09)

  • Added Boost Circular Buffer requested by Ben Goodrich for RStan

Courtesy of CRANberries, there is also a diffstat report for the most recent release

Comments and suggestions are welcome via the mailing list or the issue tracker at the GitHubGitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

November 10, 2014 11:52 AM

CRANberries

New package ionflows with initial version 1.1

Package: ionflows
Type: Package
Title: Calculate the Number of Required Flows for Semiconductor Sequencing
Version: 1.1
Date: 2014-10-21
Author: Michael Bockmayr and Jan Budczies
Depends: Biostrings
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: 2014-11-09 23:24:42 UTC; mlb47
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-10 09:55:34

More information about ionflows at CRAN

November 10, 2014 09:13 AM