Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.1.1 dated 2015-05-22 and 1.1.2 dated 2015-06-29
stochvol-1.1.1/stochvol/inst/doc/heavytails.R |only stochvol-1.1.1/stochvol/inst/doc/heavytails.Rnw |only stochvol-1.1.1/stochvol/inst/doc/heavytails.pdf |only stochvol-1.1.1/stochvol/vignettes/heavytails.Rnw |only stochvol-1.1.2/stochvol/DESCRIPTION | 10 +++++----- stochvol-1.1.2/stochvol/MD5 | 22 ++++++++++------------ stochvol-1.1.2/stochvol/NAMESPACE | 3 +++ stochvol-1.1.2/stochvol/NEWS | 3 +++ stochvol-1.1.2/stochvol/build/vignette.rds |binary stochvol-1.1.2/stochvol/data/exrates.RData |binary stochvol-1.1.2/stochvol/inst/doc/article.pdf |binary stochvol-1.1.2/stochvol/src/sampler.cpp | 4 ++-- stochvol-1.1.2/stochvol/vignettes/Makefile | 2 +- stochvol-1.1.2/stochvol/vignettes/heavytails.R |only stochvol-1.1.2/stochvol/vignettes/heavytails.pdf |only 15 files changed, 24 insertions(+), 20 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKmisc versions 0.98 dated 2015-03-30 and 0.99 dated 2015-06-29
DESCRIPTION | 14 +++++++------- MD5 | 10 ++++++---- NAMESPACE | 11 ++++++++--- NEWS | 25 ++++++++++++++++++------- R/mi.t.test.R |only man/0MKmisc-package.Rd | 14 ++++++++------ man/mi.t.test.Rd |only 7 files changed, 47 insertions(+), 27 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.1 dated 2015-05-17 and 1.2 dated 2015-06-29
HelpersMG-1.1/HelpersMG/R/getTide.R |only HelpersMG-1.1/HelpersMG/R/moon_phase.R |only HelpersMG-1.1/HelpersMG/R/temperature.periodic.R |only HelpersMG-1.1/HelpersMG/man/getTide.Rd |only HelpersMG-1.1/HelpersMG/man/moon_phase.Rd |only HelpersMG-1.1/HelpersMG/man/temperature.periodic.Rd |only HelpersMG-1.2/HelpersMG/DESCRIPTION | 10 - HelpersMG-1.2/HelpersMG/MD5 | 49 +++++---- HelpersMG-1.2/HelpersMG/NAMESPACE | 14 ++ HelpersMG-1.2/HelpersMG/NEWS | 11 +- HelpersMG-1.2/HelpersMG/R/HelpersMG-package.R | 7 - HelpersMG-1.2/HelpersMG/R/LD50.R |only HelpersMG-1.2/HelpersMG/R/LD50_fit.R |only HelpersMG-1.2/HelpersMG/R/MHalgoGen.R | 2 HelpersMG-1.2/HelpersMG/R/compare_AIC.R | 5 HelpersMG-1.2/HelpersMG/R/ind_long_lat.R | 8 - HelpersMG-1.2/HelpersMG/R/index.periodic.R |only HelpersMG-1.2/HelpersMG/R/logLik.LD50.R |only HelpersMG-1.2/HelpersMG/R/minmax.periodic.R | 104 +++++++++++++------- HelpersMG-1.2/HelpersMG/R/moon.info.R |only HelpersMG-1.2/HelpersMG/R/plot.LD50.R |only HelpersMG-1.2/HelpersMG/R/predict.LD50.R |only HelpersMG-1.2/HelpersMG/R/sun.info.R | 7 - HelpersMG-1.2/HelpersMG/R/tide.info.R |only HelpersMG-1.2/HelpersMG/man/HelpersMG-package.Rd | 7 - HelpersMG-1.2/HelpersMG/man/LD50.Rd |only HelpersMG-1.2/HelpersMG/man/compare_AIC.Rd | 5 HelpersMG-1.2/HelpersMG/man/ind_long_lat.Rd | 8 - HelpersMG-1.2/HelpersMG/man/index.periodic.Rd |only HelpersMG-1.2/HelpersMG/man/logLik.LD50.Rd |only HelpersMG-1.2/HelpersMG/man/minmax.periodic.Rd | 46 +++++--- HelpersMG-1.2/HelpersMG/man/moon.info.Rd |only HelpersMG-1.2/HelpersMG/man/plot.LD50.Rd |only HelpersMG-1.2/HelpersMG/man/predict.LD50.Rd |only HelpersMG-1.2/HelpersMG/man/sun.info.Rd | 11 +- HelpersMG-1.2/HelpersMG/man/tide.info.Rd |only 36 files changed, 192 insertions(+), 102 deletions(-)
Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on asymptotic chi-square and exact statistics. These tests were designed to reveal causality based on evidence from functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.0.2 dated 2015-03-04 and 2.1.0 dated 2015-06-29
FunChisq-2.0.2/FunChisq/src/AdjustPvalue.cpp |only FunChisq-2.0.2/FunChisq/src/ChisqDirTest.cpp |only FunChisq-2.0.2/FunChisq/src/ChisqTests.cpp |only FunChisq-2.0.2/FunChisq/src/ChisqTests.h |only FunChisq-2.0.2/FunChisq/src/ExactMultiTableTest.cpp |only FunChisq-2.0.2/FunChisq/src/ExactMultiTableTest.h |only FunChisq-2.0.2/FunChisq/src/StatDistributions.cpp |only FunChisq-2.0.2/FunChisq/src/StatDistributions.h |only FunChisq-2.0.2/FunChisq/src/TransitionTable.cpp |only FunChisq-2.0.2/FunChisq/src/TransitionTable.h |only FunChisq-2.1.0/FunChisq/DESCRIPTION | 15 FunChisq-2.1.0/FunChisq/MD5 | 37 FunChisq-2.1.0/FunChisq/NAMESPACE | 1 FunChisq-2.1.0/FunChisq/NEWS | 12 FunChisq-2.1.0/FunChisq/R/FunChisq.R | 17 FunChisq-2.1.0/FunChisq/inst/CITATION | 4 FunChisq-2.1.0/FunChisq/man/FunChisq-package.Rd | 13 FunChisq-2.1.0/FunChisq/man/cp.fun.chisq.test.Rd | 6 FunChisq-2.1.0/FunChisq/man/fun.chisq.test.Rd | 2 FunChisq-2.1.0/FunChisq/src/ExactFunctionalTest.cpp | 918 +++++++++++------ FunChisq-2.1.0/FunChisq/src/ExactFunctionalTest.h | 180 ++- FunChisq-2.1.0/FunChisq/src/Makevars |only FunChisq-2.1.0/FunChisq/src/Makevars.win |only FunChisq-2.1.0/FunChisq/src/define.h |only FunChisq-2.1.0/FunChisq/src/main.cpp | 22 FunChisq-2.1.0/FunChisq/tests/testthat/test_FunChisq.R | 9 26 files changed, 820 insertions(+), 416 deletions(-)
Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to agriculture.
Example analyses are included. Includes functions for plotting field
designs and GGE biplots.
