Mon, 05 Oct 2015

Package MultNonParam updated to version 1.2 with previous version 1.1 dated 2015-09-16

Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>

Diff between MultNonParam versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-05

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Package episensr updated to version 0.7.1 with previous version 0.7.0 dated 2015-10-01

Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. It follows the bias analysis methods and examples from the book by Lash T.L, Fox M.P, and Fink A.K. "Applying Quantitative Bias Analysis to Epidemiologic Data", 'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>

Diff between episensr versions 0.7.0 dated 2015-10-01 and 0.7.1 dated 2015-10-05

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Package alleHap updated to version 0.9.2 with previous version 0.7.2 dated 2014-08-10

Title: Allele Imputation and Haplotype Reconstruction from Pedigree Databases
Description: Simulation of alphanumeric alleles, imputation of genetic missing data and reconstruction of non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many different factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used either simulated datasets or loaded databases (in .ped file biallelic format). Haplotype reconstruction can be performed even with missing data because of alleHap, firstly imputes the genotypes. All this considering that each member (due to meiosis) should unequivocally have two alleles, one inherited from each parent.
Author: Nathan Medina-Rodriguez and Angelo Santana
Maintainer: Nathan Medina-Rodriguez <nathan.medina@ulpgc.es>

Diff between alleHap versions 0.7.2 dated 2014-08-10 and 0.9.2 dated 2015-10-05

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New package wqs with initial version 0.0.1
Package: wqs
Type: Package
Title: Weighted Quantile Sum Regression
Version: 0.0.1
Date: 2015-10-05
Author: Jenna Czarnota, David Wheeler
Maintainer: Jenna Czarnota <jennaczarnota@gmail.com>
Description: Fits weighted quantile sum regression models, calculates weighted quantile sum index and estimated component weights.
Depends: R (>= 3.2.1)
Imports: Rsolnp, glm2
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2015-10-05 19:29:59 UTC; Jenna
Repository: CRAN
Date/Publication: 2015-10-05 22:13:29

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New package qap with initial version 0.1-0
Package: qap
Title: Heuristics for the Quadratic Assignment Problem (QAP)
Version: 0.1-0
Date: 2015-10-05
Authors@R: c(person("Michael", "Hahsler", role = c("aut", "cre", "cph"), email = "mhahsler@lyle.smu.edu"), person("Franz", "Rendl", role = c("ctb", "cph")))
Description: Implements heuristics for the Quadratic Assignment Problem (QAP). Currently only a simulated annealing heuristic is available.
License: GPL-3
NeedsCompilation: yes
Packaged: 2015-10-05 14:14:37 UTC; hahsler
Author: Michael Hahsler [aut, cre, cph], Franz Rendl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Repository: CRAN
Date/Publication: 2015-10-05 22:14:30

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Package mev updated to version 1.3 with previous version 1.2 dated 2015-08-24

Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes and multivariate extreme value distributions for various parametric models.
Author: Leo Belzile [aut, cre]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>

Diff between mev versions 1.2 dated 2015-08-24 and 1.3 dated 2015-10-05

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New package luzlogr with initial version 0.1.0
Package: luzlogr
Type: Package
Title: Lightweight Logging for R Scripts
Version: 0.1.0
Date: 2015-09-29
Authors@R: person("Ben", "Bond-Lamberty", email = "bondlamberty@pnnl.gov", role = c("aut", "cre"))
Maintainer: Ben Bond-Lamberty <bondlamberty@pnnl.gov>
Description: Provides flexible but lightweight logging facilities for R scripts. Supports priority levels for logs and messages, flagging messages, capturing script output, switching logs, and logging to files or connections.
Imports: assertthat (>= 0.1)
Depends: R (>= 3.0)
License: MIT + file LICENSE
LazyData: TRUE
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-10-05 15:27:41 UTC; d3x290
Author: Ben Bond-Lamberty [aut, cre]
Repository: CRAN
Date/Publication: 2015-10-05 22:16:15

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New package HiCfeat with initial version 1.0
Package: HiCfeat
Type: Package
Title: Multiple Logistic Regression for 3D Chromatin Domain Border Analysis
Version: 1.0
Depends: R (>= 3.2.0), GenomicRanges, Matrix, glmnet, rtracklayer
Imports: IRanges, GenomeInfoDb
Date: 2015-09-23
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>
Description: We propose a multiple logistic regression model to assess the influences of genomic features such as DNA-binding proteins and functional elements on topological domain borders.
License: GPL-2
NeedsCompilation: no
Packaged: 2015-10-05 15:33:21 UTC; mourad
Repository: CRAN
Date/Publication: 2015-10-05 22:26:11

