Wed, 30 Jul 2014

Package glcm updated to version 0.3.2 with previous version 0.3.1 dated 2014-04-24

Title: Calculate textures from grey-level co-occurrence matrices (GLCMs) in R
Description: Enables calculation of image textures derived from grey-level co-occurrence matrices (GLCMs) in R. The texture calculation is coded in C++ to optimize computation time.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff

Diff between glcm versions 0.3.1 dated 2014-04-24 and 0.3.2 dated 2014-07-30

 DESCRIPTION                        |    8 +-
 MD5                                |   24 +++----
 NAMESPACE                          |    2 
 NEWS                               |    6 +
 data/L5TSR_1986.RData              |binary
 man/L5TSR_1986.Rd                  |    6 -
 man/calc_texture.Rd                |   35 +++++-----
 man/expected_textures_3x3_1x1.Rd   |   15 ++--
 man/expected_textures_5x3_n1xn2.Rd |   15 ++--
 man/expected_textures_5x7_2x3.Rd   |   15 ++--
 man/glcm-package.Rd                |    7 +-
 man/glcm.Rd                        |  123 ++++++++++++++++---------------------
 man/test_raster.Rd                 |    4 -
 13 files changed, 127 insertions(+), 133 deletions(-)

More information about glcm at CRAN
Permanent link

Package ExceedanceTools updated to version 1.2.2 with previous version 1.2.0 dated 2014-07-08

Title: Confidence regions for exceedance sets and contour lines
Description: Tools for constructing confidence regions for exceedance regions and contour lines.
Author: Joshua French
Maintainer: Joshua French

Diff between ExceedanceTools versions 1.2.0 dated 2014-07-08 and 1.2.2 dated 2014-07-30

 ExceedanceTools-1.2.0/ExceedanceTools/NEWS           |only
 ExceedanceTools-1.2.0/ExceedanceTools/R/confreg.R    |only
 ExceedanceTools-1.2.0/ExceedanceTools/man/confreg.Rd |only
 ExceedanceTools-1.2.2/ExceedanceTools/DESCRIPTION    |   10 +++++-----
 ExceedanceTools-1.2.2/ExceedanceTools/MD5            |    7 ++-----
 ExceedanceTools-1.2.2/ExceedanceTools/NAMESPACE      |    2 --
 6 files changed, 7 insertions(+), 12 deletions(-)

More information about ExceedanceTools at CRAN
Permanent link

New package DDIwR with initial version 0.1-0
Package: DDIwR
Version: 0.1-0
Date: 2014-07-30
Title: DDI related functions
Authors@R: c(person("Adrian", "Dusa", role = c("aut", "cre"), email = "dusa.adrian@unibuc.ro"))
Depends: R (>= 3.0.0)
Imports: XML, foreign
Description: This package provides useful functions for various DDI (Data Documentation Initiative) related outputs.
License: GPL (>= 2)
Packaged: 2014-07-30 18:13:41 UTC; dusadrian
Author: Adrian Dusa [aut, cre]
Maintainer: Adrian Dusa
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 22:02:08

More information about DDIwR at CRAN
Permanent link

Package metafor updated to version 1.9-4 with previous version 1.9-3 dated 2014-05-05

Title: Meta-Analysis Package for R
Description: The metafor package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer

