Title: Various programming utilities
Diff between R.utils versions 1.33.0 dated 2014-08-26 and 1.34.0 dated 2014-10-08
Description: This package provides utility methods useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 ++--
MD5 | 55 +++++++++++++++----------
NEWS | 83 ++++++++++++++++++++++++++++++++++++++-
R/Arguments.R | 21 +++++++++
R/copyDirectory.R | 24 ++++++++++-
R/countLines.R | 49 ++++++++++++++++++-----
R/downloadFile.R | 81 ++++++++++++++++++++++++++++----------
R/filePath.R | 42 ++++++++++++++++++-
R/getAbsolutePath.R | 8 +++
R/getRelativePath.R | 2
R/mkdirs.R | 28 +++++++------
R/shell.exec2.R |only
R/use.R | 27 ++++++++----
R/withOptions.R | 31 ++++++++++++--
R/withSeed.R |only
R/withSink.R |only
R/writeDataFrame.R | 12 +++++
man/countLines.Rd | 4 +
man/downloadFile.character.Rd | 2
man/filePath.Rd | 6 +-
man/getRelativePath.Rd | 2
man/shell.exec2.Rd |only
man/withOptions.Rd | 7 +++
man/withSeed.Rd |only
man/withSink.Rd |only
man/writeDataFrame.data.frame.Rd | 2
tests/absolute-relative-paths.R | 9 +++-
tests/countLines.R |only
tests/mkdirs.R |only
tests/withLocale.R | 16 +++++++
tests/withOptions.R | 19 ++++++++
tests/withSeed.R |only
tests/withSink.R |only
tests/writeDataFrame.R |only
34 files changed, 442 insertions(+), 98 deletions(-)
More information about HiDimMaxStable at CRAN
Permanent link
Title: Simulation and group sequential monitoring of randomized
multi-arm two-stage Phase IIb/III treatment efficacy trials
with time-to-event endpoints
Diff between seqDesign versions 1.0.1 dated 2014-04-17 and 1.0.2 dated 2014-10-08
Description: This package implements the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases), and applies generally to individual-randomized clinical trials with multiple active treatment groups and a shared placebo group, with a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment arm for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial outcomes (e.g., stopping early for efficacy futility); unconditional power for comparing treatment efficacy; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
Author: Michal Juraska and Doug Grove, with contributions from Xuesong Yu and Peter B. Gilbert
Maintainer: Michal Juraska
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/seqDesign.R | 12 ++++++++----
build/vignette.rds |binary
4 files changed, 15 insertions(+), 11 deletions(-)
Title: Copy number estimation from tumor genome sequencing data.
Diff between sequenza versions 2.0.0 dated 2014-04-08 and 2.1.0 dated 2014-10-08
Description: This package provides tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero
sequenza-2.0.0/sequenza/data/CPsnp.example.RData |only
sequenza-2.0.0/sequenza/inst/doc/sequenza.bib |only
sequenza-2.0.0/sequenza/inst/doc/sequenzaSNP.R |only
sequenza-2.0.0/sequenza/inst/doc/sequenzaSNP.Rnw |only
sequenza-2.0.0/sequenza/inst/doc/sequenzaSNP.pdf |only
sequenza-2.0.0/sequenza/vignettes/sequenzaSNP.Rnw |only
sequenza-2.1.0/sequenza/DESCRIPTION | 15
sequenza-2.1.0/sequenza/MD5 | 56 +--
sequenza-2.1.0/sequenza/NEWS | 14
sequenza-2.1.0/sequenza/R/analysis.R | 100 ++++--
sequenza-2.1.0/sequenza/R/bayes.R | 97 +++---
sequenza-2.1.0/sequenza/R/graphics.R | 138 +++++++-