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Package gimme updated to version 0.1-3 with previous version 0.1-2 dated 2015-09-11

Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and individual-level relations in time series data from within a structural equation modeling framework.
Author: Stephanie Lane [aut, cre, trl], Kathleen Gates [aut], Peter Molenaar [aut], Michael Hallquist [ctb], Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>

Diff between gimme versions 0.1-2 dated 2015-09-11 and 0.1-3 dated 2015-10-05

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Package future updated to version 0.8.1 with previous version 0.8.0 dated 2015-09-07

Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future versions 0.8.0 dated 2015-09-07 and 0.8.1 dated 2015-10-05

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Package dfmta updated to version 1.3-3 with previous version 1.3-2 dated 2015-04-29

Title: Phase I/II Adaptive Dose-Finding Design for MTA
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" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between dfmta versions 1.3-2 dated 2015-04-29 and 1.3-3 dated 2015-10-05

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Package dfcomb updated to version 2.1-5 with previous version 2.1-4 dated 2015-09-11

Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between dfcomb versions 2.1-4 dated 2015-09-11 and 2.1-5 dated 2015-10-05

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New package conicfit with initial version 1.0.4
Package: conicfit
Type: Package
Title: Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov
Version: 1.0.4
Encoding: UTF-8
Authors@R: c(person(given = "Jose", family = "Gama", role = c("aut","cre"),email = "rxprtgama@gmail.com"), person(given = "Nikolai", family = "Chernov", role = c("aut","cph")))
Description: Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin.
License: GPL (>= 3)
Depends: R (>= 2.7.0), pracma, geigen
Author: Jose Gama [aut, cre], Nikolai Chernov [aut, cph]
Maintainer: Jose Gama <rxprtgama@gmail.com>
Repository: CRAN
Repository/R-Forge/Project: conicfit
Repository/R-Forge/Revision: 10
Repository/R-Forge/DateTimeStamp: 2015-10-05 15:19:30
Date/Publication: 2015-10-05 22:57:57
NeedsCompilation: no
Packaged: 2015-10-05 15:25:31 UTC; rforge

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Package WRS2 updated to version 0.4-0 with previous version 0.3-2 dated 2015-07-23

Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements t-tests (independent and dependent samples), ANOVA (including between-within subject designs) and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut], Rand Wilcox [aut], Felix Schoenbrodt [ctr]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

Diff between WRS2 versions 0.3-2 dated 2015-07-23 and 0.4-0 dated 2015-10-05

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Package TreeSim updated to version 2.2 with previous version 2.1 dated 2014-09-18

Title: Simulating Phylogenetic Trees
Description: Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>

Diff between TreeSim versions 2.1 dated 2014-09-18 and 2.2 dated 2015-10-05

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New package starma with initial version 1.1
Package: starma
Type: Package
Title: Modelling STARMA Processes
Version: 1.1
Date: 2015-10-05
Author: Felix Cheysson
Maintainer: Felix Cheysson <felix@cheysson.fr>
Description: Statistical functions to identify, estimate and diagnose a STARMA model.
License: GPL-2
Imports: Rcpp (>= 0.11.1), ggplot2, scales, graphics, stats
LinkingTo: Rcpp, RcppArmadillo
Depends:
Suggests: spdep
NeedsCompilation: yes
Packaged: 2015-10-05 11:27:26 UTC; PhEMI
Repository: CRAN
Date/Publication: 2015-10-05 17:07:47

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Package rootSolve updated to version 1.6.6 with previous version 1.6.5.1 dated 2014-11-06

Title: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
Description: Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE). Includes routines that: (1) generate gradient and Jacobian matrices (full and banded), (2) find roots of non-linear equations by the Newton-Raphson method, (3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running, (4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ODEs by numerical differencing (using the method-of-lines approach). Includes fortran code.
Author: Karline Soetaert [aut, cre], yale sparse matrix package authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

Diff between rootSolve versions 1.6.5.1 dated 2014-11-06 and 1.6.6 dated 2015-10-05

 DESCRIPTION        |   15 ++++++++-------
 MD5                |   10 +++++-----
 NAMESPACE          |    6 ++++--
 R/stode.R          |    5 ++++-
 R/stodes.R         |    3 +++
 build/vignette.rds |binary
 6 files changed, 24 insertions(+), 15 deletions(-)

