Title: R Interface to FOAAS
Description: R access to the FOAAS (F... Off As A Service) web service
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Diff between rfoaas versions 0.0.4 dated 2014-10-15 and 0.0.4.20141212 dated 2014-12-13
ChangeLog | 22 ++++++++++++++++++---- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/foaas.R | 7 +++++-- man/rfoaas-package.Rd | 22 ++++++++++++++++++---- 5 files changed, 49 insertions(+), 18 deletions(-)
Title: CoxPH Model with Log Concave Baseline Distribution
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman
Diff between logconPH versions 1.3 dated 2014-10-28 and 1.4 dated 2014-12-13
logconPH-1.3/logconPH/data |only logconPH-1.3/logconPH/man/menodata.Rd |only logconPH-1.4/logconPH/DESCRIPTION | 6 logconPH-1.4/logconPH/MD5 | 21 +- logconPH-1.4/logconPH/NAMESPACE | 1 logconPH-1.4/logconPH/R/LogConcave.R | 196 +++++++++++-------- logconPH-1.4/logconPH/man/logconPH-package.Rd | 18 - logconPH-1.4/logconPH/man/logconcave.Rd | 10 - logconPH-1.4/logconPH/man/sim_Censored.Rd |only logconPH-1.4/logconPH/src/Cpp2Source/baseClass.cpp | 2 logconPH-1.4/logconPH/src/Cpp2Source/baseClass.h | 1 logconPH-1.4/logconPH/src/Cpp2Source/logconcave.cpp | 199 ++++++++++++++++++-- logconPH-1.4/logconPH/src/logconPH.cpp | 11 - 13 files changed, 333 insertions(+), 132 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang
Maintainer: Michel Lang
Diff between checkmate versions 1.5.0 dated 2014-10-18 and 1.5.1 dated 2014-12-13
DESCRIPTION | 8 - MD5 | 168 +++++++++++++++++----------------- NEWS | 6 + R/asInteger.r | 4 R/assert.r | 2 R/checkAccess.r | 3 R/checkArray.r | 3 R/checkAtomic.r | 3 R/checkAtomicVector.r | 3 R/checkCharacter.r | 3 R/checkChoice.r | 3 R/checkClass.r | 3 R/checkComplex.r | 3 R/checkCount.r | 3 R/checkDataFrame.r | 3 R/checkDirectory.r | 3 R/checkEnvironment.r | 3 R/checkFactor.r | 3 R/checkFile.r | 3 R/checkFlag.r | 3 R/checkFunction.r | 3 R/checkInt.r | 3 R/checkInteger.r | 3 R/checkIntegerish.r | 3 R/checkList.r | 3 R/checkLogical.r | 3 R/checkMatrix.r | 3 R/checkNamed.r | 3 R/checkNames.r | 8 + R/checkNull.r | 1 R/checkNumber.r | 3 R/checkNumeric.r | 3 R/checkPathForOutput.r | 5 - R/checkPercentage.r | 3 R/checkScalar.r | 3 R/checkScalarNA.r | 1 R/checkSetEqual.r | 3 R/checkString.r | 5 - R/checkSubset.r | 3 R/checkVector.r | 3 R/qassert.r | 2 man/asInteger.Rd | 4 man/assert.Rd | 2 man/checkAccess.Rd | 2 man/checkArray.Rd | 2 man/checkAtomic.Rd | 2 man/checkAtomicVector.Rd | 2 man/checkCharacter.Rd | 2 man/checkChoice.Rd | 2 man/checkClass.Rd | 2 man/checkComplex.Rd | 2 man/checkCount.Rd | 2 man/checkDataFrame.Rd | 2 man/checkDirectory.Rd | 2 man/checkEnvironment.Rd | 2 man/checkFactor.Rd | 2 man/checkFile.Rd | 2 man/checkFlag.Rd | 2 man/checkFunction.Rd | 2 man/checkInt.Rd | 2 man/checkInteger.Rd | 2 man/checkIntegerish.Rd | 2 man/checkList.Rd | 2 man/checkLogical.Rd | 2 man/checkMatrix.Rd | 2 man/checkNamed.Rd | 2 man/checkNames.Rd | 8 - man/checkNull.Rd | 2 man/checkNumber.Rd | 2 man/checkNumeric.Rd | 2 man/checkPathForOutput.Rd | 4 man/checkPercentage.Rd | 2 man/checkScalar.Rd | 2 man/checkScalarNA.Rd | 2 man/checkSetEqual.Rd | 2 man/checkString.Rd | 2 man/checkSubset.Rd | 2 man/checkVector.Rd | 2 man/qassert.Rd | 2 src/checks.c | 8 - src/helper.c | 19 +++ src/helper.h | 2 src/is_integerish.c | 2 tests/testthat/test_checkDataFrame.r | 8 + tests/testthat/test_checkIntegerish.r | 2 85 files changed, 251 insertions(+), 176 deletions(-)
Title: Constrained Optimization Via Stochastic Gradient Descent
Description: Optimize a function with constraints via a transformation of the
Lagrangian.