Author: Kevin Wright
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.11 dated 2015-03-03 and 1.12 dated 2015-06-29
DESCRIPTION | 10 +-- MD5 | 98 +++++++++++++++++++++------------------ NAMESPACE | 3 + NEWS | 23 ++++++--- R/desplot.r | 27 ++++++---- R/gge.r | 4 - build/vignette.rds |binary data/cochran.beets.txt.gz |only data/cochran.lattice.txt.gz |only data/datalist | 4 + data/jansen.apple.txt.gz |only data/jansen.carrot.txt.gz |only data/karcher.turfgrass.txt.gz |binary inst/doc/agridat_examples.Rnw | 16 +++--- inst/doc/agridat_examples.pdf |binary man/agridat.Rd | 36 +++++++++++--- man/beall.webworms.Rd | 4 - man/besag.bayesian.Rd | 2 man/besag.beans.Rd | 2 man/besag.triticale.Rd | 2 man/bliss.borers.Rd | 2 man/burgueno.alpha.Rd | 2 man/burgueno.rowcol.Rd | 3 + man/burgueno.unreplicated.Rd | 3 + man/cochran.beets.Rd |only man/cochran.latin.Rd | 2 man/cochran.lattice.Rd |only man/cochran.wireworms.Rd | 11 +++- man/connolly.potato.Rd | 10 ++- man/crowder.seeds.Rd | 27 +++++----- man/cullis.earlygen.Rd | 6 +- man/diggle.cow.Rd | 2 man/hayman.tobacco.Rd | 2 man/ilri.sheep.Rd | 2 man/jansen.apple.Rd |only man/jansen.carrot.Rd |only man/jansen.strawberry.Rd | 21 +++++--- man/jenkyn.mildew.Rd | 4 - man/karcher.turfgrass.Rd | 9 +-- man/keen.potatodamage.Rd | 9 +++ man/kempton.barley.uniformity.Rd | 2 man/lasrosas.corn.Rd | 12 ++-- man/lonnquist.maize.Rd | 2 man/mercer.wheat.uniformity.Rd | 30 ++++++++--- man/snijders.fusarium.Rd | 2 man/stroup.nin.Rd | 21 ++++++-- man/theobald.covariate.Rd | 6 +- man/turner.herbicide.Rd | 45 ++++++++++++++++- man/vold.longterm.Rd | 36 +++++++------- man/wallace.iowaland.Rd | 2 man/wedderburn.barley.Rd | 2 man/welch.bermudagrass.Rd | 14 +++-- man/wiebe.wheat.uniformity.Rd | 29 ++++++----- vignettes/agridat_examples.Rnw | 16 +++--- 54 files changed, 363 insertions(+), 202 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between spatial versions 7.3-9 dated 2015-02-11 and 7.3-10 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 11 +++-------- R/pp.R | 2 +- 4 files changed, 11 insertions(+), 16 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between rpart versions 4.1-9 dated 2015-02-11 and 4.1-10 dated 2015-06-29
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 7 ++++--- build/vignette.rds |binary inst/doc/longintro.pdf |binary inst/doc/usercode.pdf |binary tests/Examples/rpart-Ex.Rout.save | 13 ++++++------- 8 files changed, 23 insertions(+), 21 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-120 dated 2015-02-20 and 3.1-121 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 7 ++----- tests/missing.Rout.save | 2 +- 4 files changed, 10 insertions(+), 13 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between nnet versions 7.3-9 dated 2015-02-11 and 7.3-10 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 11 +++-------- 3 files changed, 9 insertions(+), 14 deletions(-)
Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut],
Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between KernSmooth versions 2.23-14 dated 2015-02-11 and 2.23-15 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 3 ++- PORTING | 5 +++++ 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between class versions 7.3-12 dated 2015-02-11 and 7.3-13 dated 2015-06-29
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 2 +- man/knn1.Rd | 4 ++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between boot versions 1.3-16 dated 2015-06-07 and 1.3-17 dated 2015-06-29
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- INDEX | 7 +------ MD5 | 10 +++++----- NAMESPACE | 6 ++++-- man/print.boot.Rd | 3 ++- 6 files changed, 20 insertions(+), 18 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver.
To see list of available hydroservers, see http://hiscentral.cuahsi.org.
The package has five data download functions: GetServices(): show all public
HydroServers from the HIS Central Catalog.
HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series
from the HIS Central catalog based on geographic bounding box, server, or keyword.
GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code, start time
and endtime, fetch a data.frame of all the observation time series data values.