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Package RcppRedis updated to version 0.1.6 with previous version 0.1.5 dated 2015-07-17

Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppRedis versions 0.1.5 dated 2015-07-17 and 0.1.6 dated 2015-10-05

 RcppRedis-0.1.5/RcppRedis/R/RcppExports.R                |only
 RcppRedis-0.1.5/RcppRedis/src/RcppExports.cpp            |only
 RcppRedis-0.1.6/RcppRedis/ChangeLog                      |   27 +++
 RcppRedis-0.1.6/RcppRedis/DESCRIPTION                    |    8 -
 RcppRedis-0.1.6/RcppRedis/MD5                            |   15 -
 RcppRedis-0.1.6/RcppRedis/README.md                      |    4 
 RcppRedis-0.1.6/RcppRedis/inst/NEWS.Rd                   |   23 ++
 RcppRedis-0.1.6/RcppRedis/inst/tests/runit.basicRtests.R |    7 
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 RcppRedis-0.1.6/RcppRedis/src/Redis.cpp                  |  117 +++++++++++++--
 10 files changed, 174 insertions(+), 27 deletions(-)

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New package logisticPCA with initial version 0.1
Package: logisticPCA
Type: Package
Title: Binary Dimensionality Reduction
Version: 0.1
Date: 2015-10-04
NeedsCompilation: yes
ByteCompile: yes
Author: Andrew J. Landgraf
Maintainer: Andrew J. Landgraf <andland@gmail.com>
Description: Dimensionality reduction techniques for binary data including logistic PCA.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/andland/logisticPCA
Imports: ggplot2
Suggests: irlba, testthat, knitr
VignetteBuilder: knitr
Packaged: 2015-10-05 14:14:15 UTC; landgraf
Repository: CRAN
Date/Publication: 2015-10-05 17:07:42

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Package gvc updated to version 0.5.0 with previous version 0.2.0 dated 2015-03-31

Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are implemented.
Author: Bastiaan Quast [aut, cre], Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>

Diff between gvc versions 0.2.0 dated 2015-03-31 and 0.5.0 dated 2015-10-05

 gvc-0.2.0/gvc/R/block_matrix.R                         |only
 gvc-0.2.0/gvc/R/minus_block_matrix.R                   |only
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 gvc-0.5.0/gvc/MD5                                      |   47 +++++---
 gvc-0.5.0/gvc/NAMESPACE                                |    9 +
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 gvc-0.5.0/gvc/R/i2e.R                                  |   19 +++
 gvc-0.5.0/gvc/R/nrca.R                                 |   36 +-----
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 35 files changed, 240 insertions(+), 81 deletions(-)

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New package smallarea with initial version 0.1
Package: smallarea
Type: Package
Title: Fits a Fay Herriot Model
Version: 0.1
Date: 2015-10-03
Author: Abhishek Nandy
Maintainer: Abhishek Nandy <nandy006@umn.edu>
Description: Inference techniques for Fay Herriot Model.
License: GPL (>= 2)
Depends: MASS
Packaged: 2015-10-05 03:16:17 UTC; abhishek
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-10-05 12:37:47

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New package SimDesign with initial version 0.3
Package: SimDesign
Title: Structure for Organizing Monte Carlo Simulation Designs
Version: 0.3
Date: 2015-10-04
Authors@R: person("Phil", "Chalmers", email = "rphilip.chalmers@gmail.com", role = c("aut", "cre"))
Description: Provides tools to help organize Monte Carlo simulations in R. The tools provided control the structure and back-end of the Monte Carlo simulations by utilizing a generate-analyse-summarise strategy. The functions control common simulation issues such as re-simulating non-convergent results, support parallel back-end computations, save and restore temporary files, aggregate results across independent nodes, and provide native support for debugging.
VignetteBuilder: knitr
Depends: R (>= 3.2.1)
Imports: foreach, methods, parallel
Suggests: knitr
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2015-10-05 00:59:14 UTC; phil
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Repository: CRAN
Date/Publication: 2015-10-05 12:37:41

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Package riskRegression updated to version 1.1.7 with previous version 1.1.1 dated 2014-12-10

Title: Risk Regression Models for Survival Analysis with Competing Risks
Description: Risk regression models for survival analysis with and without competing risks.
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>