sequenza-2.1.0/sequenza/R/misc.R | 5
sequenza-2.1.0/sequenza/R/model.R | 21 +
sequenza-2.1.0/sequenza/R/next.R | 24 -
sequenza-2.1.0/sequenza/R/workflows.R | 218 ++++++++++----
sequenza-2.1.0/sequenza/build/vignette.rds |binary
sequenza-2.1.0/sequenza/data/CP.example.RData |binary
sequenza-2.1.0/sequenza/data/example.seqz.rda |binary
sequenza-2.1.0/sequenza/exec/sequenza-utils.py | 338 ++++++++++++++++------
sequenza-2.1.0/sequenza/inst/doc/sequenza.R | 8
sequenza-2.1.0/sequenza/inst/doc/sequenza.Rnw | 80 ++---
sequenza-2.1.0/sequenza/inst/doc/sequenza.pdf |binary
sequenza-2.1.0/sequenza/man/CP.data.Rd | 9
sequenza-2.1.0/sequenza/man/baf.bayes.Rd | 13
sequenza-2.1.0/sequenza/man/baf.model.fit.Rd | 6
sequenza-2.1.0/sequenza/man/chromosome.view.Rd | 2
sequenza-2.1.0/sequenza/man/cp.plot.Rd | 23 -
sequenza-2.1.0/sequenza/man/find.breaks.Rd | 10
sequenza-2.1.0/sequenza/man/get.ci.Rd | 10
sequenza-2.1.0/sequenza/man/workflows.Rd | 32 +-
sequenza-2.1.0/sequenza/vignettes/sequenza.Rnw | 80 ++---
32 files changed, 899 insertions(+), 400 deletions(-)
Title: Spatial geostatistics; some geostatistical and radial basis
functions, prediction and cross validation; design of optimal
spatial sampling networks based on geostatistical modelling
Diff between geospt versions 0.5-0 dated 2012-04-24 and 1.0-0 dated 2014-10-08
Description: This package contains functions for: estimation of the
variogram through trimmed mean, radial basis functions
(optimization, prediction and cross-validation), summary
statistics from cross-validation, pocket plot, and design of
optimal sampling networks through sequential and simultaneous
points methods
Author: Carlos Melo
Maintainer: Alí Santacruz
geospt-0.5-0/geospt/R/Dis.R |only
geospt-0.5-0/geospt/man/Dis.Rd |only
geospt-1.0-0/geospt/DESCRIPTION | 17 ++-
geospt-1.0-0/geospt/MD5 | 69 ++++++++--------
geospt-1.0-0/geospt/NAMESPACE | 17 +++
geospt-1.0-0/geospt/R/RBF.phi.R | 2
geospt-1.0-0/geospt/R/bp.with.outlier.label.R | 8 -
geospt-1.0-0/geospt/R/criterio.cv.R | 13 +--
geospt-1.0-0/geospt/R/extractFormula.R |only
geospt-1.0-0/geospt/R/graph.rbf.R | 112 ++++++++++++++++++++++----
geospt-1.0-0/geospt/R/network.design.r |only
geospt-1.0-0/geospt/R/pocket.plot.R | 41 +++++----
geospt-1.0-0/geospt/R/rbf.R | 61 +++++++++-----
geospt-1.0-0/geospt/R/rbf.cv.R | 8 -
geospt-1.0-0/geospt/R/rbf.cv1.R |only
geospt-1.0-0/geospt/R/rbf.tcv.R | 9 +-
geospt-1.0-0/geospt/R/seqPtsOptNet.R | 46 ++++++++--
geospt-1.0-0/geospt/R/simPtsOptNet.R | 39 ++++++---
geospt-1.0-0/geospt/demo |only
geospt-1.0-0/geospt/inst |only
geospt-1.0-0/geospt/man/COSha10.Rd | 22 ++---
geospt-1.0-0/geospt/man/COSha10map.Rd | 4
geospt-1.0-0/geospt/man/COSha30.Rd | 22 ++---
geospt-1.0-0/geospt/man/COSha30map.Rd | 4
geospt-1.0-0/geospt/man/RBF.phi.Rd | 4
geospt-1.0-0/geospt/man/criterio.cv.Rd | 18 ++--
geospt-1.0-0/geospt/man/est.variograms.Rd | 6 -
geospt-1.0-0/geospt/man/extractFormula.Rd |only
geospt-1.0-0/geospt/man/geospt-package.Rd | 6 -
geospt-1.0-0/geospt/man/graph.rbf.Rd | 61 +++++++++-----
geospt-1.0-0/geospt/man/lalib.Rd | 4
geospt-1.0-0/geospt/man/network.design.Rd |only
geospt-1.0-0/geospt/man/pocket.plot.Rd | 18 ++--