Diff between metafor versions 1.9-3 dated 2014-05-05 and 1.9-4 dated 2014-07-30

 metafor-1.9-3/metafor/inst/doc/metafor.Rnw                                 |only
 metafor-1.9-3/metafor/inst/doc/metafor_diagram.Rnw                         |only
 metafor-1.9-3/metafor/tests/testthat/test_rma.mh_vs_metan_dat.bcg.r        |only
 metafor-1.9-3/metafor/tests/testthat/test_rma.peto_vs_metan_dat.bcg.r      |only
 metafor-1.9-3/metafor/tests/testthat/test_rma.uni_vs_metan_dat.bcg.r       |only
 metafor-1.9-3/metafor/vignettes/incl                                       |only
 metafor-1.9-3/metafor/vignettes/metafor.Rnw                                |only
 metafor-1.9-3/metafor/vignettes/metafor_diagram.Rnw                        |only
 metafor-1.9-4/metafor/DESCRIPTION                                          |   19 
 metafor-1.9-4/metafor/MD5                                                  |   83 
 metafor-1.9-4/metafor/NAMESPACE                                            |    3 
 metafor-1.9-4/metafor/NEWS                                                 |   76 
 metafor-1.9-4/metafor/R/metafor.R                                          | 1597 ++++++----
 metafor-1.9-4/metafor/build/vignette.rds                                   |binary
 metafor-1.9-4/metafor/data/dat.bourassa1996.rda                            |only
 metafor-1.9-4/metafor/data/dat.riley2003.rda                               |only
 metafor-1.9-4/metafor/inst/doc/metafor.pdf.asis                            |only
 metafor-1.9-4/metafor/inst/doc/metafor_diagram.pdf.asis                    |only
 metafor-1.9-4/metafor/man/addpoly.default.Rd                               |    6 
 metafor-1.9-4/metafor/man/addpoly.rma.Rd                                   |    6 
 metafor-1.9-4/metafor/man/confint.rma.Rd                                   |   23 
 metafor-1.9-4/metafor/man/cumul.Rd                                         |    2 
 metafor-1.9-4/metafor/man/dat.bourassa1996.Rd                              |only
 metafor-1.9-4/metafor/man/dat.fine1993.Rd                                  |    2 
 metafor-1.9-4/metafor/man/dat.hasselblad1998.Rd                            |    2 
 metafor-1.9-4/metafor/man/dat.konstantopoulos2011.Rd                       |   18 
 metafor-1.9-4/metafor/man/dat.riley2003.Rd                                 |only
 metafor-1.9-4/metafor/man/forest.cumul.rma.Rd                              |    6 
 metafor-1.9-4/metafor/man/forest.default.Rd                                |    8 
 metafor-1.9-4/metafor/man/forest.rma.Rd                                    |    8 
 metafor-1.9-4/metafor/man/funnel.Rd                                        |    4 
 metafor-1.9-4/metafor/man/labbe.Rd                                         |    4 
 metafor-1.9-4/metafor/man/metafor-package.Rd                               |   10 
 metafor-1.9-4/metafor/man/plot.cumul.rma.Rd                                |only
 metafor-1.9-4/metafor/man/predict.rma.Rd                                   |    6 
 metafor-1.9-4/metafor/man/print.escalc.Rd                                  |    4 
 metafor-1.9-4/metafor/man/print.rma.uni.Rd                                 |    4 
 metafor-1.9-4/metafor/man/radial.Rd                                        |    4 
 metafor-1.9-4/metafor/man/replmiss.Rd                                      |only
 metafor-1.9-4/metafor/man/rma.glmm.Rd                                      |    8 
 metafor-1.9-4/metafor/man/rma.mh.Rd                                        |    4 
 metafor-1.9-4/metafor/man/rma.mv.Rd                                        |   12 
 metafor-1.9-4/metafor/man/rma.peto.Rd                                      |    4 
 metafor-1.9-4/metafor/man/rma.uni.Rd                                       |   25 
 metafor-1.9-4/metafor/man/trimfill.Rd                                      |    4 
 metafor-1.9-4/metafor/man/weights.rma.Rd                                   |    4 
 metafor-1.9-4/metafor/tests/testthat/test_metan_vs_rma.mh_with_dat.bcg.r   |only
 metafor-1.9-4/metafor/tests/testthat/test_metan_vs_rma.peto_with_dat.bcg.r |only
 metafor-1.9-4/metafor/tests/testthat/test_metan_vs_rma.uni_with_dat.bcg.r  |only
 metafor-1.9-4/metafor/tests/testthat/test_regression_with_rma.r            |only
 metafor-1.9-4/metafor/tests/testthat/test_rma_vs_direct_computation.r      |only
 metafor-1.9-4/metafor/tests/testthat/test_rma_vs_lm_and_lme.r              |only
 metafor-1.9-4/metafor/vignettes/metafor.pdf.asis                           |only
 metafor-1.9-4/metafor/vignettes/metafor_diagram.pdf.asis                   |only
 54 files changed, 1222 insertions(+), 734 deletions(-)