Diff between riskRegression versions 1.1.1 dated 2014-12-10 and 1.1.7 dated 2015-10-05

 riskRegression-1.1.1/riskRegression/src/matrix.h                                |only
 riskRegression-1.1.7/riskRegression/DESCRIPTION                                 |   17 
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 riskRegression-1.1.7/riskRegression/NAMESPACE                                   |   23 +
 riskRegression-1.1.7/riskRegression/R/CSC.R                                     |  180 ++++++----
 riskRegression-1.1.7/riskRegression/R/FGR.R                                     |    8 
 riskRegression-1.1.7/riskRegression/R/coef.riskRegression.R                     |    2 
 riskRegression-1.1.7/riskRegression/R/plot.CauseSpecificCox.R                   |   34 +
 riskRegression-1.1.7/riskRegression/R/plot.predictedRisk.R                      |    2 
 riskRegression-1.1.7/riskRegression/R/plot.riskRegression.R                     |    9 
 riskRegression-1.1.7/riskRegression/R/plotEffects.R                             |    9 
 riskRegression-1.1.7/riskRegression/R/predict.CauseSpecificCox.R                |    2 
 riskRegression-1.1.7/riskRegression/R/predict.FGR.R                             |    2 
 riskRegression-1.1.7/riskRegression/R/predict.riskRegression.R                  |    5 
 riskRegression-1.1.7/riskRegression/R/print.CauseSpecificCox.R                  |   12 
 riskRegression-1.1.7/riskRegression/R/print.FGR.R                               |    2 
 riskRegression-1.1.7/riskRegression/R/print.riskRegression.R                    |    2 
 riskRegression-1.1.7/riskRegression/R/print.subjectWeights.R                    |    2 
 riskRegression-1.1.7/riskRegression/R/print.timevarCoefList.R                   |    2 
 riskRegression-1.1.7/riskRegression/R/riskRegression-package.R                  |    4 
 riskRegression-1.1.7/riskRegression/R/riskRegression.R                          |   11 
 riskRegression-1.1.7/riskRegression/R/subjectWeights.R                          |   14 
 riskRegression-1.1.7/riskRegression/R/summary.FGR.R                             |    2 
 riskRegression-1.1.7/riskRegression/R/summary.riskRegression.R                  |    2 
 riskRegression-1.1.7/riskRegression/man/CSC.Rd                                  |   78 ++--
 riskRegression-1.1.7/riskRegression/man/FGR.Rd                                  |   44 +-
 riskRegression-1.1.7/riskRegression/man/Melanoma.Rd                             |   21 -
 riskRegression-1.1.7/riskRegression/man/plot.riskRegression.Rd                  |   52 +-
 riskRegression-1.1.7/riskRegression/man/plotEffects.Rd                          |   58 +--
 riskRegression-1.1.7/riskRegression/man/predict.riskRegression.Rd               |   21 -
 riskRegression-1.1.7/riskRegression/man/riskRegression.Rd                       |  100 ++---
 riskRegression-1.1.7/riskRegression/man/subjectWeights.Rd                       |   61 +--
 riskRegression-1.1.7/riskRegression/src/matrix.c                                |    2 
 riskRegression-1.1.7/riskRegression/src/riskregression.h                        |   50 ++
 riskRegression-1.1.7/riskRegression/tests/test-FGR.R                            |   21 +
 riskRegression-1.1.7/riskRegression/tests/testthat/CauseSpecificCoxRegression.R |    7 
 riskRegression-1.1.7/riskRegression/tests/testthat/brier.R                      |    4 
 37 files changed, 547 insertions(+), 389 deletions(-)

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Package prodlim updated to version 1.5.5 with previous version 1.5.1 dated 2014-12-10

Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>

Diff between prodlim versions 1.5.1 dated 2014-12-10 and 1.5.5 dated 2015-10-05

 prodlim-1.5.1/prodlim/R/contrastMethods.R           |only
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 prodlim-1.5.5/prodlim/R/lifeTab.survival.R          |    4 
 prodlim-1.5.5/prodlim/R/plot.Hist.R                 |    3 
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 prodlim-1.5.5/prodlim/R/predict.prodlim.R           |   77 ++---
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 prodlim-1.5.5/prodlim/man/atRisk.Rd                 |   61 +---
 prodlim-1.5.5/prodlim/man/backGround.Rd             |   31 +-
 prodlim-1.5.5/prodlim/man/confInt.Rd                |   47 +--
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 prodlim-1.5.5/prodlim/man/leaveOneOut.Rd            |   16 -
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 prodlim-1.5.5/prodlim/man/meanNeighbors.Rd          |   11 
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 prodlim-1.5.5/prodlim/man/neighborhood.Rd           |   49 +--
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 prodlim-1.5.5/prodlim/man/plot.Hist.Rd              |   85 ++----
 prodlim-1.5.5/prodlim/man/plot.prodlim.Rd           |  275 ++++++++++----------
 prodlim-1.5.5/prodlim/man/plotCompetingRiskModel.Rd |   12 
 prodlim-1.5.5/prodlim/man/plotIllnessDeathModel.Rd  |   18 -
 prodlim-1.5.5/prodlim/man/predict.prodlim.Rd        |   94 +++---
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 71 files changed, 1708 insertions(+), 1554 deletions(-)

