Title: Vectorised Tools for URL Handling and Parsing
Diff between urltools versions 0.5 dated 2014-12-09 and 0.6 dated 2014-12-22
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes
Maintainer: Oliver Keyes
urltools-0.5/urltools/man/url_param.Rd |only
urltools-0.5/urltools/src/Makevars |only
urltools-0.6/urltools/DESCRIPTION | 8 -
urltools-0.6/urltools/MD5 | 38 ++++---
urltools-0.6/urltools/NAMESPACE | 4
urltools-0.6/urltools/NEWS |only
urltools-0.6/urltools/R/RcppExports.R | 59 ++++++++++-
urltools-0.6/urltools/R/urltools.R | 3
urltools-0.6/urltools/README.md | 3
urltools-0.6/urltools/inst/doc/urltools.R | 2
urltools-0.6/urltools/inst/doc/urltools.Rmd | 4
urltools-0.6/urltools/inst/doc/urltools.html | 4
urltools-0.6/urltools/man/extract_host.Rd |only
urltools-0.6/urltools/man/extract_parameter.Rd |only
urltools-0.6/urltools/man/replace_parameter.Rd |only
urltools-0.6/urltools/man/urltools.Rd | 4
urltools-0.6/urltools/src/RcppExports.cpp | 40 +++++++-
urltools-0.6/urltools/src/encoding.cpp |only
urltools-0.6/urltools/src/encoding.h | 53 +---------
urltools-0.6/urltools/src/parsing.cpp |only
urltools-0.6/urltools/src/parsing.h | 99 +-------------------
urltools-0.6/urltools/src/urltools.cpp | 97 ++++++++++++++++---
urltools-0.6/urltools/tests/testthat/test_parsing.R | 12 ++
urltools-0.6/urltools/vignettes/urltools.Rmd | 4
24 files changed, 241 insertions(+), 193 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Diff between TDA versions 1.2 dated 2014-10-14 and 1.3 dated 2014-12-22
Description: This package provides tools for the statistical analysis of persistent homology and for density clustering.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria
Maintainer: Fabrizio Lecci
DESCRIPTION | 8
MD5 | 59 ++---
NEWS | 5
R/clusterTree.R | 59 ++++-
R/findKtree.R | 26 +-
R/gridDiag.R | 68 +++--
R/maxPersistence.R | 2
R/plot.clusterTree.R | 34 ++
R/plot.diagram.R | 11
R/plot.maxPersistence.R | 3
R/plotRule.R | 7
R/ripsArbitDiag.R | 5
R/ripsL2Diag.R | 15 +
build/vignette.rds |binary
inst/doc/article.Rnw | 11
inst/doc/article.pdf |binary
man/TDA-package.Rd | 4
man/bootstrapDiagram.Rd | 2
man/clusterTree.Rd | 18 -
man/gridDiag.Rd | 60 +++--
man/plot.clusterTree.Rd | 2
man/plot.diagram.Rd | 13 -
man/summary.diagram.Rd | 6
src/diag.cpp | 114 +++++++++-
src/gudhi/Persistent_cohomology.h | 58 ++++-
src/gudhi/Persistent_cohomology/Persistent_cohomology_column.h | 6
src/gudhi/Simplex_tree.h | 6
src/tdautils/dionysusUtils.h |only
src/tdautils/gridUtils.h | 6
src/tdautils/phatUtils.h | 27 ++
vignettes/article.Rnw | 11
31 files changed, 467 insertions(+), 179 deletions(-)
Title: Kriging-based Inversion for Deterministic and Noisy Computer
Experiments
Diff between KrigInv versions 1.3 dated 2012-08-10 and 1.3.1 dated 2014-12-22
Description: Criteria and algorithms for sequentially estimating level sets of a multivariate numerical function, possibly observed with noise.