More information about metafor at CRAN
Permanent link

New package tmap with initial version 0.6
Package: tmap
Maintainer: Martijn Tennekes
License: GPL-3
Title: Thematic Maps
Type: Package
LazyLoad: yes
Author: Martijn Tennekes
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, way to create all kinds of thematic maps, such as choropleths and bubble maps.
Version: 0.6
Date: 2014-06-30
Depends: R (>= 3.0)
Imports: rgeos, grid, gridBase, sp, rgdal, classInt, RColorBrewer, igraph, fields, vegan
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-07-30 15:47:53 UTC; vt
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 18:25:21

More information about tmap at CRAN
Permanent link

Package miceadds updated to version 0.14-9 with previous version 0.13-7 dated 2014-06-27

Title: Some additional multiple imputation functions, especially for mice
Description: The package miceadds contains some auxiliary functions for multiple imputation which complements existing functionality in R. In addition to some utility functions, main features include plausible value imputation, multilevel imputation functions, imputation using partial least squares (PLS) for high dimensional predictors and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch

Diff between miceadds versions 0.13-7 dated 2014-06-27 and 0.14-9 dated 2014-07-30

 DESCRIPTION                  |   10 ++--
 MD5                          |   24 ++++++----
 NAMESPACE                    |    7 ++-
 R/Rutils.R                   |   10 ++++
 R/load.data.R                |only
 R/mi.anova.R                 |   97 ++++++++++++++++++++++++++++++++++++-------
 R/save.data.R                |only
 R/write.pspp.R               |    1 
 inst/NEWS                    |   35 +++++++++++----
 man/load.Rdata.Rd            |   30 +++++++++++--
 man/load.data.Rd             |only
 man/mi.anova.Rd              |   38 +++++++++-------
 man/miceadds-package.Rd      |    2 
 man/save.data.Rd             |only
 man/write.mice.imputation.Rd |    2 
 15 files changed, 193 insertions(+), 63 deletions(-)

More information about miceadds at CRAN
Permanent link

Package GetoptLong updated to version 0.0.5 with previous version 0.0.4 dated 2014-06-17

Title: Parse 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 0.0.4 dated 2014-06-17 and 0.0.5 dated 2014-07-30

 DESCRIPTION                          |    8 +-
 MD5                                  |   20 +++--
 NEWS                                 |    8 ++
 R/GetoptLong.R                       |  117 +++++++++++++++++++++--------------
 R/zzz.R                              |only
 inst/doc/GetoptLong.pdf              |binary
 inst/doc/variable_interpolation.R    |    2 
 inst/doc/variable_interpolation.Rnw  |    2 
 inst/doc/variable_interpolation.pdf  |binary
 inst/tests/test.R                    |only
 inst/tests/test_GetoptLong.R         |    7 ++
 vignettes/variable_interpolation.Rnw |    2 
 12 files changed, 106 insertions(+), 60 deletions(-)

More information about GetoptLong at CRAN
Permanent link

Package codep updated to version 0.4-1 with previous version 0.2-2 dated 2013-09-05

Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional feature.
Author: Guillaume Guenard and Pierre Legendre, with contributions from Bertrand Pages
Maintainer: Guillaume Guenard