Author: Steven Pollack
Maintainer: Steven Pollack
Diff between blowtorch versions 1.0.1 dated 2014-05-08 and 1.0.2 dated 2014-12-13
blowtorch-1.0.1/blowtorch/inst/tests |only blowtorch-1.0.2/blowtorch/.Rinstignore | 2 blowtorch-1.0.2/blowtorch/DESCRIPTION | 10 ++- blowtorch-1.0.2/blowtorch/MD5 | 50 ++++++++++-------- blowtorch-1.0.2/blowtorch/NAMESPACE | 2 blowtorch-1.0.2/blowtorch/README.md | 21 ++++++- blowtorch-1.0.2/blowtorch/inst/examples |only blowtorch-1.0.2/blowtorch/inst/final_project |only blowtorch-1.0.2/blowtorch/man/SGD.Rd | 26 +++++---- blowtorch-1.0.2/blowtorch/man/addDots.Rd | 3 - blowtorch-1.0.2/blowtorch/man/aggregateConstraints.Rd | 3 - blowtorch-1.0.2/blowtorch/man/aggregateGradients.Rd | 3 - blowtorch-1.0.2/blowtorch/man/aggregateHessians.Rd | 3 - blowtorch-1.0.2/blowtorch/man/blowtorch.Rd | 3 - blowtorch-1.0.2/blowtorch/man/buildDh.Rd | 8 ++ blowtorch-1.0.2/blowtorch/man/build_h.Rd | 8 ++ blowtorch-1.0.2/blowtorch/man/gradientDescent.Rd | 8 ++ blowtorch-1.0.2/blowtorch/man/multiplot.Rd | 3 - blowtorch-1.0.2/blowtorch/man/plot.SGD.Rd | 3 - blowtorch-1.0.2/blowtorch/tests |only 20 files changed, 103 insertions(+), 53 deletions(-)
Title: Multitaper Spectral Analysis Tools
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim
Maintainer: Karim Rahim
Diff between multitaper versions 1.0-8 dated 2013-10-01 and 1.0-9 dated 2014-12-13
DESCRIPTION | 16 +++++----- MD5 | 68 +++++++++++++++++++++++----------------------- R/demod.R | 17 ++++++++--- R/dpss.R | 3 -- R/dpssHelpers.R | 3 -- R/dropFreqs.R | 3 -- R/multitaper.R | 29 +++++++++++++++---- R/multitaperHelper.R | 3 -- R/plots.R | 3 -- R/plotsHelper.R | 3 -- R/sineTaper.R | 7 ++-- R/utility.R | 8 ----- inst |only man/CETdaily.Rd | 4 -- man/CETmonthly.Rd | 4 -- man/HadCRUTnh.Rd | 4 -- man/centre.Rd | 3 -- man/demod.dpss.Rd | 14 +++++---- man/dpss.Rd | 2 - man/dpssToEigenvalues.Rd | 2 - man/dropFreqs.Rd | 4 -- man/mlco2.Rd | 2 - man/mtm.coh.Rd | 3 -- man/multitaper-package.Rd |only man/multitaperTrend.Rd | 3 -- man/percivalAR4.Rd | 3 -- man/plot.mtm.Rd | 2 - man/plot.mtm.coh.Rd | 2 - man/sineTaper.Rd | 5 +-- man/spec.mtm.Rd | 8 +++-- man/willamette.Rd | 3 -- src/Makevars | 3 -- src/Makevars.win | 3 -- src/djt.f | 3 -- src/dpss.f90 | 3 -- src/sine.f | 5 +-- 36 files changed, 118 insertions(+), 130 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [cre, aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham
Diff between httr versions 0.5 dated 2014-09-02 and 0.6.0 dated 2014-12-13
