Sat, 30 Aug 2014

Package survivalMPL updated to version 0.1.1 with previous version 0.1.0 dated 2014-04-03

Title: Penalised Maximum Likelihood for Survival Analysis Models
Description: Estimate the regression coefficients and the baseline hazard of proportional hazard Cox models using maximum penalised likelihood. A 'non-parametric' smooth estimate of the baseline hazard function is provided.
Author: Dominique-Laurent Couturier, Jun Ma, Stephane Heritier.
Maintainer: Dominique-Laurent Couturier

Diff between survivalMPL versions 0.1.0 dated 2014-04-03 and 0.1.1 dated 2014-08-30

 DESCRIPTION                |   10 +++++-----
 MD5                        |    6 +++---
 R/coxph.r                  |    2 +-
 man/survivalMPL-package.Rd |    2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

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Package nsRFA updated to version 0.7-12 with previous version 0.7-11 dated 2013-12-16

Title: Non-supervised Regional Frequency Analysis
Description: A collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology. The package refers to the index-value method and, more precisely, helps the hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions with similar growth curves; (3) fit distribution functions to the empirical regional growth curves.
Author: Alberto Viglione [aut, cre], Jonathan R. M. Hosking [ctb], Francesco Laio [ctb], Alan Miller [ctb], Eric Gaume [ctb], Olivier Payrastre [ctb], Jose Luis Salinas [ctb], Chi Cong N'guyen [ctb], Karine Halbert [ctb]
Maintainer: Alberto Viglione

Diff between nsRFA versions 0.7-11 dated 2013-12-16 and 0.7-12 dated 2014-08-30

 DESCRIPTION                        |   22 
 MD5                                |   29 
 R/BayesianMCMC.R                   | 2906 ++++++++++++++++++-------------------
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 19 files changed, 1591 insertions(+), 1500 deletions(-)

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Package jvmr updated to version 2.11.2.1 with previous version 2.11.1.1 dated 2014-06-25

Title: Integration of R, Java, and Scala
Description: Cross-platform, self-contained, and bi-directional interface between R and Scala, Java, and other JVM-based languages.
Author: David B. Dahl [aut, cre], Scala developers [ctb] (see http://scala-lang.org/), beanshell2 developers [ctb] (see https://code.google.com/p/beanshell2/), jline2 developers [ctb] (see https://github.com/jline/jline2)
Maintainer: David B. Dahl

Diff between jvmr versions 2.11.1.1 dated 2014-06-25 and 2.11.2.1 dated 2014-08-30

 jvmr-2.11.1.1/jvmr/inst/COPYRIGHT                                        |only
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 jvmr-2.11.2.1/jvmr/MD5                                                   |   23 +++----
 jvmr-2.11.2.1/jvmr/NAMESPACE                                             |    6 ++
 jvmr-2.11.2.1/jvmr/NEWS                                                  |   11 +++
 jvmr-2.11.2.1/jvmr/R/main.R                                              |   29 ++++++----
 jvmr-2.11.2.1/jvmr/R/onLoad.R                                            |    4 -
 jvmr-2.11.2.1/jvmr/R/version.R                                           |    2 
 jvmr-2.11.2.1/jvmr/R/zzz.R                                               |   11 +++
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 jvmr-2.11.2.1/jvmr/java                                                  |only
 12 files changed, 66 insertions(+), 34 deletions(-)

More information about jvmr at CRAN
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Package frailtypack updated to version 2.7 with previous version 2.6.1 dated 2014-07-23

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

Diff between frailtypack versions 2.6.1 dated 2014-07-23 and 2.7 dated 2014-08-30

 DESCRIPTION                        |   40 
 MD5                                |  187 ++--
 NEWS                               |   11 
 R/Cmeasures.R                      |    2 
 R/additivePenal.R                  |  132 +--
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 R/plot.nestedPenal.additivePenal.R |   74 +
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 R/print.frailtyPenal.R             |   18 
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 R/survival.R                       |  109 +-
 demo/frailtypack_additivePenal.R   |    6 
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 demo/frailtypack_jointPenal.R      |   41 
 demo/frailtypack_nestedPenal.R     |   14 
 man/Cmeasures.Rd                   |    6 
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 src/funcpaMultivCpm.f90            |  132 +--
 src/funcpaMultivSplines.f90        |  297 +++----
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 src/funcpajsplines.f90             |  204 ++--
 src/funcpajsplines_intcens.f90     |    4 
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 src/funcpas_tps.f90                |    4 
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 src/funcpasweib_log.f90            |  113 --
 src/joint.f90                      |  211 ++---
 src/multiveJoint.f90               |   44 -
 src/nested.f90                     |   19 
 src/risque.f90                     |   60 +
 src/survival.f90                   |  246 +++++
 95 files changed, 4826 insertions(+), 4263 deletions(-)