Diff between codep versions 0.2-2 dated 2013-09-05 and 0.4-1 dated 2014-07-30

 DESCRIPTION          |    8 
 MD5                  |   16 -
 NAMESPACE            |    2 
 R/eigenmap.R         |  135 ++++++++++---
 R/gcd.R              |only
 man/codep-package.Rd |    6 
 man/eigenmap.Rd      |  192 +++++++++++++------
 man/gcd.Rd           |only
 man/mca.Rd           |    4 
 src/permut.c         |  499 ++++++++++++++++++++++++---------------------------
 10 files changed, 492 insertions(+), 370 deletions(-)

More information about codep at CRAN
Permanent link

Package arulesNBMiner updated to version 0.1-4 with previous version 0.1-2 dated 2012-03-19

Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Description: NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets presented in "Michael Hahsler. A model-based frequency constraint for mining associations from transaction data. Data Mining and Knowledge Discovery, 13(2):137-166, September 2006." In addition an extension for NB-precise rules is implemented.
Author: Michael Hahsler
Maintainer: Michael Hahsler

Diff between arulesNBMiner versions 0.1-2 dated 2012-03-19 and 0.1-4 dated 2014-07-30

 arulesNBMiner-0.1-2/arulesNBMiner/java/Association.class         |only
 arulesNBMiner-0.1-2/arulesNBMiner/java/Itemset.class             |only
 arulesNBMiner-0.1-2/arulesNBMiner/java/NBMiner.class             |only
 arulesNBMiner-0.1-2/arulesNBMiner/java/R_result.class            |only
 arulesNBMiner-0.1-2/arulesNBMiner/java/Rule.class                |only
 arulesNBMiner-0.1-2/arulesNBMiner/java/SparseSetOfItemsets.class |only
 arulesNBMiner-0.1-2/arulesNBMiner/java/arulesNBMiner.jar         |only
 arulesNBMiner-0.1-4/arulesNBMiner/DESCRIPTION                    |   26 +++++-----
 arulesNBMiner-0.1-4/arulesNBMiner/MD5                            |   21 ++------
 arulesNBMiner-0.1-4/arulesNBMiner/NAMESPACE                      |    2 
 arulesNBMiner-0.1-4/arulesNBMiner/R/NBMinerParameters.R          |   26 ++++++----
 arulesNBMiner-0.1-4/arulesNBMiner/data/Agrawal.rda               |binary
 arulesNBMiner-0.1-4/arulesNBMiner/inst/java/arulesNBMiner.jar    |binary
 arulesNBMiner-0.1-4/arulesNBMiner/java/Makefile                  |    8 +--
 arulesNBMiner-0.1-4/arulesNBMiner/man/NBMinerParameters.Rd       |    2 
 15 files changed, 47 insertions(+), 38 deletions(-)

More information about arulesNBMiner at CRAN
Permanent link

Package twostageTE updated to version 1.01 with previous version 1.0 dated 2013-05-24

Title: Two-Stage Threshold Estimation
Description: Implements a variety of nonparametric methods for computing one-stage and two-stage confidence intervals, as well as point estimates of threshold values.
Author: Shawn Mankad, George Michailidis, Moulinath Banerjee
Maintainer: Shawn Mankad

Diff between twostageTE versions 1.0 dated 2013-05-24 and 1.01 dated 2014-07-30

 DESCRIPTION                                    |   14 ++--
 MD5                                            |   30 +++++-----
 R/estimateDeriv.R                              |   74 ++++++++++++-------------
 R/estimateSigmaSq.R                            |   31 ++++++----
 R/likelihoodConfidenceInterval.R               |   54 +++++++++---------
 R/linearBootstrapConfidenceInterval_stageTwo.R |   28 ++++-----
 R/pava.R                                       |   72 ++++++++++++------------
 R/plot.twostageTE.R                            |    6 +-
 R/print.twostageTE.R                           |    4 -
 R/stageOneAnalysis.R                           |   14 ++--
 R/stageTwoAnalysis.R                           |   28 ++++-----
 R/summary.twostageTE.R                         |    8 +-
 R/threshold_estimate_ir.R                      |   30 +++++-----
 R/threshold_estimate_locLinear.R               |   12 ++--
 R/waldConfidenceInterval_ir_stageOne.R         |   28 ++++-----
 R/waldConfidenceInterval_ir_stageTwo.R         |   34 +++++------
 16 files changed, 237 insertions(+), 230 deletions(-)