Author: Clement Chevalier, Victor Picheny and David Ginsbourger
Maintainer: Clement Chevalier
DESCRIPTION | 23 ++++++-----
MD5 | 78 +++++++++++++++++++-------------------
NAMESPACE | 7 ++-
R/print_uncertainty_1d.R | 9 +++-
man/EGI.Rd | 11 ++---
man/EGIparallel.Rd | 6 +-
man/bichon_optim.Rd | 4 -
man/computeAuxVariables_noChol.Rd | 4 -
man/computeAuxVariables_update.Rd | 4 -
man/computeQuickKrigcov.Rd | 4 -
man/computeRealVolumeConstant.Rd | 9 ++--
man/integration_design.Rd | 6 +-
man/jn_optim.Rd | 6 +-
man/max_infill_criterion.Rd | 4 -
man/max_sur.Rd | 6 +-
man/max_sur_parallel.Rd | 6 +-
man/max_timse.Rd | 6 +-
man/max_timse_parallel.Rd | 6 +-
man/max_vorob_parallel.Rd | 6 +-
man/precomputeUpdateData.Rd | 4 -
man/predict_nobias_km.Rd | 4 -
man/predict_update_km.Rd | 4 -
man/predict_update_km_parallel.Rd | 4 -
man/print_uncertainty.Rd | 4 -
man/print_uncertainty_1d.Rd | 8 +--
man/print_uncertainty_2d.Rd | 4 -
man/print_uncertainty_nd.Rd | 4 -
man/ranjan_optim.Rd | 4 -
man/sur_optim.Rd | 6 +-
man/sur_optim_parallel.Rd | 6 +-
man/sur_optim_parallel2.Rd | 6 +-
man/timse_optim.Rd | 6 +-
man/timse_optim_parallel.Rd | 6 +-
man/timse_optim_parallel2.Rd | 6 +-
man/tmse_optim.Rd | 4 -
man/tsee_optim.Rd | 4 -
man/update_km.Rd | 4 -
man/vorob_optim_parallel.Rd | 6 +-
man/vorob_optim_parallel2.Rd | 6 +-
man/vorob_threshold.Rd | 7 +--
40 files changed, 164 insertions(+), 148 deletions(-)
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods
Diff between GLDEX versions 2.0.0.1 dated 2014-11-01 and 2.0.0.2 dated 2014-12-22
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/pgl.R | 2 +-
man/GLDEX.package.Rd | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Diff between etasFLP versions 1.1.1 dated 2014-10-30 and 1.2.0 dated 2014-12-22
Description: Estimation of the components of an ETAS model for earthquake description.
Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood.
The two estimation steps are alternated until convergence is obtained.
For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi
ChangeLog | 14 +
DESCRIPTION | 8
MD5 | 18 +
NAMESPACE | 2
R/etas.starting.R |only
R/plot.etasclass.R | 427 +++++++++++++++++++++++++++++++++++++++++++---
man/etas.starting.Rd |only
man/etasFLP-package.Rd | 8
man/etasclass.Rd | 7
man/plot.etasclass.Rd | 84 ++++++++-
src/fortran_etas_code.f90 | 290 +++++--------------------------
11 files changed, 582 insertions(+), 276 deletions(-)
Title: Dynamic Documents for R
Diff between rmarkdown versions 0.3.3 dated 2014-09-17 and 0.4.2 dated 2014-12-22
Description: Convert R Markdown documents into a variety of formats
including HTML, MS Word, PDF, and Beamer.
Author: JJ Allaire, Jonathan McPherson, Yihui Xie, Hadley Wickham, Joe Cheng,
Jeff Allen
Maintainer: JJ Allaire
default.html | 7
tmp/cranberry1a3865c87e5a/rmarkdown-0.3.3/rmarkdown/inst/rmd/h/bootstrap-2.3.2 |only
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/DESCRIPTION | 8
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/MD5 | 121 +++++-----
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/NAMESPACE | 1
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/NEWS |only
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/html_dependencies.R | 17 -
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/html_extras.R | 7
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/ioslides_presentation.R | 2
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/output_format.R | 4
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/pandoc.R | 26 +-
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/pdf_document.R | 12
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/render.R | 8
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/shiny.R | 103 ++++++--
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/slidy_presentation.R | 2
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/tufte_handout.R | 5
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/R/util.R | 22 +
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/NOTICE | 54 ++++
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd | 2
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex | 5
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmd/beamer/default.tex | 17 -
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmd/h/bootstrap-3.3.1 |only
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmd/h/default.html | 8
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmd/ioslides/ioslides-13.5.1/theme/css/default.css | 5
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmd/ioslides/ioslides_presentation.lua | 1
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/inst/rmd/latex/default.tex | 64 ++---
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/man/metadata.Rd | 11
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/man/pandoc_args.Rd | 8
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/man/pdf_document.Rd | 1
tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/man/run.Rd | 18 +
30 files changed, 377 insertions(+), 162 deletions(-)
Title: Data sets and scripts for Modeling Psychophysical Data in R.
Diff between MPDiR versions 0.1-15 dated 2014-03-26 and 0.1-16 dated 2014-12-22
Description: Data sets and scripts for Modeling Psychophysical Data in R (Springer).
