Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see: (i) "Life tables
with covariates: Dynamic model for nonlinear analysis of longitudinal data"
by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80),
<DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of
longitudinal data on aging and mortality" by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(iii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.3.2 dated 2016-07-01 and 1.3.4 dated 2016-09-04
stpm-1.3.2/stpm/R/simdata_gen_cont.R |only stpm-1.3.2/stpm/R/spm_gen.R |only stpm-1.3.2/stpm/data/longdat.csv.gz |only stpm-1.3.2/stpm/data/vitstat.csv.gz |only stpm-1.3.2/stpm/man/simdata_gen.Rd |only stpm-1.3.2/stpm/man/spm_gen.Rd |only stpm-1.3.2/stpm/vignettes/stpm-vignette.html |only stpm-1.3.4/stpm/DESCRIPTION | 9 - stpm-1.3.4/stpm/MD5 | 33 +++--- stpm-1.3.4/stpm/NAMESPACE | 4 stpm-1.3.4/stpm/R/simdata_gamma_frailty.R | 3 stpm-1.3.4/stpm/R/simdata_pobs_cont.R |only stpm-1.3.4/stpm/R/spm_pobs.R |only stpm-1.3.4/stpm/R/spm_projection.R | 35 ++++++ stpm-1.3.4/stpm/R/spm_time-dependent.R | 10 + stpm-1.3.4/stpm/build |only stpm-1.3.4/stpm/data/longdat.csv |only stpm-1.3.4/stpm/data/vitstat.csv |only stpm-1.3.4/stpm/inst |only stpm-1.3.4/stpm/man/sim_pobs.Rd |only stpm-1.3.4/stpm/man/simdata_gamma_frailty.Rd | 2 stpm-1.3.4/stpm/man/spm_pobs.Rd |only stpm-1.3.4/stpm/src/spm_integral_MD.cpp | 136 +++++++++++++++++++-------- stpm-1.3.4/stpm/vignettes/stpm-vignette.Rmd | 27 ++--- 24 files changed, 179 insertions(+), 80 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [ctb],
Dirk Eddelbuettel [ctb] (ziggurat rnorm sources),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 1.9.16 dated 2016-07-21 and 1.10.0 dated 2016-09-04
spaMM-1.10.0/spaMM/DESCRIPTION | 8 spaMM-1.10.0/spaMM/MD5 | 128 + spaMM-1.10.0/spaMM/NAMESPACE | 13 spaMM-1.10.0/spaMM/R/GLM.fit.R | 2 spaMM-1.10.0/spaMM/R/HLCor.R | 100 - spaMM-1.10.0/spaMM/R/HLFactorList.R | 10 spaMM-1.10.0/spaMM/R/HLfit.R | 1210 ------------------ spaMM-1.10.0/spaMM/R/HLfit_Internals.R | 809 ++++++------ spaMM-1.10.0/spaMM/R/HLfit_b_internals.R |only spaMM-1.10.0/spaMM/R/HLfit_body.R |only spaMM-1.10.0/spaMM/R/HLframes.R | 31 spaMM-1.10.0/spaMM/R/LevenbergMstep.R | 27 spaMM-1.10.0/spaMM/R/MakeCovEst.R | 53 spaMM-1.10.0/spaMM/R/RcppExports.R | 4 spaMM-1.10.0/spaMM/R/auglinmodfit.R | 832 +++++------- spaMM-1.10.0/spaMM/R/calc.p_v.R | 32 spaMM-1.10.0/spaMM/R/confint.R | 37 spaMM-1.10.0/spaMM/R/corrHLfit-internals.R | 8 spaMM-1.10.0/spaMM/R/corrHLfit.R | 32 spaMM-1.10.0/spaMM/R/corrMM.LRT.R | 47 spaMM-1.10.0/spaMM/R/correlationFns.R | 33 spaMM-1.10.0/spaMM/R/dispGammaGLM.R | 1 spaMM-1.10.0/spaMM/R/extractors.R | 125 + spaMM-1.10.0/spaMM/R/fitme.R | 114 - spaMM-1.10.0/spaMM/R/iterateSmooth.R | 29 spaMM-1.10.0/spaMM/R/locoptim.R | 8 spaMM-1.10.0/spaMM/R/locoptimthroughsmooth.R | 4 spaMM-1.10.0/spaMM/R/mapMM.R | 2 spaMM-1.10.0/spaMM/R/negbin.R | 3 spaMM-1.10.0/spaMM/R/predict.R | 122 + spaMM-1.10.0/spaMM/R/predictor.R | 5 spaMM-1.10.0/spaMM/R/preprocess.R | 498 +++++-- spaMM-1.10.0/spaMM/R/preprocess_internals.R |only spaMM-1.10.0/spaMM/R/simulate.HL.R | 18 spaMM-1.10.0/spaMM/R/spaMM.data.R | 7 spaMM-1.10.0/spaMM/R/structures.R |only spaMM-1.10.0/spaMM/R/summary.HL.R | 78 - spaMM-1.10.0/spaMM/R/update.HL.R | 15 spaMM-1.10.0/spaMM/R/utils.R | 8 spaMM-1.10.0/spaMM/data/crack.RData |only spaMM-1.10.0/spaMM/inst/NEWS.Rd | 36 spaMM-1.10.0/spaMM/man/COMPoisson.Rd | 2 spaMM-1.10.0/spaMM/man/HLCor.Rd | 2 spaMM-1.10.0/spaMM/man/HLfit.Rd | 66 spaMM-1.10.0/spaMM/man/Loaloa.Rd | 53 spaMM-1.10.0/spaMM/man/Matern.corr.Rd | 12 spaMM-1.10.0/spaMM/man/corMatern.Rd | 2 spaMM-1.10.0/spaMM/man/corrHLfit.Rd | 2 spaMM-1.10.0/spaMM/man/corrMatrix.Rd | 2 spaMM-1.10.0/spaMM/man/extractors.Rd | 18 spaMM-1.10.0/spaMM/man/fitme.Rd | 39 spaMM-1.10.0/spaMM/man/inverse.Gamma.Rd |only spaMM-1.10.0/spaMM/man/member_extractors.Rd |only spaMM-1.10.0/spaMM/man/options.Rd | 4 spaMM-1.10.0/spaMM/man/phiHGLM.Rd |only spaMM-1.10.0/spaMM/man/plot.HL.Rd | 2 spaMM-1.10.0/spaMM/man/predict.Rd | 13 spaMM-1.10.0/spaMM/man/salamander.Rd | 10 spaMM-1.10.0/spaMM/man/spaMM-conventions.Rd |only spaMM-1.10.0/spaMM/man/spaMM-internal-Rcpp.Rd | 1 spaMM-1.10.0/spaMM/man/spaMM-internal.Rd | 38 spaMM-1.10.0/spaMM/man/spaMM.Rd | 12 spaMM-1.10.0/spaMM/man/update.Rd | 16 spaMM-1.10.0/spaMM/src/RcppExports.cpp | 13 spaMM-1.10.0/spaMM/src/spaMM_linear.cpp | 39 spaMM-1.10.0/spaMM/tests/testthat/test-COMPoisson.R | 6 spaMM-1.10.0/spaMM/tests/testthat/test-blackbox.R |only spaMM-1.10.0/spaMM/tests/testthat/test-dhglm.R |only spaMM-1.10.0/spaMM/tests/testthat/test-predVar.R | 8 spaMM-1.10.0/spaMM/tests/testthat/test-random-slope.R | 2 spaMM-1.9.16/spaMM/R/plotdhglm.R |only 71 files changed, 2182 insertions(+), 2669 deletions(-)
Title: Functions and R Code to Accompany Derivatives Markets
Description: A set of pricing and expository functions that should
be useful in teaching a course on financial derivatives.
Author: Robert McDonald [aut, cre, cph]
Maintainer: Robert McDonald <rmcd1024@gmail.com>
Diff between derivmkts versions 0.2.1 dated 2016-06-27 and 0.2.2 dated 2016-09-04
derivmkts-0.2.1/derivmkts/inst/test |only derivmkts-0.2.1/derivmkts/vignettes/derivmkts.tex |only derivmkts-0.2.1/derivmkts/vignettes/rlistings.tex |only derivmkts-0.2.2/derivmkts/DESCRIPTION | 6 derivmkts-0.2.2/derivmkts/MD5 | 41 derivmkts-0.2.2/derivmkts/NAMESPACE | 8 derivmkts-0.2.2/derivmkts/NEWS.md | 15 derivmkts-0.2.2/derivmkts/R/asianmontecarlo.R | 6 derivmkts-0.2.2/derivmkts/R/binom.R | 18 derivmkts-0.2.2/derivmkts/R/compound.R |only derivmkts-0.2.2/derivmkts/build/vignette.rds |binary derivmkts-0.2.2/derivmkts/inst/doc/Notes-on-vectorization.R |only derivmkts-0.2.2/derivmkts/inst/doc/Notes-on-vectorization.Rnw |only derivmkts-0.2.2/derivmkts/inst/doc/Notes-on-vectorization.pdf |only derivmkts-0.2.2/derivmkts/inst/doc/derivmkts-vignette.R | 141 --- derivmkts-0.2.2/derivmkts/inst/doc/derivmkts-vignette.Rnw | 456 +++------- derivmkts-0.2.2/derivmkts/inst/doc/derivmkts-vignette.pdf |binary derivmkts-0.2.2/derivmkts/man/binom.Rd | 5 derivmkts-0.2.2/derivmkts/man/compound.Rd |only derivmkts-0.2.2/derivmkts/tests/testthat/barrier_tests.R | 1 derivmkts-0.2.2/derivmkts/tests/testthat/compound_tests.R |only derivmkts-0.2.2/derivmkts/tests/testthat/option_testvalues.Rdata |binary derivmkts-0.2.2/derivmkts/tests/testthat/test.R | 1 derivmkts-0.2.2/derivmkts/vignettes/Notes-on-vectorization.Rnw |only derivmkts-0.2.2/derivmkts/vignettes/derivmkts-vignette.Rnw | 456 +++------- derivmkts-0.2.2/derivmkts/vignettes/derivmkts.bib | 68 + 26 files changed, 498 insertions(+), 724 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.6 dated 2016-07-19 and 0.12.7 dated 2016-09-04