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New package PsiHat with initial version 1.0
Package: PsiHat
Type: Package
Title: Several Local False Discovery Rate Estimators
Version: 1.0
Date: 2015-09-30
Author: Alaa Ali, Kyle Leckett, Marta Padilla, David R. Bickel (contributions from Bradley Efron, Brit B. Turnbull, Balasubramanian Narasimhan from package locfdr).
Maintainer: Marta Padilla <padilla.mpf@gmail.com>
Description: Suite of R functions for the estimation of local false discovery rate (LFDR) using several methods.
License: GPL-3
Depends: methods, qvalue, splines
URL: http://www.r-project.org, http://www.bioconductor.org, http://www.statomics.com
NeedsCompilation: no
Packaged: 2015-10-05 09:59:01 UTC; martapadilla
Repository: CRAN
Date/Publication: 2015-10-05 12:58:12

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Package pec updated to version 2.4.7 with previous version 2.4.4 dated 2014-12-05

Title: Prediction Error Curves for Risk Prediction Models in Survival Analysis
Description: Validation of risk predictions obtained from survival models and competing risk models based on censored data using inverse weighting and cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>

Diff between pec versions 2.4.4 dated 2014-12-05 and 2.4.7 dated 2015-10-05

 pec-2.4.4/pec/data/GBSG2.RData                  |only
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 pec-2.4.7/pec/NAMESPACE                         |   63 ++
 pec-2.4.7/pec/R/R2.R                            |    2 
 pec-2.4.7/pec/R/calPlot.R                       |  625 +++++++++++++++--------
 pec-2.4.7/pec/R/cindex.R                        |   92 +--
 pec-2.4.7/pec/R/crps.R                          |    2 
 pec-2.4.7/pec/R/ibs.R                           |    2 
 pec-2.4.7/pec/R/ipcw.R                          |   16 
 pec-2.4.7/pec/R/marginal.prodlim.R              |    6 
 pec-2.4.7/pec/R/pec-package.R                   |    5 
 pec-2.4.7/pec/R/pec.R                           |   78 +-
 pec-2.4.7/pec/R/plot.Cindex.R                   |    2 
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 pec-2.4.7/pec/R/predictSurvProb.penfitS3.R      |    2 
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 pec-2.4.7/pec/man/pecCtree.Rd                   |    4 
 pec-2.4.7/pec/man/pecRpart.Rd                   |   11 
 pec-2.4.7/pec/man/plot.calibrationPlot.Rd       |only
 pec-2.4.7/pec/man/plot.pec.Rd                   |  118 ++--
 pec-2.4.7/pec/man/plotPredictEventProb.Rd       |   85 +--
 pec-2.4.7/pec/man/plotPredictSurvProb.Rd        |   84 +--
 pec-2.4.7/pec/man/predictEventProb.Rd           |   43 -
 pec-2.4.7/pec/man/predictLifeYearsLost.Rd       |   49 -
 pec-2.4.7/pec/man/predictRestrictedMeanTime.Rd  |only
 pec-2.4.7/pec/man/predictSurvProb.Rd            |  103 ++-
 pec-2.4.7/pec/man/print.pec.Rd                  |   24 
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 pec-2.4.7/pec/man/selectCox.Rd                  |   31 -
 pec-2.4.7/pec/man/selectFGR.Rd                  |   35 -
 pec-2.4.7/pec/man/simCost.Rd                    |    7 
 pec-2.4.7/pec/man/wallyPlot.Rd                  |only
 pec-2.4.7/pec/src/auc.c                         |only
 84 files changed, 1949 insertions(+), 1788 deletions(-)

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New package geofd with initial version 1.0
Package: geofd
Version: 1.0
Author: Ramon Giraldo <rgiraldoh@unal.edu.co>, Pedro Delicado <pedro.delicado@upc.edu>, Jorge Mateu <mateu@mat.uji.es>
Maintainer: Pedro Delicado <pedro.delicado@upc.edu>
Title: Spatial Prediction for Function Value Data
Description: Kriging based methods are used for predicting functional data (curves) with spatial dependence.
License: GPL-2
Depends: fda, geoR
Repository: CRAN
Date: 2015-09-21
NeedsCompilation: no
Packaged: 2015-10-05 09:09:31 UTC; delicado
Date/Publication: 2015-10-05 12:58:15