The data.frame has two columns: time and DataValue. This function has an optional "daily"
parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily
values. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a HydroServer Lite ODM database
via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.0.0 dated 2015-05-05 and 1.2.3 dated 2015-06-29
DESCRIPTION | 21 - MD5 | 44 +- NAMESPACE | 4 R/AddMethods.R | 2 R/GetServices.R | 1 R/GetSiteInfo.R | 748 ++++++++++++++++++++++++++----------- R/GetSites.R | 365 +++++++++++++----- R/GetValues.R | 425 +++++++++++++++++---- R/GetVariables.R | 174 +++++++- R/HISCentral_GetSeriesCatalog.R |only R/HISCentral_GetSites.R |only R/MakeSOAPEnvelope.R | 6 R/PackageDocumentation.R |only R/WaterOneFlowNamespace.R |only README.md | 12 build |only inst |only man/GetSiteInfo.Rd | 94 ++++ man/GetSites.Rd | 40 + man/GetValues.Rd | 43 ++ man/GetVariables.Rd | 23 + man/HISCentral_GetSeriesCatalog.Rd |only man/HISCentral_GetSites.Rd |only man/MakeSOAPEnvelope.Rd | 3 man/WaterML-package.Rd |only man/WaterOneFlowNamespace.Rd |only vignettes |only 27 files changed, 1569 insertions(+), 436 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.2.0 dated 2015-05-26 and 0.3.0 dated 2015-06-29
DESCRIPTION | 16 + MD5 | 70 ++++---- NAMESPACE | 12 + R/bugs.R | 27 +-- R/data.docu.R | 19 +- R/extract.old.R | 2 R/main.R | 151 +++++++++++------- R/parser.R |only R/s3.correlations.R |only R/s3.generics.R | 108 +++++++++++- R/s3.methods.R | 139 ++++++++++++++-- R/stan.R | 342 +++++++++++++++++++++++------------------ R/support.export.R | 150 +++++++++++++---- R/support.internal.R | 102 ++++-------- data/kidney.rda |binary man/VarCorr.Rd | 3 man/brm.Rd | 118 +++++++++----- man/brm.data.Rd | 16 + man/brm.pars.Rd | 11 + man/brm.plot.Rd | 3 man/brms-package.Rd | 2 man/brmsfit-class.Rd | 6 man/cor.ar.Rd |only man/cor.arma.Rd |only man/cor.brms.Rd |only man/cor.ma.Rd |only man/epilepsy.Rd | 2 man/fixef.Rd | 3 man/hypothesis.Rd |only man/inhaler.Rd | 2 man/kidney.Rd | 15 - man/ngrps.Rd | 5 man/par.names.Rd |only man/plot.brmsfit.Rd | 3 man/posterior.samples.Rd |only man/print.brmsfit.Rd | 3 man/ranef.Rd | 7 man/summary.brmsfit.Rd | 3 tests/testthat/tests.parser.R |only tests/testthat/tests.stan.R | 35 +++- tests/testthat/tests.support.R | 6 41 files changed, 916 insertions(+), 465 deletions(-)
Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Description: Functions to obtain the operational characteristics of
bioequivalence studies with 2-stage designs via simulations
- Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use both point estimate (PE) and mse from stage 1
also for the power monitoring steps.
- The third function power.2stage.fC() calculates power and sample-size
distribution of 2-stage BE studies with a futility criterion
for the PE or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
This function has a sibling power.2stage.pAF(), which performs exactly as
described in A.Fuglsang 2014
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between Power2Stage versions 0.3-1 dated 2015-01-23 and 0.4-1 dated 2015-06-29
Power2Stage-0.3-1/Power2Stage/R/sampsiz.R |only Power2Stage-0.4-1/Power2Stage/DESCRIPTION | 54 ++--- Power2Stage-0.4-1/Power2Stage/MD5 | 41 ++-- Power2Stage-0.4-1/Power2Stage/NAMESPACE | 6 Power2Stage-0.4-1/Power2Stage/NEWS | 25 ++ Power2Stage-0.4-1/Power2Stage/R/power.R | 6 Power2Stage-0.4-1/Power2Stage/R/power_2stage.R | 71 +++---- Power2Stage-0.4-1/Power2Stage/R/power_2stage_DL.R |only Power2Stage-0.4-1/Power2Stage/R/power_2stage_GS.R | 47 +--- Power2Stage-0.4-1/Power2Stage/R/power_2stage_KM.R | 61 ++---- Power2Stage-0.4-1/Power2Stage/R/power_2stage_SSR.R | 70 ++----- Power2Stage-0.4-1/Power2Stage/R/power_2stage_fC.R | 86 +++----- Power2Stage-0.4-1/Power2Stage/R/power_2stage_parallel.R | 126 +++++-------- Power2Stage-0.4-1/Power2Stage/R/power_2stage_parallel_AF.R | 81 ++------ Power2Stage-0.4-1/Power2Stage/R/print_pwrtsd_s3.R |only Power2Stage-0.4-1/Power2Stage/R/sampsiz2.R | 28 +- Power2Stage-0.4-1/Power2Stage/R/sampsiz_n0.R | 6 Power2Stage-0.4-1/Power2Stage/man/power.2stage.GS.Rd | 58 +++-- Power2Stage-0.4-1/Power2Stage/man/power.2stage.KM.Rd | 23 +- Power2Stage-0.4-1/Power2Stage/man/power.2stage.Rd | 71 +++++-- Power2Stage-0.4-1/Power2Stage/man/power.2stage.fC.Rd | 57 ++++- Power2Stage-0.4-1/Power2Stage/man/power.2stage.p.Rd | 35 ++- Power2Stage-0.4-1/Power2Stage/man/power.2stage.ssr.Rd | 30 +-- 23 files changed, 503 insertions(+), 479 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between tree versions 1.0-35 dated 2014-03-03 and 1.0-36 dated 2015-06-29
ChangeLog | 6 ++++++ DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 5 +++++ tests/Examples/tree-Ex.Rout.save | 12 ++++++------ 5 files changed, 28 insertions(+), 17 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between RODBC versions 1.3-11 dated 2015-02-26 and 1.3-12 dated 2015-06-29
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 46 +++++++++++++++++++++++----------------------- NAMESPACE | 1 + R/RODBC.R | 3 ++- R/sql.R | 3 ++- build/vignette.rds |binary inst/doc/RODBC.pdf |binary man/odbc.Rd | 3 ++- man/odbcClose.Rd | 3 ++- man/odbcConnect.Rd | 3 ++- man/odbcDataSources.Rd | 2 +- man/odbcGetInfo.Rd | 3 ++- man/odbcSetAutoCommit.Rd | 2 +- man/setSqlTypeInfo.Rd | 2 +- man/sqlColumns.Rd | 3 ++- man/sqlCopy.Rd | 3 ++- man/sqlDrop.Rd | 3 ++- man/sqlFetch.Rd | 3 ++- man/sqlQuery.Rd | 3 ++- man/sqlSave.Rd | 3 ++- man/sqlTables.Rd | 3 ++- man/sqlTypeInfo.Rd | 3 ++- src/RODBC.c | 41 +++++++++++++++++++++++------------------ 24 files changed, 87 insertions(+), 63 deletions(-)
Title: Penalized Smoothing Splines
Description: Smoothing splines with penalties on order m derivatives.
Author: S original by Jim Ramsey <ramsay@psych.mcgill.ca>.
R port by Brian Ripley <ripley@stats.ox.ac.uk>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between pspline versions 1.0-16 dated 2013-04-16 and 1.0-17 dated 2015-06-29
ChangeLog | 5 +++++ DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 +++ 4 files changed, 17 insertions(+), 9 deletions(-)
Title: Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data
Description: Estimation/multiple imputation programs for mixed categorical
and continuous data.
Author: Original by Joseph L. Schafer <jls@stat.psu.edu>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between mix versions 1.0-8 dated 2010-01-03 and 1.0-9 dated 2015-06-29
ChangeLog | 9 +++++++++ DESCRIPTION | 17 +++++++++-------- MD5 |only NAMESPACE | 2 ++ R/mix.R | 2 +- data/stlouis.rda |binary 6 files changed, 21 insertions(+), 9 deletions(-)
Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13 and 4.4)
and Brian Ripley <ripley@stats.ox.ac.uk> (version 4.13).
Note that maintainers are not available to give advice on using a
package they did not author.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between gee versions 4.13-18 dated 2012-03-14 and 4.13-19 dated 2015-06-29
ChangeLog | 10 ++++++++++ DESCRIPTION | 21 +++++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 4 +++- R/ugee.R | 6 ++---- src/ugee.c | 18 ++++++++++++++++++ src/ugee.h | 3 --- tests/Examples/gee-Ex.Rout.save | 13 +++++++------ 8 files changed, 58 insertions(+), 31 deletions(-)
Title: Tools for Inference with Set-Theoretic Comparative Methods
Description: Provides a number of functions for carrying out
inference with set-theoretic comparative methods, including
facilities for examining causal paths, assessing the sensitivity
of results to measurement and model specification error,
and performing Random Forest Comparative Analysis.