geospt-1.0-0/geospt/man/rbf.Rd | 51 +++++------
geospt-1.0-0/geospt/man/rbf.cv.Rd | 34 +++++--
geospt-1.0-0/geospt/man/rbf.cv1.Rd |only
geospt-1.0-0/geospt/man/rbf.tcv.Rd | 35 ++++----
geospt-1.0-0/geospt/man/samplePts.Rd | 14 +--
geospt-1.0-0/geospt/man/seqPtsOptNet.Rd | 52 +++++++-----
geospt-1.0-0/geospt/man/simPtsOptNet.Rd | 36 ++++++--
40 files changed, 532 insertions(+), 301 deletions(-)
Title: Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
Diff between pvclust versions 1.2-2 dated 2011-04-13 and 1.3-0 dated 2014-10-08
Description: pvclust is a package for assessing the uncertainty in
hierarchical cluster analysis. It provides AU (approximately
unbiased) p-values as well as BP (boostrap probability) values
computed via multiscale bootstrap resampling.
Author: Ryota Suzuki
Maintainer: Ryota Suzuki
DESCRIPTION | 15
MD5 |only
R/pvclust.R | 892 +++++++++++++++++++++++++--------------------------
man/lung.Rd | 2
man/msfit.Rd | 2
man/msplot.Rd | 2
man/plot.pvclust.Rd | 2
man/print.pvclust.Rd | 2
man/pvclust.Rd | 411 +++++++++++------------
man/pvpick.Rd | 2
man/seplot.Rd | 2
11 files changed, 676 insertions(+), 656 deletions(-)
Title: Convex Clustering Methods and Clustering Indexes
Diff between cclust versions 0.6-18 dated 2014-01-26 and 0.6-19 dated 2014-10-08
Description: Convex Clustering methods, including K-means algorithm,
On-line Update algorithm (Hard Competitive Learning) and Neural Gas
algorithm (Soft Competitive Learning), and calculation of several
indexes for finding the number of clusters in a data set.
Author: Evgenia Dimitriadou [aut],
Kurt Hornik [ctb, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/Rindexes.R | 4 ++--
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Selecting variable subsets
Diff between subselect versions 0.12-3 dated 2013-07-09 and 0.12-4 dated 2014-10-08
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima
subselect-0.12-3/subselect/src/Makevars.in |only
subselect-0.12-4/subselect/DESCRIPTION | 23 ++++++-----------
subselect-0.12-4/subselect/MD5 | 31 ++++++++++++------------
subselect-0.12-4/subselect/build |only
subselect-0.12-4/subselect/inst/CHANGELOG | 4 +++
subselect-0.12-4/subselect/inst/doc/subselect.R |only
subselect-0.12-4/subselect/src/CCRcrt.h | 7 +++--
subselect-0.12-4/subselect/src/ErrMReals.h | 13 +++++-----
subselect-0.12-4/subselect/src/MStcrt.h | 5 ++-
subselect-0.12-4/subselect/src/Qforms.h | 3 +-
subselect-0.12-4/subselect/src/RMcrt.cpp | 3 +-
subselect-0.12-4/subselect/src/RMcrt.h | 5 ++-
subselect-0.12-4/subselect/src/RVcrt.cpp | 3 +-
subselect-0.12-4/subselect/src/RVcrt.h | 9 +++---
subselect-0.12-4/subselect/src/SR_datatrnsf.cpp | 3 ++
subselect-0.12-4/subselect/src/SpecialArrays.h | 7 +++--
subselect-0.12-4/subselect/src/Sscma.cpp | 7 +++--
subselect-0.12-4/subselect/src/Wrkf1.cpp | 8 ++++--
18 files changed, 74 insertions(+), 57 deletions(-)
Title: Models for analysing moult in birds
Diff between moult versions 1.3 dated 2013-08-08 and 1.4 dated 2014-10-08
Description: Functions to estimate start and duration of moult from moult
data (of types 1 to 5), based on models developed in Underhill
and Zucchini (1988, 1990). Allows modelling parameters as
functions of covariates.