httr-0.5/httr/R/sysdata.rda |only httr-0.5/httr/man/new_token.Rd |only httr-0.6.0/httr/DESCRIPTION | 31 - httr-0.6.0/httr/MD5 | 218 ++++++------ httr-0.6.0/httr/NAMESPACE | 23 + httr-0.6.0/httr/R/body.R | 16 httr-0.6.0/httr/R/config.r | 7 httr-0.6.0/httr/R/content-parse.r | 50 +- httr-0.6.0/httr/R/content.r | 3 httr-0.6.0/httr/R/doctor.R |only httr-0.6.0/httr/R/envvar.R | 49 +- httr-0.6.0/httr/R/handle-pool.r | 31 + httr-0.6.0/httr/R/handle-url.r | 2 httr-0.6.0/httr/R/headers.r | 10 httr-0.6.0/httr/R/http-post.r | 4 httr-0.6.0/httr/R/http-verb.R |only httr-0.6.0/httr/R/media-guess.r | 29 - httr-0.6.0/httr/R/oauth-app.r | 4 httr-0.6.0/httr/R/oauth-init.R | 16 httr-0.6.0/httr/R/oauth-listener.r | 4 httr-0.6.0/httr/R/oauth-server-side.R |only httr-0.6.0/httr/R/oauth-signature.r | 8 httr-0.6.0/httr/R/oauth-token-utils.R | 33 + httr-0.6.0/httr/R/oauth-token.r | 283 +++++++++------- httr-0.6.0/httr/R/perform.R | 18 - httr-0.6.0/httr/R/progress.R | 18 - httr-0.6.0/httr/R/response.r | 2 httr-0.6.0/httr/R/safe-callback.R |only httr-0.6.0/httr/R/upload-file.r | 3 httr-0.6.0/httr/R/url.r | 2 httr-0.6.0/httr/R/verbose.r | 5 httr-0.6.0/httr/R/write-function.R | 50 ++ httr-0.6.0/httr/R/zzz.R | 5 httr-0.6.0/httr/README.md | 18 - httr-0.6.0/httr/build/vignette.rds |binary httr-0.6.0/httr/demo/00Index | 1 httr-0.6.0/httr/demo/oauth1-withings.r |only httr-0.6.0/httr/demo/oauth2-linkedin.r | 22 - httr-0.6.0/httr/inst/cacert.pem | 9 httr-0.6.0/httr/inst/doc/api-packages.Rmd | 58 +++ httr-0.6.0/httr/inst/doc/api-packages.html | 70 +++ httr-0.6.0/httr/inst/doc/quickstart.Rmd | 2 httr-0.6.0/httr/inst/doc/quickstart.html | 172 +++++---- httr-0.6.0/httr/man/BROWSE.Rd | 5 httr-0.6.0/httr/man/DELETE.Rd | 5 httr-0.6.0/httr/man/GET.Rd | 6 httr-0.6.0/httr/man/HEAD.Rd | 6 httr-0.6.0/httr/man/PATCH.Rd | 3 httr-0.6.0/httr/man/POST.Rd | 3 httr-0.6.0/httr/man/PUT.Rd | 3 httr-0.6.0/httr/man/Token-class.Rd | 20 - httr-0.6.0/httr/man/VERB.Rd |only httr-0.6.0/httr/man/add_headers.Rd | 3 httr-0.6.0/httr/man/authenticate.Rd | 3 httr-0.6.0/httr/man/brew_dr.Rd |only httr-0.6.0/httr/man/cache_info.Rd | 3 httr-0.6.0/httr/man/config.Rd | 3 httr-0.6.0/httr/man/content.Rd | 3 httr-0.6.0/httr/man/content_type.Rd | 5 httr-0.6.0/httr/man/cookies.Rd | 3 httr-0.6.0/httr/man/guess_media.Rd | 10 httr-0.6.0/httr/man/handle.Rd | 3 httr-0.6.0/httr/man/handle_pool.Rd | 11 httr-0.6.0/httr/man/has_content.Rd | 3 httr-0.6.0/httr/man/headers.Rd | 3 httr-0.6.0/httr/man/hmac_sha1.Rd | 3 httr-0.6.0/httr/man/http_condition.Rd | 3 httr-0.6.0/httr/man/http_error.Rd | 3 httr-0.6.0/httr/man/http_status.Rd | 3 httr-0.6.0/httr/man/httr.Rd | 3 httr-0.6.0/httr/man/httr_options.Rd | 3 httr-0.6.0/httr/man/init_oauth1.0.Rd | 3 httr-0.6.0/httr/man/init_oauth2.0.Rd | 6 httr-0.6.0/httr/man/insensitive.Rd | 3 httr-0.6.0/httr/man/jwt_signature.Rd |only httr-0.6.0/httr/man/modify_url.Rd | 3 httr-0.6.0/httr/man/oauth1.0_token.Rd | 11 httr-0.6.0/httr/man/oauth2.0_token.Rd | 11 httr-0.6.0/httr/man/oauth_app.Rd | 10 httr-0.6.0/httr/man/oauth_callback.Rd | 3 httr-0.6.0/httr/man/oauth_endpoint.Rd | 6 httr-0.6.0/httr/man/oauth_endpoints.Rd | 3 httr-0.6.0/httr/man/oauth_exchanger.Rd | 3 httr-0.6.0/httr/man/oauth_listener.Rd | 3 httr-0.6.0/httr/man/oauth_service_token.Rd |only httr-0.6.0/httr/man/oauth_signature.Rd | 3 httr-0.6.0/httr/man/parse_http_date.Rd | 3 httr-0.6.0/httr/man/parse_media.Rd | 3 httr-0.6.0/httr/man/parse_url.Rd | 3 httr-0.6.0/httr/man/progress.Rd | 3 httr-0.6.0/httr/man/response.Rd | 3 httr-0.6.0/httr/man/revoke_all.Rd |only httr-0.6.0/httr/man/safe_callback.Rd |only httr-0.6.0/httr/man/set_config.Rd | 3 httr-0.6.0/httr/man/set_cookies.Rd | 3 httr-0.6.0/httr/man/sign_oauth.Rd | 6 httr-0.6.0/httr/man/status_code.Rd | 3 httr-0.6.0/httr/man/timeout.Rd | 3 httr-0.6.0/httr/man/upload_file.Rd | 5 httr-0.6.0/httr/man/url_ok.Rd | 3 httr-0.6.0/httr/man/url_success.Rd | 3 httr-0.6.0/httr/man/use_proxy.Rd | 3 httr-0.6.0/httr/man/user_agent.Rd | 3 httr-0.6.0/httr/man/verbose.Rd | 3 httr-0.6.0/httr/man/with_config.Rd | 3 httr-0.6.0/httr/man/write_disk.Rd | 3 httr-0.6.0/httr/man/write_function.Rd | 3 httr-0.6.0/httr/man/write_stream.Rd |only httr-0.6.0/httr/src/writer.c | 24 + httr-0.6.0/httr/tests/testthat/test-body.r | 21 + httr-0.6.0/httr/tests/testthat/test-config.r | 35 + httr-0.6.0/httr/tests/testthat/test-header.r | 6 httr-0.6.0/httr/tests/testthat/test-oauth-cache.R | 10 httr-0.6.0/httr/tests/testthat/test-oauth-server-side.R |only httr-0.6.0/httr/tests/testthat/test-ssl.R |only httr-0.6.0/httr/tests/testthat/test-url.r | 6 httr-0.6.0/httr/vignettes/api-packages.Rmd | 58 +++ httr-0.6.0/httr/vignettes/quickstart.Rmd | 2 118 files changed, 1099 insertions(+), 591 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui
Diff between boral versions 0.5 dated 2014-09-18 and 0.6 dated 2014-12-13
DESCRIPTION | 8 MD5 | 46 - R/auxilaryfunctions.R | 956 +++++++++++++++++++++++------------------ R/boral.jags.R | 415 +++++++++-------- inst/NEWS.Rd | 100 ++-- man/boral-package.Rd | 14 man/boral.Rd | 106 ++-- man/calc.condlogLik.Rd | 31 - man/calc.logLik.lv0.Rd | 49 +- man/calc.marglogLik.Rd | 41 + man/create.life.Rd | 13 man/ds.residuals.Rd | 4 man/fitted.boral.Rd | 4 man/get.dic.Rd | 4 man/get.enviro.cor.Rd | 16 man/get.hpdintervals.Rd | 9 man/get.measures.Rd | 17 man/get.more.measures.Rd | 22 man/get.residual.cor.Rd | 20 man/lvsplot.Rd | 3 man/make.jagsboralmodel.Rd | 32 - man/make.jagsboralnullmodel.Rd | 24 - man/plot.boral.Rd | 6 man/summary.boral.Rd | 3 24 files changed, 1094 insertions(+), 849 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-22 0.1-9.2
2013-09-08 0.1-9.1
2012-05-02 0.1-9
2011-11-17 0.1-8