Author: Chris Krogslund [aut, cre]
Maintainer: Chris Krogslund <ckrogslund@berkeley.edu>
Diff between stcm versions 0.1.0 dated 2015-04-02 and 0.1.1 dated 2015-06-29
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- R/caret_infer.R | 6 +++--- R/cond_expand.R | 2 +- R/fsqca_sim.R | 2 +- R/fsqca_sim_inclcut.R | 4 ++-- R/get_qca_datasets.R | 6 +++--- R/hicks_20.R | 2 +- R/hicks_29.R | 2 +- R/meas_error.R | 4 ++-- R/mod_error.R | 6 +++--- R/paths_summary.R | 21 ++++++++++----------- R/rfca.R | 10 +++++----- man/fsqca_sim.Rd | 2 +- man/hicks_20.Rd | 2 +- man/hicks_29.Rd | 2 +- man/rfca.Rd | 6 +++--- 17 files changed, 59 insertions(+), 60 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers.
Among available features there are: pattern searching
(e.g. via regular expressions), random string generation,
string collation, transliteration, concatenation,
date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 0.5-4 dated 2015-06-28 and 0.5-5 dated 2015-06-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 +++--- configure | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
V. Shcherbakov;
G.C. Shen;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.42-1 dated 2015-06-05 and 1.42-2 dated 2015-06-29
DESCRIPTION | 18 +-- MD5 | 237 ++++++++++++++++++++++----------------------- NAMESPACE | 10 + NEWS | 108 ++++++++++++++++++++ R/First.R | 65 ++++++------ R/affine.R | 13 -- R/clusterinfo.R | 11 ++ R/formulae.R | 26 ++++ R/images.R | 51 +++++++-- R/kppm.R | 149 +++++++++++++++++++++++----- R/lppm.R | 8 + R/mincontrast.R | 4 R/objsurf.R | 2 R/options.R | 6 + R/pcf.R | 31 +++-- R/pcfinhom.R | 47 +++++--- R/plot.fv.R | 8 + R/plot.im.R | 24 ++-- R/ppmclass.R | 7 - R/randomNS.R | 38 ++++++- R/resolve.defaults.R | 2 R/rose.R | 79 +++++++++++++-- R/rotmean.R | 9 + R/summary.im.R | 16 +-- R/tess.R | 52 ++++----- R/triangulate.R |only R/update.ppm.R | 14 -- R/wingeom.R | 63 ++++++++--- README.md | 37 ++++--- build/vignette.rds |binary data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/cells.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary inst/CITATION | 4 inst/doc/BEGINNER.txt | 17 ++- inst/doc/datasets.Rnw | 2 inst/doc/datasets.pdf |binary inst/doc/getstart.R | 42 +++---- inst/doc/getstart.Rnw | 32 +++--- inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.R | 42 +++---- inst/doc/shapefiles.Rnw | 2 inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 4 inst/doc/updates.Rnw | 45 +++++++- inst/doc/updates.pdf |binary man/clusterfit.Rd | 7 + man/density.ppp.Rd | 10 - man/fitted.lppm.Rd |only man/fitted.ppm.Rd | 2 man/kppm.Rd | 9 + man/padimage.Rd | 22 +++- man/quad.ppm.Rd | 5 man/rCauchy.Rd | 15 ++ man/rMatClust.Rd | 16 ++- man/rThomas.Rd | 15 ++ man/rVarGamma.Rd | 15 ++ man/rose.Rd | 51 ++++++++- man/rotmean.Rd | 23 +++- man/spatstat-internal.Rd | 27 +++-- man/spatstat-package.Rd | 81 ++++++++++++--- man/tess.Rd | 7 + man/triangulate.owin.Rd |only man/update.kppm.Rd | 49 +++++---- tests/alltests.R | 10 + vignettes/datasets.Rnw | 2 vignettes/getstart.Rnw | 32 +++--- vignettes/packagesizes.txt | 3 vignettes/shapefiles.Rnw | 2 vignettes/updates.Rnw | 45 +++++++- 121 files changed, 1265 insertions(+), 508 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.2 dated 2015-06-10 and 4.5 dated 2015-06-29