More information about twostageTE at CRAN
Permanent link

Package Surrogate updated to version 0.1-2 with previous version 0.1-1 dated 2014-05-11

Title: Evaluation of surrogate endpoints in clinical trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst

Diff between Surrogate versions 0.1-1 dated 2014-05-11 and 0.1-2 dated 2014-07-30

 DESCRIPTION                           |   10 +++----
 MD5                                   |   45 ++++++++++++++++++++++------------
 NEWS                                  |    5 +++
 R/BifixedContCont.R                   |    3 +-
 R/FixedContContIT.r                   |    5 +++
 R/ICABinBin.R                         |only
 R/MarginalProbs.R                     |only
 R/MixedContContIT.R                   |    2 -
 R/RandVec.R                           |only
 R/SimDataCounterfactualsBinBin.R      |only
 R/SimDataSTSBinBin.R                  |only
 R/minSurrBinBin.R                     |only
 R/plot.InfoTheoretic.R                |    1 
 R/plot_ICABinBin.R                    |only
 R/summary_ICABinBin.R                 |only
 man/ARMD.Rd                           |    2 -
 man/FixedContContIT.Rd                |    3 +-
 man/ICABinBin.Rd                      |only
 man/ICAContCont.Rd                    |    5 ++-
 man/MICAContCont.Rd                   |    6 +++-
 man/MarginalProbs.Rd                  |only
 man/MinSurrBinBin.Rd                  |only
 man/MinSurrContCont.Rd                |    2 -
 man/MixedContContIT.Rd                |    4 ---
 man/RandVec.Rd                        |only
 man/Sim.Data.Counterfactuals.Rd       |    5 ++-
 man/Sim.Data.CounterfactualsBinBin.Rd |only
 man/Sim.Data.STSBinBin.Rd             |only
 man/plot.CausalInference.Rd           |    6 ++--
 man/plot.ICABinBin.Rd                 |only
 man/summary.gen.Rd                    |    4 +++
 31 files changed, 69 insertions(+), 39 deletions(-)

More information about Surrogate at CRAN
Permanent link

Package CRF updated to version 0.3-8 with previous version 0.3-7 dated 2014-05-06

Title: CRF - Conditional Random Fields
Description: This package implements modeling and computational tools for conditional random fields model (CRF) as well as other probabilistic undirected graphical models of discrete data with pairwise and unary potentials.
Author: Ling-Yun Wu [aut, cre]
Maintainer: Ling-Yun Wu