Author: Kenneth Knoblauch and Laurence T. Maloney
Maintainer: Ken Knoblauch
DESCRIPTION | 12 +++----
MD5 | 36 +++++++++++------------
R/polmer.R | 73 +++---------------------------------------------
data/Chromatic.rda |binary
data/ConfRates.rda |binary
data/Context.rda |binary
data/CorticalCells.rda |binary
data/Faces.rda |binary
data/Faces2.rda |binary
data/Gabor.rda |binary
data/Grue.rda |binary
data/HSP.rda |binary
data/ModelFest.df.rda |binary
data/Motion.rda |binary
data/StairCase.rda |binary
data/Vernier.rda |binary
inst/NEWS | 4 ++
inst/scripts/Ch9.R | 74 +++++++++++++++++++++++++++++++++++++++++++++++++
man/polmer.Rd | 25 +++++-----------
19 files changed, 116 insertions(+), 108 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Diff between MixGHD versions 1.2 dated 2014-12-10 and 1.3 dated 2014-12-22
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MSGHD, mixture of multiple scaled generalized hyperbolic distributions. The cMSGHD is a MSGHD with convex contour plots. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/MCGHD.R | 2 +-
R/MGHD.R | 2 +-
R/MSGHD.R | 2 +-
R/Selection.R | 22 +++++++++++-----------
R/cMSGHD.R | 2 +-
man/DA.Rd | 8 ++++----
man/MCGHD.Rd | 4 ++--
man/MGHD.Rd | 6 +++---
man/MGHFA.Rd | 6 +++---
man/MSGHD.Rd | 6 +++---
man/Selection.Rd | 6 +++---
man/cMSGHD.Rd | 6 +++---
14 files changed, 53 insertions(+), 53 deletions(-)
Title: A Comprehensive, General Purpose Population Genetics Analysis
Package
Diff between diveRsity versions 1.9.5 dated 2014-04-29 and 1.9.73 dated 2014-12-22
Description: Allows the calculation of both genetic diversity partition
statistics,genetic differentiation statistics and locus
informativeness for ancestry assignment. It also provides users
with various option to calculate bootstrapped 95% confidence
intervals both across loci, for pairwise population comparisons
and to plot these results interactively. V1.2 and up provides
parallel computing capabilities and pairwise results without
bootstrapping. Weir and Cockerham's 1984 F-statistics are now
also calculated. Various plotting features are also provided.
Chi-square tests of genetic heterogeneity are also provided.
Functionality for the calculation of various diversity
parameters is also possible for RAD-seq derived SNP data sets
containing thousands of marker loci. A shiny application for
the development of microsatellite multiplexes is also available
Author: Kevin Keenan
Maintainer: Kevin Keenan
diveRsity-1.9.5/diveRsity/R/diveRsity-code.R |only
diveRsity-1.9.5/diveRsity/man/difPlot.rd |only
diveRsity-1.9.5/diveRsity/man/div.part.Rd |only
diveRsity-1.9.5/diveRsity/man/in.calc.Rd |only
diveRsity-1.9.5/diveRsity/man/readGenepop.user.Rd |only
diveRsity-1.9.5/diveRsity/man/snp2gp.Rd |only
diveRsity-1.9.73/diveRsity/DESCRIPTION | 46
diveRsity-1.9.73/diveRsity/MD5 | 100 +
diveRsity-1.9.73/diveRsity/NAMESPACE | 10
diveRsity-1.9.73/diveRsity/R/RcppExports.R | 74 -
diveRsity-1.9.73/diveRsity/R/arp2gen.R |only
diveRsity-1.9.73/diveRsity/R/bigDivPart.R |only
diveRsity-1.9.73/diveRsity/R/chiCalc.R |only
diveRsity-1.9.73/diveRsity/R/corPlot.R |only
diveRsity-1.9.73/diveRsity/R/corPlotter.R |only
diveRsity-1.9.73/diveRsity/R/diffCalc.R |only
diveRsity-1.9.73/diveRsity/R/diffPlot.R |only
diveRsity-1.9.73/diveRsity/R/divBasic.R |only
diveRsity-1.9.73/diveRsity/R/divMigrate.R |only
diveRsity-1.9.73/diveRsity/R/divMigrateOnline.R |only
diveRsity-1.9.73/diveRsity/R/divOnline.R |only