Author: Birgit Erni
Maintainer: Birgit Erni
DESCRIPTION | 12 +--
MD5 | 17 ++--
NAMESPACE | 2
NEWS | 4 +
R/predict.moult.R | 197 ++++++++++++++++++++++++++++++++-------------------
build |only
inst/doc/moult.R |only
inst/doc/moult.Rnw |only
man/predict.moult.Rd | 188 +++++++++++++++++++++++++-----------------------
man/weavers.Rd | 102 +++++++++++++++++---------
vignettes |only
11 files changed, 312 insertions(+), 210 deletions(-)
Title: General Frailty models: shared, joint and nested frailty models
with prediction
Diff between frailtypack versions 2.7 dated 2014-08-30 and 2.7.1 dated 2014-10-08
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
DESCRIPTION | 6
MD5 | 6
R/epoce.R | 394 +++++++++++++++++++++++++++----------------------------
R/frailtyPenal.R | 6
4 files changed, 207 insertions(+), 205 deletions(-)
Title: Threads Environment for R
Diff between Rdsm versions 2.0.2 dated 2013-08-20 and 2.1.1 dated 2014-10-08
Description: Provides a threads-type programming environment for R.
The package gives the R programmer the clearer, more concise
shared memory world view, and in some cases gives superior
performance as well. In addition, it enables parallel processing on
very large, out-of-core matrices.
Author: Norm Matloff
Maintainer: Norm Matloff
README | 2
tmp/cranberry6e8840a1a800/Rdsm-2.0.2/Rdsm/man/shmcls.Rd |only
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/DESCRIPTION | 10
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/MD5 | 39 +
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/NAMESPACE | 5
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/R/Rdsm.R | 219 +++++++---
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/AdjXform.R | 28 +
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/BSort.R | 10
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/Burst.R |only
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/KMeans.R | 8
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/MMul.R | 60 ++
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/PDist.R | 9
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/inst/examples/README |only
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/Rdsm-package.Rd | 57 +-
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/getidxs.Rd | 7
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/getmatrix.Rd |only
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/loadex.Rd |only
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/makebarr.Rd | 6
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/mgrinit.Rd | 17
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/mgrmakelock.Rd | 6
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/mgrmakevar.Rd | 13
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/rdsmlock.Rd | 46 --
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/readsync.Rd |only
tmp/cranberry6e8840a1a800/Rdsm-2.1.1/Rdsm/man/stoprdsm.Rd |only
24 files changed, 361 insertions(+), 181 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial
trading strategies.
Author: Jeffrey A. Ryan
Maintainer: ORPHANED
Diff between quantmod versions 0.4-1 dated 2014-10-03 and 0.4-2 dated 2014-10-08
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ R/TA.R | 6 ------ R/getSymbols.R | 27 --------------------------- R/getSymbols.skeleton.R | 1 - R/newTA.R | 7 +++++-- man/getSymbols.FRED.Rd | 2 -- man/getSymbols.MySQL.Rd | 10 +--------- man/getSymbols.Rd | 10 ++-------- man/getSymbols.google.Rd | 2 -- man/getSymbols.rda.Rd | 2 -- man/getSymbols.yahoo.Rd | 2 -- man/quantmod-package.Rd | 10 +++++----- 13 files changed, 30 insertions(+), 83 deletions(-)
Title: A Grammar of Data Manipulation
Diff between dplyr versions 0.3 dated 2014-10-04 and 0.3.0.1 dated 2014-10-08
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 6 ++---
MD5 | 14 +++++------
inst/doc/databases.html | 20 ++++++++---------
inst/doc/introduction.html | 16 ++++++-------
inst/doc/memory.html | 48 ++++++++++++++++++++---------------------
inst/doc/nse.html | 4 +--
inst/doc/window-functions.html | 12 +++++-----
tests/testthat/test-mutate.r | 6 ++++-
8 files changed, 65 insertions(+), 61 deletions(-)