Diff between CRF versions 0.3-7 dated 2014-05-06 and 0.3-8 dated 2014-07-30

 DESCRIPTION               |   14 +--
 MD5                       |  126 ++++++++++++++++-----------------
 NAMESPACE                 |    2 
 data/Chain.RData          |binary
 data/Clique.RData         |binary
 data/Loop.RData           |binary
 data/Rain.RData           |binary
 data/Small.RData          |binary
 data/Tree.RData           |binary
 man/CRF-package.Rd        |  171 ++++++++++++++++++----------------------------
 man/Chain.Rd              |    1 
 man/Clique.Rd             |    1 
 man/Loop.Rd               |    1 
 man/Rain.Rd               |    7 -
 man/Small.Rd              |    1 
 man/Tree.Rd               |    1 
 man/clamp.crf.Rd          |   33 ++++----
 man/clamp.reset.Rd        |   15 +---
 man/crf.nll.Rd            |   44 +++++------
 man/crf.update.Rd         |   69 ++++++++----------
 man/decode.block.Rd       |   23 ++----
 man/decode.chain.Rd       |    9 +-
 man/decode.conditional.Rd |   17 +---
 man/decode.cutset.Rd      |   18 +---
 man/decode.exact.Rd       |    6 -
 man/decode.greedy.Rd      |   12 +--
 man/decode.icm.Rd         |   15 +---
 man/decode.ilp.Rd         |   12 +--
 man/decode.junction.Rd    |    9 +-
 man/decode.lbp.Rd         |   18 +---
 man/decode.marginal.Rd    |   13 +--
 man/decode.sample.Rd      |   13 +--
 man/decode.trbp.Rd        |   18 +---
 man/decode.tree.Rd        |    9 +-
 man/duplicate.crf.Rd      |   10 +-
 man/get.logPotential.Rd   |   16 +---
 man/get.potential.Rd      |   13 +--
 man/infer.chain.Rd        |   18 +---
 man/infer.conditional.Rd  |   26 ++----
 man/infer.cutset.Rd       |   24 ++----
 man/infer.exact.Rd        |   15 +---
 man/infer.junction.Rd     |   18 +---
 man/infer.lbp.Rd          |   27 ++-----
 man/infer.sample.Rd       |   22 ++---
 man/infer.trbp.Rd         |   27 ++-----
 man/infer.tree.Rd         |   18 +---
 man/make.crf.Rd           |   74 ++++++++-----------
 man/make.features.Rd      |   46 +++++-------
 man/make.par.Rd           |   17 +---
 man/mrf.nll.Rd            |   32 +++-----
 man/mrf.stat.Rd           |   17 ++--
 man/mrf.update.Rd         |    9 +-
 man/sample.chain.Rd       |   13 +--
 man/sample.conditional.Rd |   21 ++---
 man/sample.cutset.Rd      |   19 ++---
 man/sample.exact.Rd       |   13 +--
 man/sample.gibbs.Rd       |   15 +---
 man/sample.junction.Rd    |   13 +--
 man/sample.tree.Rd        |   13 +--
 man/sub.crf.Rd            |   27 +++----
 man/train.crf.Rd          |   38 ++++------
 man/train.mrf.Rd          |   24 ++----
 src/JunctionTree.cpp      |    2 
 src/misc.h                |    3 
 64 files changed, 570 insertions(+), 738 deletions(-)

More information about CRF at CRAN
Permanent link

Package BLCOP updated to version 0.2.8 with previous version 0.2.7 dated 2014-01-07

Title: Black-Litterman and copula-opinion pooling frameworks
Description: An implementation of the Black-Litterman Model and Atilio Meucci's copula opinion pooling framework. This should be regarded as a beta release.
Author: Francisco Gochez
Maintainer: Mango Solutions

Diff between BLCOP versions 0.2.7 dated 2014-01-07 and 0.2.8 dated 2014-07-30

 DESCRIPTION                   |    8 ++++----
 MD5                           |   13 +++++++------
 NAMESPACE                     |    3 ++-
 NEWS                          |    3 +++
 build/vignette.rds            |binary
 inst/RUnit/runit.buildviews.R |    2 +-
 inst/doc/BLCOP.pdf            |binary
 inst/doc/BlackLitterman.pdf   |only
 8 files changed, 17 insertions(+), 12 deletions(-)

More information about BLCOP at CRAN
Permanent link

Package btf updated to version 1.1 with previous version 1.0 dated 2014-07-15

Title: Estimates univariate function via Bayesian trend filtering
Description: Trend filtering uses the generalized lasso framework to fit an adaptive polynomial of degree k to estimate the function f_0 at each input x_i in the model: y_i = f_0(x_i) + epsilon_i, for i = 1, ..., n, and epsilon_i is sub-Gaussian with E(epsilon_i) = 0. Bayesian trend filtering adapts the genlasso framework to a fully Bayesian hierarchical model, estimating the penalty parameter lambda within a tractable Gibbs sampler.
Author: Edward A. Roualdes
Maintainer: Edward A. Roualdes