2011-11-16 0.1-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-24 1.3
2011-09-20 1.2
2011-05-03 1.1
2011-04-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-24 1.6-2
2013-04-19 1.6-1
2012-02-19 1.6-0
2012-01-07 1.5-0
2011-03-11 1.4-0
2010-03-01 1.3-1
2010-02-06 1.3-0
2007-10-12 1.2-6
2007-09-30 1.2-5
2006-09-29 1.2-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-01 1.0
Title: In-source Documentation for R
Description: A Doxygen-like in-source documentation system
for Rd, collation, and NAMESPACE.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham
Diff between roxygen2 versions 4.0.2 dated 2014-09-02 and 4.1.0 dated 2014-12-13
DESCRIPTION | 8 +-- MD5 | 77 ++++++++++++++++------------- NAMESPACE | 3 - R/RcppExports.R | 8 +++ R/description.R | 11 +++- R/minidesc.R | 2 R/object.R | 3 - R/rd-file-api.R | 2 R/rd-tag-api.R | 9 +++ R/roclet-collate.R | 15 +++-- R/roclet-namespace.R | 2 R/roclet-rd.R | 6 +- R/safety.R | 1 R/utils.R | 2 build/vignette.rds |binary inst/doc/rd.Rmd | 8 ++- inst/doc/rd.html | 8 ++- man/is_s3_generic.Rd | 3 - man/namespace_roclet.Rd | 3 - man/new_roclet.Rd | 3 - man/object.Rd | 3 - man/rd_roclet.Rd | 3 - man/register-parser.Rd | 3 - man/roc_proc_text.Rd | 3 - man/roxygen.Rd | 3 - man/roxygenize.Rd | 3 - man/source_package.Rd | 3 - man/update_collate.Rd | 12 +++- src/RcppExports.cpp | 30 +++++++++++ src/parser.cpp |only src/roxygen.h |only tests/testthat/roxygen-block-1.R |only tests/testthat/roxygen-block-2.R |only tests/testthat/roxygen-example-1.R |only tests/testthat/test-collate.R | 21 +++++++ tests/testthat/test-cpp-parser.R |only tests/testthat/test-describein.R | 26 +++++++++ tests/testthat/test-srcref-comment.R |only tests/testthat/test-wrapFieldIfNecessary.R | 10 +++ tests/testthat/testCollateNoIncludes |only vignettes/rd.Rmd | 8 ++- vignettes/rd.md | 8 ++- 42 files changed, 235 insertions(+), 75 deletions(-)
Title: UI for the RGP genetic programming framework
Description: RGP UI provides as modern web-based user interface to the modular
Genetic Programming (GP) system RGP.
Author: Oliver Flasch
Maintainer: Oliver Flasch
Diff between rgpui versions 0.1-1 dated 2014-03-14 and 0.1-2 dated 2014-12-13
DESCRIPTION | 10 MD5 | 10 NAMESPACE | 3 R/webgui.R | 5 man/rgpuiHtml.Rd | 1598 ++++++++++++++++++++++++-------------------- man/symbolicRegressionUi.Rd | 9 6 files changed, 895 insertions(+), 740 deletions(-)
Title: Design and analysis of mixture experiments
Description: Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson
Maintainer: John Lawson
Diff between mixexp versions 1.1.8 dated 2014-11-11 and 1.1.9 dated 2014-12-13
DESCRIPTION | 14 +++++++------- MD5 | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-)