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Package diagonals updated to version 0.4.0 with previous version 0.3.0 dated 2015-06-15

Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>

Diff between diagonals versions 0.3.0 dated 2015-06-15 and 0.4.0 dated 2015-10-05

 diagonals-0.3.0/diagonals/R/diag.R              |only
 diagonals-0.3.0/diagonals/man/diag-set.Rd       |only
 diagonals-0.4.0/diagonals/DESCRIPTION           |    6 
 diagonals-0.4.0/diagonals/MD5                   |   20 -
 diagonals-0.4.0/diagonals/NEWS                  |    6 
 diagonals-0.4.0/diagonals/R/fatdiag.R           |  139 ++++++----
 diagonals-0.4.0/diagonals/R/matricise.R         |only
 diagonals-0.4.0/diagonals/README.md             |    1 
 diagonals-0.4.0/diagonals/build/vignette.rds    |binary
 diagonals-0.4.0/diagonals/inst/doc/fatdiag.html |  323 +++++++++++++++++-------
 diagonals-0.4.0/diagonals/man/fatdiag.Rd        |   12 
 diagonals-0.4.0/diagonals/man/matricise.Rd      |only
 diagonals-0.4.0/diagonals/tests                 |only
 13 files changed, 357 insertions(+), 150 deletions(-)

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Package dbscan updated to version 0.9-5 with previous version 0.9-4 dated 2015-09-17

Title: Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph], Sunil Arya [ctb, cph], David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between dbscan versions 0.9-4 dated 2015-09-17 and 0.9-5 dated 2015-10-05

 DESCRIPTION               |   14 ++++-----
 MD5                       |   41 ++++++++++++++--------------
 NAMESPACE                 |    1 
 R/optics.R                |   66 +++++++++++++++++++++++-----------------------
 README.md                 |only
 inst/NEWS                 |    8 ++++-
 inst/tests/test-lof.R     |   11 +++++--
 inst/tests/test-optics.R  |   26 +++++++++++++++---
 man/dbscan.Rd             |    2 +
 man/lof.Rd                |    1 
 man/optics.Rd             |   17 +++++++++--
 src/ANN.cpp               |    6 ++--
 src/R_kNN.cpp             |    7 ++--
 src/R_optics.cpp          |   44 ++++++++++++++++++------------
 src/R_regionQuery.cpp     |    2 -
 src/kd_dump.cpp           |    2 -
 src/kd_fix_rad_search.cpp |   10 +++---
 src/kd_pr_search.cpp      |   12 ++++----
 src/kd_search.cpp         |   12 ++++----
 src/kd_util.cpp           |   10 +++---
 src/pr_queue.h            |   10 +++---
 src/pr_queue_k.h          |    2 -
 22 files changed, 177 insertions(+), 127 deletions(-)

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Package cate updated to version 1.0.4 with previous version 1.0.3 dated 2015-09-09

Title: High Dimensional Factor Analysis and Confounder Adjusted Testing and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut], Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>

Diff between cate versions 1.0.3 dated 2015-09-09 and 1.0.4 dated 2015-10-05

 DESCRIPTION                 |   10 -
 MD5                         |   37 +++----
 NAMESPACE                   |    1 
 R/adjust_functions.R        |   21 ++--
 R/cate.R                    |  225 +++++++++++++++++++++++++++++++-------------
 R/factor_functions.R        |    1 
 R/other_methods.R           |   81 +++++++++------
 R/simulate_functions.R      |    5 
 build/vignette.rds          |binary
 inst/doc/cate-vignette.R    |   21 ++--
 inst/doc/cate-vignette.Rnw  |   43 +++++---
 inst/doc/cate-vignette.pdf  |binary
 man/adjust.latent.Rd        |    8 -
 man/cate.Rd                 |   54 +++++++---
 man/est.confounder.num.Rd   |   15 +-
 man/gen.sim.data.Rd         |    4 
 man/gender.sm.Rd            |    1 
 man/parse.cate.formula.Rd   |only
 man/wrapper.Rd              |   32 +++---
 vignettes/cate-vignette.Rnw |   43 +++++---
 20 files changed, 397 insertions(+), 205 deletions(-)

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