diveRsity-1.9.73/diveRsity/R/divPart.R |only
diveRsity-1.9.73/diveRsity/R/divRatio.R |only
diveRsity-1.9.73/diveRsity/R/divSimCo.R |only
diveRsity-1.9.73/diveRsity/R/fastDivPart.R |only
diveRsity-1.9.73/diveRsity/R/fileReader.R |only
diveRsity-1.9.73/diveRsity/R/fstOnly.R |only
diveRsity-1.9.73/diveRsity/R/fstWC.R |only
diveRsity-1.9.73/diveRsity/R/gpSampler.R |only
diveRsity-1.9.73/diveRsity/R/haploDiv.R |only
diveRsity-1.9.73/diveRsity/R/hweFun.R |only
diveRsity-1.9.73/diveRsity/R/inCalc.R |only
diveRsity-1.9.73/diveRsity/R/microPlexer.R |only
diveRsity-1.9.73/diveRsity/R/multiplot.R |only
diveRsity-1.9.73/diveRsity/R/plotter.R |only
diveRsity-1.9.73/diveRsity/R/polyIn.R |only
diveRsity-1.9.73/diveRsity/R/pre.divLowMemory.R |only
diveRsity-1.9.73/diveRsity/R/preBigDiv.R |only
diveRsity-1.9.73/diveRsity/R/pwDivCalc.R |only
diveRsity-1.9.73/diveRsity/R/readGenepop.R |only
diveRsity-1.9.73/diveRsity/R/readGenepopX.R |only
diveRsity-1.9.73/diveRsity/R/rgp.R |only
diveRsity-1.9.73/diveRsity/R/snp2gen.R |only
diveRsity-1.9.73/diveRsity/R/statCalc.R |only
diveRsity-1.9.73/diveRsity/R/writeBoot.R |only
diveRsity-1.9.73/diveRsity/build/vignette.rds |binary
diveRsity-1.9.73/diveRsity/data/Test_data.rda |binary
diveRsity-1.9.73/diveRsity/data/pop_stats.rda |binary
diveRsity-1.9.73/diveRsity/inst/diveRsity-online/server.R | 943 +++++---------
diveRsity-1.9.73/diveRsity/inst/diveRsity-online/ui.R | 174 +-
diveRsity-1.9.73/diveRsity/inst/doc/diveRsity.pdf |binary
diveRsity-1.9.73/diveRsity/man/Tab.Rd |only
diveRsity-1.9.73/diveRsity/man/bsFun.Rd | 3
diveRsity-1.9.73/diveRsity/man/chiCalc.Rd | 105 -
diveRsity-1.9.73/diveRsity/man/corPlot.rd | 82 -
diveRsity-1.9.73/diveRsity/man/corPlotter.Rd |only
diveRsity-1.9.73/diveRsity/man/diffCalc.Rd | 13
diveRsity-1.9.73/diveRsity/man/diffCalcHarm.Rd |only
diveRsity-1.9.73/diveRsity/man/diffPlot.rd |only
diveRsity-1.9.73/diveRsity/man/divBasic.Rd | 138 +-
diveRsity-1.9.73/diveRsity/man/divMigrate.Rd | 114 -
diveRsity-1.9.73/diveRsity/man/divMigrateOnline.Rd |only
diveRsity-1.9.73/diveRsity/man/divRatio.Rd | 146 +-
diveRsity-1.9.73/diveRsity/man/divSimCo.Rd |only
diveRsity-1.9.73/diveRsity/man/fastDivPart.Rd | 199 +-
diveRsity-1.9.73/diveRsity/man/genos2mat.Rd |only
diveRsity-1.9.73/diveRsity/man/hweFun.Rd |only
diveRsity-1.9.73/diveRsity/man/inCalc.Rd | 160 +-
diveRsity-1.9.73/diveRsity/man/multiplot.Rd |only
diveRsity-1.9.73/diveRsity/man/pwTabMerge.Rd |only
diveRsity-1.9.73/diveRsity/man/snp2gen.Rd |only
diveRsity-1.9.73/diveRsity/man/statCalc.Rd | 5
diveRsity-1.9.73/diveRsity/man/tabMerge.Rd |only
diveRsity-1.9.73/diveRsity/src/RcppExports.cpp | 79 +
diveRsity-1.9.73/diveRsity/src/Tab.cpp |only
diveRsity-1.9.73/diveRsity/src/diffCalcHarm.cpp |only
diveRsity-1.9.73/diveRsity/src/genos2mat.cpp |only
diveRsity-1.9.73/diveRsity/src/pwHt.cpp | 39
diveRsity-1.9.73/diveRsity/src/pwTabMerge.cpp |only
diveRsity-1.9.73/diveRsity/src/tabMerge.cpp |only
80 files changed, 1184 insertions(+), 1246 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.1 dated 2014-12-19 and 0.2.2 dated 2014-12-22
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
R/vardchanges.R | 5 +++--
R/vardcros.R | 4 ++--
R/vardom.R | 4 ++--
R/vardom_othstr.R | 4 ++--
R/vardomh.R | 2 +-
inst/CITATION | 4 ++--
inst/NEWS | 4 ++++
man/vardchanges.Rd | 10 ++++++----
man/vardcros.Rd | 10 ++++++----
man/vardom.Rd | 4 +++-
man/vardomh.Rd | 4 +++-
man/vardpoor-package.Rd | 6 +++---