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Package Peptides updated to version 1.0 with previous version 0.4 dated 2014-03-26

Title: Calculate indices and theoretical physicochemical properties of peptides and protein sequences
Description: Calculate physicochemical properties and indices from aminoacid sequences of peptides and proteins. Include also utilities for read and plot GROMACS output files .XVG.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio

Diff between Peptides versions 0.4 dated 2014-03-26 and 1.0 dated 2014-08-30

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 46 files changed, 590 insertions(+), 386 deletions(-)

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Package parsedate updated to version 1.0.3 with previous version 1.0.2 dated 2014-08-28

Title: Recognize and parse dates in various formats, including all ISO 8601 formats
Description: Parse dates automatically, without the need of specifying a format. Currently it includes the git date parser. It can also recognize and parse all ISO 8601 formats.
Author: Gabor Csardi, Linus Torvalds
Maintainer: Gabor Csardi

Diff between parsedate versions 1.0.2 dated 2014-08-28 and 1.0.3 dated 2014-08-30

 DESCRIPTION           |    6 +++---
 MD5                   |    6 +++---
 R/parsedate-package.r |    3 +--
 tests/testthat.R      |    4 +++-
 4 files changed, 10 insertions(+), 9 deletions(-)

More information about parsedate at CRAN
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New package archivist with initial version 1.0
Package: archivist
Version: 1.0
Type: Package
Title: Tools for storing, restoring and searching for R objects
Authors@R: c( person("Przemyslaw", "Biecek", role = c("aut", "cre"), email = "przemyslaw.biecek@gmail.com"), person("Marcin", "Kosinski", role = c("aut"), email = "m.p.kosinski@gmail.com") )
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Repository: CRAN
License: GPL-2
LazyLoad: yes
LazyData: yes
Depends: R (>= 3.0.0), RSQLite, DBI, lubridate, jsonlite
Imports: RCurl, digest, httr
BugReports: https://github.com/pbiecek/archivist/issues
Packaged: 2014-08-30 18:30:21 UTC; pbiecek
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek
NeedsCompilation: no
Date/Publication: 2014-08-30 23:00:41

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Package sirt updated to version 0.47-36 with previous version 0.46-15 dated 2014-08-05

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch

Diff between sirt versions 0.46-15 dated 2014-08-05 and 0.47-36 dated 2014-08-30

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 sirt-0.47-36/sirt/man/polychoric2.Rd                          |    2 
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 sirt-0.47-36/sirt/man/rasch.mirtlc.Rd                         |  178 ++
 sirt-0.47-36/sirt/man/rasch.mml.Rd                            |   21 
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 sirt-0.47-36/sirt/man/rasch.pml.Rd                            |   10 
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 sirt-0.47-36/sirt/man/smirt.Rd                                |    3 
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 sirt-0.47-36/sirt/man/yen.q3.Rd                               |   20 
 74 files changed, 2302 insertions(+), 1139 deletions(-)

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Package PopGenome updated to version 2.0.9 with previous version 2.0.8 dated 2014-07-31

Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: PopGenome is an R-package for Population Genetic & Genomic Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer

Diff between PopGenome versions 2.0.8 dated 2014-07-31 and 2.0.9 dated 2014-08-30

 DESCRIPTION                                           |    8 
 MD5                                                   |   43 ++---
 NEWS                                                  |   13 +
 R/PopGplot.R                                          |    4 
 R/Whop_readVCF.R                                      |   26 +--
 R/concatenate.R                                       |   24 +-
 R/fstcalc.R                                           |    4 
 R/get_gff_info.R                                      |   18 +-
 R/get_segsites.R                                      |    2 
 R/linkdisequ_FAST.R                                   |   18 +-
 R/readData.R                                          |   43 +++--
 R/readVCF.R                                           |  152 ++++++++++++++----
 R/set.synnonsyn.R                                     |   17 +-
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 R/splitting.data.R                                    |    5 
 inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary
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 man/PopGplot.Rd                                       |    4 
 man/Whop_readVCF.Rd                                   |    2 
 man/readVCF.Rd                                        |    9 -
 src/find_lines.c                                      |  101 +++++++++++
 src/myReadVCFC.c                                      |  103 ++++++++++--
 src/whopgenome/whopgen_codemat.cpp                    |    2 
 23 files changed, 466 insertions(+), 132 deletions(-)

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Package mcIRT updated to version 0.41 with previous version 0.40 dated 2014-03-15

Title: IRT models for multiple choice items (mcIRT)
Description: This package provides functions to estimate two popular IRT-models: The Nominal Response Model (Bock 1972) and the quite recently developed Nested Logit Model (Suh & Bolt 2010). These are two models to examine multiple-choice items and other multicategorial response formats.
Author: Manuel Reif
Maintainer: Manuel Reif