Diff between btf versions 1.0 dated 2014-07-15 and 1.1 dated 2014-07-30

 DESCRIPTION |   10 +++++-----
 MD5         |    4 ++--
 R/btf.R     |    9 +++++++--
 3 files changed, 14 insertions(+), 9 deletions(-)

More information about btf at CRAN
Permanent link

Package mwa updated to version 0.3.2 with previous version 0.3.1 dated 2014-06-15

Title: MWA package for causal inference in spatiotemporal event data
Description: MWA grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte

Diff between mwa versions 0.3.1 dated 2014-06-15 and 0.3.2 dated 2014-07-30

 DESCRIPTION                   |    8 +--
 MD5                           |    8 +--
 R/mwa.R                       |  100 ++++++++++++++++++++++++++++++++----------
 inst/java/WakeCounter.jar     |binary
 inst/javasrc/WakeCounter.java |    2 
 5 files changed, 87 insertions(+), 31 deletions(-)

More information about mwa at CRAN
Permanent link

Package SSDforR updated to version 1.4.6 with previous version 1.4.5 dated 2014-06-20

Title: SSD for R to analyze single system data
Description: Package to visually and statistically analyze single system data
Author: Charles Auerbach,PHD Wendy Zeitlin Schudrich,PHD Wurzweiler School of Social Work
Maintainer: Charles Auerbach

Diff between SSDforR versions 1.4.5 dated 2014-06-20 and 1.4.6 dated 2014-07-30

 SSDforR-1.4.5/SSDforR/R/abautoacf.r  |only
 SSDforR-1.4.5/SSDforR/R/abautopacf.r |only
 SSDforR-1.4.5/SSDforR/R/arimadiff.r  |only
 SSDforR-1.4.5/SSDforR/R/arimama.r    |only
 SSDforR-1.4.6/SSDforR/DESCRIPTION    |    6 +++---
 SSDforR-1.4.6/SSDforR/MD5            |   12 ++++++------
 SSDforR-1.4.6/SSDforR/R/ABautoacf.R  |only
 SSDforR-1.4.6/SSDforR/R/ABautopacf.R |only
 SSDforR-1.4.6/SSDforR/R/Arimadiff.R  |only
 SSDforR-1.4.6/SSDforR/R/Arimama.R    |only
 SSDforR-1.4.6/SSDforR/R/Effectsize.R |   35 +++++++++++++++++++++++------------
 11 files changed, 32 insertions(+), 21 deletions(-)

More information about SSDforR at CRAN
Permanent link

Package RbioRXN updated to version 1.3.1 with previous version 1.3 dated 2014-06-17

Title: RbioRXN - process Rhea, KEGG, MetaCyc, Unipathway biochemical reaction data
Description: RbioRXN is an R package that facilitates retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway. The package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min

Diff between RbioRXN versions 1.3 dated 2014-06-17 and 1.3.1 dated 2014-07-30

 DESCRIPTION                   |    8 
 MD5                           |   10 
 R/instantiate.rhea.R          |  534 +++++++++++++++++++++---------------------
 data/example.rda              |binary
 man/RbioRXN-package.Rd        |    4 
 man/parse.metacyc.compound.Rd |    9 
 6 files changed, 289 insertions(+), 276 deletions(-)

More information about RbioRXN at CRAN
Permanent link

New package extlasso with initial version 0.1
Package: extlasso
Type: Package
Title: Maximum penalized likelihood estimation with extended lasso penalty
Version: 0.1
Date: 2014-26-06
Author: B N Mandal and Jun Ma
Maintainer: B N Mandal
Depends: R (>= 3.1.1)
Description: The package estimates coefficients of extended LASSO penalized linear regression and generalized linear models. Currently lasso and elastic net penalized linear regression and generalized linear models are considered. The package currently utilizes an accurate approximation of L1 penalty and then a modified Jacobi algorithm to estimate the coefficients. There is provision for plotting of the solutions and predictions of coefficients at given values of lambda. The package also contains functions for cross validation to select a suitable lambda value given the data. The package also provides a function for estimation in fused lasso penalized linear regression.
License: GPL (>= 2)
Packaged: 2014-07-30 05:44:05 UTC; User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 07:58:08