man/variance_est.Rd | 2 ++
man/varpoord.Rd | 2 +-
16 files changed, 59 insertions(+), 44 deletions(-)
Title: Target Inhibition Interaction using Maximization and
Minimization Averaging
Diff between timma versions 0.99.0 dated 2014-12-09 and 1.0.0 dated 2014-12-22
Description: Target Inhibition Interaction using Maximization/Minimization
Averaging
Author: Liye
Maintainer: Liye He
DESCRIPTION | 7 +-
MD5 | 53 +++++++++++++++------
R/ci.R |only
R/drawGraph.R | 83 +++++++++++++++++++++++++++-------
R/drugRank.R | 3 +
R/kiba.R |only
R/miller_drug_response.R |only
R/miller_drugs.R |only
R/miller_interaction_binary.R |only
R/miller_sensitivity.R |only
R/miller_targets.R |only
R/sffsBinary.R | 16 +++---
R/sffsBinary1.R | 14 +++--
R/sffsBinary2.R | 14 +++--
R/sffsCategory.R | 14 +++--
R/sffsCategory1.R | 14 +++--
R/sffsCategoryWeighted.R | 14 +++--
R/sffsCategoryWeighted1.R | 15 +++---
R/timma.R | 30 ++++++++----
data/ci.rda |only
data/datalist |only
data/kiba.rda |only
data/miller_drug_response.rda |only
data/miller_drugs.rda |only
data/miller_interaction_binary.rda |only
data/miller_sensitivity.rda |only
data/tyner_interaction_binary.rda |binary
data/tyner_interaction_multiclass.rda |binary
data/tyner_sensitivity.rda |binary
man/ci.Rd |only
man/drawGraph.Rd | 7 ++
man/kiba.Rd |only
man/miller_drug_response.Rd |only
man/miller_drugs.Rd |only
man/miller_interaction_binary.Rd |only
man/miller_sensitivity.Rd |only
man/miller_targets.Rd |only
man/timma.Rd | 6 ++
38 files changed, 200 insertions(+), 90 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Diff between gets versions 0.1 dated 2014-10-15 and 0.2 dated 2014-12-22
Description: Automated multi-path General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting structural breaks in the mean. The mean can be specified as an autoregressive model with covariates (an 'AR-X' model), and the variance can be specified as a log-variance model with covariates (a 'log-ARCH-X' model). The four main functions of the package are arx, getsm, getsv and isat. The first function, arx, estimates an AR-X model with log-ARCH-X errors. The second function, getsm, undertakes GETS model selection of the mean specification of an arx object. The third function, getsv, undertakes GETS model selection of the log-variance specification of an arx object. The fourth function, isat, undertakes GETS model selection of an indicator saturated mean specification.
Author: Felix Pretis, James Reade, Genaro Sucarrat
Maintainer: Genaro Sucarrat
gets-0.1/gets/R/glog.ep.R |only
gets-0.1/gets/R/regs.mean.R |only
gets-0.1/gets/R/regs.var.R |only
gets-0.1/gets/man/glog.ep.Rd |only
gets-0.1/gets/man/regs.mean.Rd |only
gets-0.1/gets/man/regs.var.Rd |only
gets-0.2/gets/DESCRIPTION | 18
gets-0.2/gets/MD5 | 76 +-
gets-0.2/gets/NAMESPACE | 6
gets-0.2/gets/NEWS | 41 +
gets-0.2/gets/R/arx.R | 575 ++++++++++++--------
gets-0.2/gets/R/coef.arx.R | 55 +
gets-0.2/gets/R/coef.gets.R | 14
gets-0.2/gets/R/diagnostics.R |only
gets-0.2/gets/R/dropvar.R |only
gets-0.2/gets/R/eqwma.R | 8
gets-0.2/gets/R/fitted.arx.R | 35 +
gets-0.2/gets/R/fitted.gets.R | 8
gets-0.2/gets/R/getsm.R | 1010 ++++++++++++++++++------------------
gets-0.2/gets/R/getsv.R | 940 +++++++++++++++++----------------
gets-0.2/gets/R/isat.R |only
gets-0.2/gets/R/isatvar.R |only
gets-0.2/gets/R/leqwma.R | 6
gets-0.2/gets/R/plot.arx.R |only
gets-0.2/gets/R/plot.gets.R |only
gets-0.2/gets/R/print.arx.R | 22