seqminer-4.2/seqminer/demo/workflow.R |only seqminer-4.5/seqminer/ChangeLog | 14 seqminer-4.5/seqminer/DESCRIPTION | 13 seqminer-4.5/seqminer/MD5 | 97 +++--- seqminer-4.5/seqminer/NAMESPACE | 4 seqminer-4.5/seqminer/R/seqminer.R | 149 ++++++++-- seqminer-4.5/seqminer/README.md | 2 seqminer-4.5/seqminer/configure | 42 +- seqminer-4.5/seqminer/configure.ac | 23 - seqminer-4.5/seqminer/configure.win | 2 seqminer-4.5/seqminer/demo/00Index | 4 seqminer-4.5/seqminer/demo/annotate.R |only seqminer-4.5/seqminer/demo/meta.workflow.R |only seqminer-4.5/seqminer/demo/vcf.workflow.R |only seqminer-4.5/seqminer/inst/rvtests/cfh.refFlat.txt |only seqminer-4.5/seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz |only seqminer-4.5/seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz.tbi |only seqminer-4.5/seqminer/man/SeqMiner.Rd | 16 - seqminer-4.5/seqminer/man/annotateGene.Rd | 13 seqminer-4.5/seqminer/man/annotatePlain.Rd | 8 seqminer-4.5/seqminer/man/annotateVcf.Rd | 8 seqminer-4.5/seqminer/man/download.annotation.resource.Rd |only seqminer-4.5/seqminer/man/getCovPair.Rd | 21 - seqminer-4.5/seqminer/man/getRefBase.Rd | 11 seqminer-4.5/seqminer/man/hasIndex.Rd | 8 seqminer-4.5/seqminer/man/isDirWritable.Rd |only seqminer-4.5/seqminer/man/isInRange.Rd | 7 seqminer-4.5/seqminer/man/isURL.Rd |only seqminer-4.5/seqminer/man/makeAnnotationParameter.Rd | 4 seqminer-4.5/seqminer/man/readVCFToListByGene.Rd | 32 -- seqminer-4.5/seqminer/man/readVCFToListByRange.Rd | 29 - seqminer-4.5/seqminer/man/readVCFToMatrixByGene.Rd | 19 - seqminer-4.5/seqminer/man/readVCFToMatrixByRange.Rd | 16 - seqminer-4.5/seqminer/man/rvmeta.readCovByRange.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.readDataByGene.Rd | 22 - seqminer-4.5/seqminer/man/rvmeta.readDataByRange.Rd | 19 - seqminer-4.5/seqminer/man/rvmeta.readNullModel.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.readScoreByRange.Rd | 11 seqminer-4.5/seqminer/man/rvmeta.readSkewByRange.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.writeCovData.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.writeScoreData.Rd | 11 seqminer-4.5/seqminer/man/tabix.createIndex.Rd | 18 - seqminer-4.5/seqminer/man/tabix.createIndex.meta.Rd | 4 seqminer-4.5/seqminer/man/tabix.createIndex.vcf.Rd | 4 seqminer-4.5/seqminer/man/tabix.read.Rd | 7 seqminer-4.5/seqminer/man/tabix.read.header.Rd | 7 seqminer-4.5/seqminer/man/tabix.read.table.Rd | 13 seqminer-4.5/seqminer/man/validateAnnotationParameter.Rd | 9 seqminer-4.5/seqminer/man/verifyFilename.Rd |only seqminer-4.5/seqminer/src/Makevars.in | 2 seqminer-4.5/seqminer/src/Makevars.win | 2 seqminer-4.5/seqminer/src/Profiler.cpp | 27 + seqminer-4.5/seqminer/src/Profiler.h | 6 seqminer-4.5/seqminer/src/SimpleTimer.h | 138 +++++++++ seqminer-4.5/seqminer/src/rvMetaLoader.cpp | 44 ++ 55 files changed, 585 insertions(+), 333 deletions(-)