Diff between mcIRT versions 0.40 dated 2014-03-15 and 0.41 dated 2014-08-30

 DESCRIPTION       |   11 ++++++-----
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 NAMESPACE         |    1 -
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 R/Infnrm.R        |   17 +++++++++++------
 R/reshMG.R        |   29 ++++++++++++++++++++---------
 data/examp1.RData |binary
 7 files changed, 52 insertions(+), 32 deletions(-)

More information about mcIRT at CRAN
Permanent link

Package TDMR updated to version 1.2 with previous version 1.1 dated 2014-06-06

Title: Tuned Data Mining in R
Description: Tuned Data Mining in R (TDMR) performs a complete tuning of a data mining task.
Author: Wolfgang Konen , Patrick Koch
Maintainer: Wolfgang Konen

Diff between TDMR versions 1.1 dated 2014-06-06 and 1.2 dated 2014-08-30

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More information about TDMR at CRAN
Permanent link

Package PP updated to version 0.5 with previous version 0.2-1 dated 2013-12-29

Title: Person Parameter estimation
Description: The PP package includes estimation of (MLE, WLE, MAP, EAP, ROBUST) person parameters for the 1,2,3,4-PL model and the GPCM (generalized partial credit model). The parameters are estimated under the assumption that the item parameters are known and fixed. The package could be useful when items from an itempool/itembank with known item parameters are administered to a new population of testtakers and an ability estimation for every testtaker is needed.
Author: Manuel Reif
Maintainer: Manuel Reif

Diff between PP versions 0.2-1 dated 2013-12-29 and 0.5 dated 2014-08-30

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More information about PP at CRAN
Permanent link

Package RSiteCatalyst updated to version 1.4.0 with previous version 1.3.3 dated 2014-04-12

Title: R Client for Adobe Analytics API v1.4
Description: Functions for accessing the Adobe Analytics Reporting API
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch

Diff between RSiteCatalyst versions 1.3.3 dated 2014-04-12 and 1.4.0 dated 2014-08-30

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Package rmmseg4j (with last version 0.2-0) was removed from CRAN

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

2012-07-22 0.2-0
2012-06-18 0.1-0

Permanent link
Package transmission (with last version 0.2.0) was removed from CRAN

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

2014-06-13 0.2.0

Permanent link
Package transnet (with last version 0.1) was removed from CRAN

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

2012-11-13 0.1

Permanent link
Package EpiModel updated to version 1.0.2 with previous version 1.0.1 dated 2014-07-29

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with tools available for expansion to model complex epidemic processes.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Li Wang [ctb]
Maintainer: Samuel Jenness

Diff between EpiModel versions 1.0.1 dated 2014-07-29 and 1.0.2 dated 2014-08-30

 DESCRIPTION                       |    8 
 MD5                               |  120 ++++++------
 NAMESPACE                         |    5 
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 man/icm.Rd                        |    8 
 man/merge.icm.Rd                  |    2 
 man/merge.netsim.Rd               |    2 
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 tests/testthat/test-dcm.R         |   42 ++--
 tests/testthat/test-diagnostics.R |   42 ++++
 tests/testthat/test-icm.R         |   30 +--
 tests/testthat/test-merge.R       |    4 
 tests/testthat/test-netattr.R     |   22 +-
 tests/testthat/test-netsim.R      |   20 +-
 tests/testthat/test-netvary.R     |only
 vignettes/Intro.Rnw               |   11 -
 64 files changed, 831 insertions(+), 704 deletions(-)

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2007-02-11 0.8.4.2

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Package sns updated to version 0.9.1 with previous version 0.9 dated 2014-08-25

Title: Stochastic Newton Sampler (SNS)
Description: Multivariate, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability densities. SNS is a Metropolis-Hastings variant, where the proposal function is a local Gaussian approximation to the density obtained via a second order Taylor expansion around the current point. The mean of the Gaussian proposal is taken as the full Newton-Raphson step from the current point. During burn-in, Newton-Raphson optimization is performed to get close to the mode of the pdf which is unique due to convexity.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Asad Hasan

Diff between sns versions 0.9 dated 2014-08-25 and 0.9.1 dated 2014-08-30

 DESCRIPTION     |   14 +++++++-------
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 NEWS            |    9 +++++++--
 R/sns.R         |    8 ++++++--
 man/bayesGLM.Rd |    4 ++--
 man/ess.Rd      |    6 +++---
 man/sns.Rd      |   14 +++++++-------
 7 files changed, 38 insertions(+), 29 deletions(-)

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New package apc with initial version 1.0
Package: apc
Type: Package
Title: Age-period-cohort analysis
Version: 1.0
Date: 2014-08-29
Author: Bent Nielsen
Maintainer: Bent Nielsen
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
License: GPL-3
Packaged: 2014-08-29 23:41:27 UTC; Nielsen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-30 06:52:00

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