gets-0.2/gets/R/print.gets.R | 56 +
gets-0.2/gets/R/residuals.gets.R | 13
gets-0.2/gets/R/skewness.test.R | 21
gets-0.2/gets/R/summary.arx.R | 3
gets-0.2/gets/R/summary.gets.R | 3
gets-0.2/gets/R/vcov.arx.R | 30 -
gets-0.2/gets/R/vcov.gets.R | 7
gets-0.2/gets/man/arx.Rd | 85 +--
gets-0.2/gets/man/coef.arx.Rd | 70 +-
gets-0.2/gets/man/coef.gets.Rd | 103 +--
gets-0.2/gets/man/diagnostics.Rd |only
gets-0.2/gets/man/dropvar.Rd |only
gets-0.2/gets/man/eqwma.Rd | 37 -
gets-0.2/gets/man/gets-package.Rd | 43 +
gets-0.2/gets/man/getsm.Rd | 98 +--
gets-0.2/gets/man/hpdata.Rd | 10
gets-0.2/gets/man/info.criterion.Rd | 14
gets-0.2/gets/man/isat.Rd |only
gets-0.2/gets/man/isatvar.Rd |only
gets-0.2/gets/man/jb.test.Rd | 1
gets-0.2/gets/man/ols.Rd | 4
47 files changed, 1874 insertions(+), 1538 deletions(-)
Title: General-to-Specific (GETS) Model Selection
Diff between AutoSEARCH versions 1.3 dated 2014-10-22 and 1.4 dated 2014-12-22
Description: Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or of a log-ARCH-X model of the error. NOTE: The package has been succeeded by the package gets, also available on the CRAN, which is intended to be more user-friendly, faster and easier to extend. AutoSEARCH will continue to be maintained, but the development focus will switch to gets. Users are therefore encouraged to consider gets instead.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 5 +++++
man/AutoSEARCH-package.Rd | 4 ++--
man/ols.fit1.Rd | 2 +-
man/regs.mean.sm.Rd | 1 -
man/regs.vol.sm.Rd | 2 --
7 files changed, 18 insertions(+), 16 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-09-08 1.2
2010-01-28 1.1
2009-12-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-03 0.9.1
2011-12-15 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-11 0.14.3.11
2013-08-07 0.13.8
2013-03-14 0.13.03
2013-01-04 0.13.01
2012-06-19 0.12.06
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-05-02 0.0.1
Title: Manipulations of Triangular Meshes Based on the VCGLIB API
Diff between Rvcg versions 0.10 dated 2014-12-16 and 0.10.1 dated 2014-12-22
Description: Operations on triangular meshes based on VCGLIB. This package
integrates nicely with the R-package "rgl" to render the meshes processed
by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL
license, and it is the base of most of the software tools of the Visual
Computing Lab of the Italian National Research Council Institute ISTI
(http://vcg.isti.cnr.it), like metro and MeshLab.
The vcglib source is pulled from
trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work
with options determined by the configure script as well as
to work with the header files included by RcppEigen.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager
DESCRIPTION | 12 +---
MD5 | 24 ++++-----
R/Rvcg-package.R | 4 -
R/vcgImport.r | 52 ++++++++++++++++---
R/vcgIsosurface.r | 21 ++++---
R/vcgUniformRemesh.r | 1
inst/NEWS.Rd | 12 ++++
man/Rvcg-package.Rd | 4 -
man/vcgIsosurface.Rd | 11 +---
man/vcgUniformRemesh.Rd | 1
src/RallRead.cpp | 56 +++++++++++++--------
src/Rmarch.cpp | 16 ++----
src/vcglib/vcg/complex/algorithms/point_sampling.h | 1
13 files changed, 137 insertions(+), 78 deletions(-)
Title: Inference for Hidden Markov and Semi-Markov Models
Diff between mhsmm versions 0.4.12 dated 2014-01-09 and 0.4.14 dated 2014-12-22
Description: Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. Suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.