More information about extlasso at CRAN
Permanent link

Package Rdrools (with last version 0.0.2) was removed from CRAN

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

2011-11-29 0.0.2
2011-11-26 0.0.1

Permanent link
Package Rdroolsjars (with last version 0.0.1) was removed from CRAN

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

2011-11-26 0.0.1

Permanent link
Package swirl updated to version 2.2.14 with previous version 2.2.9 dated 2014-05-30

Title: Learn R, in R.
Description: swirl turns the R console into an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.
Author: Nick Carchedi [aut, cre], Bill Bauer [aut], Gina Grdina [aut], Sean Kross [aut]
Maintainer: Nick Carchedi

Diff between swirl versions 2.2.9 dated 2014-05-30 and 2.2.14 dated 2014-07-30

 DESCRIPTION                        |   10 +-
 MD5                                |   81 ++++++++--------
 NAMESPACE                          |    6 +
 R/answerTests2.R                   |   16 ++-
 R/email_info.R                     |only
 R/install_course.R                 |   59 +++++++++++-
 R/instructionSet.R                 |   80 +++++++++++++---
 R/menu.R                           |   40 ++++++--
 R/parse_content.R                  |    3 
 R/phrases.R                        |   74 +++++++++------
 R/progress.R                       |    2 
 R/swirl.R                          |  181 +++++++++++++++++++++++++++++--------
 R/utilities.R                      |   34 ++++++
 man/AnswerTests.Rd                 |    4 
 man/InstallCourses.Rd              |only
 man/any_of_exprs.Rd                |   14 +-
 man/bye.Rd                         |    2 
 man/email_admin.Rd                 |only
 man/expr_creates_var.Rd            |    2 
 man/expr_identical_to.Rd           |    2 
 man/expr_is_a.Rd                   |    2 
 man/expr_uses_func.Rd              |    2 
 man/func_of_newvar_equals.Rd       |    2 
 man/info.Rd                        |    2 
 man/install_course_directory.Rd    |   12 ++
 man/install_course_dropbox.Rd      |   12 ++
 man/install_course_github.Rd       |   12 ++
 man/install_course_google_drive.Rd |   12 ++
 man/install_course_url.Rd          |   12 ++
 man/install_course_zip.Rd          |   12 ++
 man/install_from_swirl.Rd          |   25 ++++-
 man/main.Rd                        |    2 
 man/nxt.Rd                         |    2 
 man/omnitest.Rd                    |    2 
 man/play.Rd                        |    2 
 man/reset.Rd                       |only
 man/skip.Rd                        |    2 
 man/submit.Rd                      |only
 man/swirl.Rd                       |    2 
 man/uninstall_course.Rd            |   13 ++
 man/val_has_length.Rd              |    2 
 man/val_matches.Rd                 |    2 
 man/var_is_a.Rd                    |    2 
 man/zip_course.Rd                  |   13 ++
 44 files changed, 583 insertions(+), 176 deletions(-)

More information about swirl at CRAN
Permanent link

New package rareGE with initial version 0.1
Package: rareGE
Type: Package
Title: Testing Gene-Environment Interaction for Rare Genetic Variants
Version: 0.1
Date: 2014-07-28
Author: Han Chen
Maintainer: Han Chen
Description: Tests gene-environment interaction for rare genetic variants using Sequence Kernel Association Test (SKAT) type gene-based tests. Includes two tests for the interaction term only, and one joint test for genetic main effects and gene-environment interaction.
License: GPL-3
Imports: MASS, nlme, survey
URL: http://www.hsph.harvard.edu/han-chen/
Packaged: 2014-07-29 19:59:09 UTC; hanchen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 06:57:34

More information about rareGE at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.