Author: Jared O'Connell
Maintainer: Jared O'Connell
ChangeLog | 38 +++++++++++--------
DESCRIPTION | 15 ++-----
MD5 | 79 ++++++++++++++++++++---------------------
README |only
build/vignette.rds |binary
inst/CITATION | 3 -
inst/doc/DHMM1.Rnw | 3 +
inst/doc/DHMM2.Rnw | 4 +-
man/addStates.Rd | 2 -
man/dmvnorm.hsmm.Rd | 2 -
man/dnorm.hsmm.Rd | 2 -
man/dpois.hsmm.Rd | 2 -
man/gammafit.Rd | 2 -
man/hmmfit.Rd | 2 -
man/hmmspec.Rd | 2 -
man/hsmmfit.Rd | 2 -
man/hsmmspec.Rd | 2 -
man/mstep.mvnorm.Rd | 2 -
man/mstep.norm.Rd | 2 -
man/mstep.pois.Rd | 2 -
man/plot.hsmm.Rd | 2 -
man/plot.hsmm.data.Rd | 2 -
man/predict.hmm.Rd | 2 -
man/predict.hmmspec.Rd | 2 -
man/predict.hsmm.Rd | 2 -
man/predict.hsmmspec.Rd | 2 -
man/print.hmm.Rd | 2 -
man/print.hmmspec.Rd | 2 -
man/print.hsmmspec.Rd | 2 -
man/rmvnorm.hsmm.Rd | 2 -
man/rnorm.hsmm.Rd | 2 -
man/rpois.hsmm.Rd | 2 -
man/sim.mc.Rd | 2 -
man/simulate.hmmspec.Rd | 2 -
man/simulate.hsmmspec.Rd | 2 -
man/summary.hmm.Rd | 2 -
man/summary.hsmm.Rd | 2 -
vignettes/DHMM1.Rnw | 3 +
vignettes/DHMM2.Rnw | 4 +-
vignettes/fig/dhmm-clsfig1.pdf |binary
vignettes/fig/dhmm-clsfig2.pdf |binary
41 files changed, 105 insertions(+), 102 deletions(-)
Title: Helsinki Open Data R Tools
Diff between helsinki versions 0.9.22 dated 2014-12-19 and 0.9.24 dated 2014-12-22
Description: Tools for accessing various open data sources in the Helsinki
region in Finland. Current data sources include
the Real Estate Department (district maps),
the Environmental Services Authority,
Service Map API,
Linked Events API and
Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen, Leo Lahti, Joona Lehtomaki
Maintainer: Juuso Parkkinen
helsinki-0.9.22/helsinki/R/demography.R |only
helsinki-0.9.22/helsinki/R/economy.R |only
helsinki-0.9.22/helsinki/man/get_economic_indicators.Rd |only
helsinki-0.9.22/helsinki/man/get_population_projection.Rd |only
helsinki-0.9.24/helsinki/DESCRIPTION | 12
helsinki-0.9.24/helsinki/MD5 | 17
helsinki-0.9.24/helsinki/NAMESPACE | 2
helsinki-0.9.24/helsinki/inst/extras/demography.R |only
helsinki-0.9.24/helsinki/inst/extras/economy.R |only
helsinki-0.9.24/helsinki/vignettes/figure/hsy_ramava-1.png |only
helsinki-0.9.24/helsinki/vignettes/helsinki_tutorial.Rmd | 37 -
helsinki-0.9.24/helsinki/vignettes/helsinki_tutorial.html | 367 +++++--------
helsinki-0.9.24/helsinki/vignettes/helsinki_tutorial.md | 284 +++-------
13 files changed, 277 insertions(+), 442 deletions(-)
Title: Neural Networks in R using the Stuttgart Neural Network
Simulator (SNNS)
Diff between RSNNS versions 0.4-5 dated 2014-05-23 and 0.4-6 dated 2014-12-22
Description: The Stuttgart Neural Network Simulator (SNNS) is a library
containing many standard implementations of neural networks. This
package wraps the SNNS functionality to make it available from
within R. Using the RSNNS low-level interface, all of the
algorithmic functionality and flexibility of SNNS can be accessed.
Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and
learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir and José M. BenÃtez
Maintainer: Christoph Bergmeir
ChangeLog | 9
DESCRIPTION | 15 -
MD5 | 218 +++++++--------
NAMESPACE | 44 +--
R/art1.R | 2
R/art2.R | 2
R/artmap.R | 2
R/assoz.R | 2
R/dlvq.R | 2
R/elman.R | 2
R/jordan.R | 2
R/mlp.R | 2
R/rbf.R | 2
R/rbfDDA.R | 2
R/reg_class.R | 2
R/rsnns.R | 10
R/som.R | 2
R/util.R | 15 -
demo/iris.R | 4
demo/mlp_irisSnnsR.R | 4
demo/mlp_iris_tuning.R | 4
demo/pruning_iris.R | 4
demo/pruning_irisSnnsR.R | 5
demo/rbf_irisSnnsR.R | 4
demo/rbf_sin.R | 38 +-
demo/rbf_sinSnnsR.R | 126 ++++-----
man/RSNNS-package.Rd | 236 +++++++----------
man/SnnsR-class.Rd | 57 +---
man/SnnsRObject-createNet.Rd | 31 --
man/SnnsRObject-createPatSet.Rd | 20 -
man/SnnsRObject-extractNetInfo.Rd | 20 -
man/SnnsRObject-extractPatterns.Rd | 16 -
man/SnnsRObject-genericPredictCurrPatSet.Rd | 18 -
man/SnnsRObject-getAllHiddenUnits.Rd | 17 -
man/SnnsRObject-getAllInputUnits.Rd | 17 -
man/SnnsRObject-getAllOutputUnits.Rd | 17 -
man/SnnsRObject-getAllUnits.Rd | 11
man/SnnsRObject-getAllUnitsTType.Rd | 29 --
man/SnnsRObject-getCompleteWeightMatrix.Rd | 15 -
man/SnnsRObject-getInfoHeader.Rd | 12
man/SnnsRObject-getSiteDefinitions.Rd | 12
man/SnnsRObject-getTypeDefinitions.Rd | 12
man/SnnsRObject-getUnitDefinitions.Rd | 12
man/SnnsRObject-getUnitsByName.Rd | 14 -
man/SnnsRObject-getWeightMatrix.Rd | 24 -
man/SnnsRObject-initializeNet.Rd | 20 -
man/SnnsRObject-predictCurrPatSet.Rd | 27 -
man/SnnsRObject-resetRSNNS.Rd | 12
man/SnnsRObject-setTTypeUnitsActFunc.Rd | 21 -
man/SnnsRObject-setUnitDefaults.Rd | 33 +-
man/SnnsRObject-somPredictComponentMaps.Rd | 16 -
man/SnnsRObject-somPredictCurrPatSetWinners.Rd | 40 +-
man/SnnsRObject-somPredictCurrPatSetWinnersSpanTree.Rd | 23 -
man/SnnsRObject-train.Rd | 76 ++---
man/SnnsRObject-whereAreResults.Rd | 26 -
man/SnnsRObjectFactory.Rd | 15 -
man/SnnsRObjectMethodCaller.Rd | 73 ++---
man/analyzeClassification.Rd | 89 ++----
man/art1.Rd | 182 +++++--------
man/art2.Rd | 109 +++----
man/artmap.Rd | 158 ++++-------
man/assoz.Rd | 84 ++----
man/confusionMatrix.Rd | 23 -
man/decodeClassLabels.Rd | 36 +-
man/denormalizeData.Rd | 24 -
man/dlvq.Rd | 112 +++-----
man/elman.Rd | 111 +++----
man/encodeClassLabels.Rd | 21 -
man/exportToSnnsNetFile.Rd | 15 -
man/extractNetInfo.Rd | 25 -
man/getNormParameters.Rd | 19 -
man/getSnnsRDefine.Rd | 17 -
man/getSnnsRFunctionTable.Rd | 15 -
man/inputColumns.Rd | 11
man/jordan.Rd | 142 ++++------
man/matrixToActMapList.Rd | 28 --
man/mlp.Rd | 136 ++++-----
man/normTrainingAndTestSet.Rd | 43 +--
man/normalizeData.Rd | 42 +--
man/outputColumns.Rd | 11
man/plotActMap.Rd | 11
man/plotIterativeError.Rd | 20 -
man/plotROC.Rd | 16 -
man/plotRegressionError.Rd | 18 -
man/predict.rsnns.Rd | 15 -
man/print.rsnns.Rd | 11
man/rbf.Rd | 135 +++------
man/rbfDDA.Rd | 86 ++----
man/readPatFile.Rd | 14 -
man/readResFile.Rd | 13
man/resolveSnnsRDefine.Rd | 17 -
man/rsnnsObjectFactory.Rd | 84 ++----
man/savePatFile.Rd | 15 -
man/setSnnsRSeedValue.Rd | 12
man/snnsData.Rd | 12
man/som.Rd | 149 ++++------
man/splitForTrainingAndTest.Rd | 27 -
man/summary.rsnns.Rd | 29 --
man/toNumericClassLabels.Rd | 10
man/train.Rd | 40 +-
man/vectorToActMap.Rd | 25 -
man/weightMatrix.Rd | 19 -
src/SnnsCLib.cpp | 60 ++++
src/SnnsCLibWrapper.cpp | 3
src/cc_glob.cpp | 2
src/kernel.cpp | 3
src/kr_io.cpp | 2
src/learn_f.cpp | 22 +
src/prun_f.cpp | 40 +-
src/u_lrand48.cpp | 29 +-
110 files changed, 1758 insertions(+), 2130 deletions(-)
Title: Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
Diff between pvclust versions 1.3-1 dated 2014-12-05 and 1.3-2 dated 2014-12-22
Description: An implementation of multiscale bootstrap resampling for
assessing the uncertainty in hierarchical cluster analysis.
It provides AU (approximately unbiased) p-value as well as
BP (bootstrap probability) value for each cluster in a dendrogram.
Author: Ryota Suzuki
Maintainer: Ryota Suzuki
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/pvclust.R | 10 +++++++---
3 files changed, 13 insertions(+), 9 deletions(-)