ChangeLog | 207 +++++++++--- DESCRIPTION | 8 MD5 | 115 +++--- R/Rcpp.package.skeleton.R | 2 README.md | 13 build/Rcpp.pdf |binary inst/NEWS.Rd | 45 ++ inst/doc/Rcpp-FAQ.Rnw | 4 inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.Rnw | 12 inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 16 inst/examples/FastLM/fastLMviaArmadillo.r | 4 inst/examples/FastLM/lmArmadillo.R | 36 ++ inst/examples/FastLM/lmGSL.R | 53 +++ inst/examples/RcppGibbs/RcppGibbs.R | 73 ++++ inst/examples/RcppGibbs/timeRNGs.R | 89 +++++ inst/examples/RcppInline/RcppInlineExample.r | 22 + inst/examples/RcppInline/RcppInlineWithLibsExamples.r | 229 ++++++++++++- inst/examples/RcppInline/UncaughtExceptions.r | 17 - inst/examples/RcppInline/external_pointer.r | 63 +++ inst/examples/SugarPerformance/sugarBenchmarks.R | 2 inst/examples/functionCallback/newApiExample.r | 21 + inst/include/Rcpp.h | 3 inst/include/Rcpp/Environment.h | 46 ++ inst/include/Rcpp/Module.h | 2 inst/include/Rcpp/String.h | 85 +---- inst/include/Rcpp/config.h | 4 inst/include/Rcpp/exceptions.h | 2 inst/include/Rcpp/internal/NAComparator.h | 16 inst/include/Rcpp/macros/dispatch.h | 78 +++- inst/include/Rcpp/proxy/FieldProxy.h | 6 inst/include/Rcpp/r/headers.h | 9 inst/include/Rcpp/r_cast.h | 2 inst/include/Rcpp/vector/Vector.h | 26 + inst/unitTests/cpp/String.cpp | 8 inst/unitTests/cpp/Vector.cpp | 28 + inst/unitTests/cpp/dispatch.cpp |only inst/unitTests/cpp/language.cpp | 2 inst/unitTests/cpp/rmath.cpp | 300 ++++++++++++++++++ inst/unitTests/runit.String.R | 4 inst/unitTests/runit.Vector.R | 26 + inst/unitTests/runit.dispatch.R |only inst/unitTests/runit.quickanddirty.R |only inst/unitTests/runit.rmath.R | 187 +++++++++++ man/Rcpp.package.skeleton.Rd | 7 man/compileAttributes.Rd | 2 src/attributes.cpp | 51 +-- src/barrier.cpp | 6 tests/doRUnit.R | 4 vignettes/Rcpp-FAQ.Rnw | 4 vignettes/Rcpp-package.Rnw | 12 vignettes/Rcpp.bib | 16 60 files changed, 1620 insertions(+), 347 deletions(-)
Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. Can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre],
Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>
Diff between nplr versions 0.1-4 dated 2015-08-01 and 0.1-5 dated 2016-09-04
nplr-0.1-4/nplr/vignettes/nplrApp.png |only nplr-0.1-5/nplr/DESCRIPTION | 12 +++--- nplr-0.1-5/nplr/MD5 | 32 +++++++++--------- nplr-0.1-5/nplr/NAMESPACE | 14 ++++---- nplr-0.1-5/nplr/NEWS | 4 ++ nplr-0.1-5/nplr/R/AllGenerics.R | 2 - nplr-0.1-5/nplr/R/helpers.R | 59 +++++++++++++++++++++++----------- nplr-0.1-5/nplr/R/nplr.R | 15 +++++--- nplr-0.1-5/nplr/R/summary.nplr.R |only nplr-0.1-5/nplr/build/vignette.rds |binary nplr-0.1-5/nplr/inst/doc/nplr.Rnw | 18 ++++++---- nplr-0.1-5/nplr/inst/doc/nplr.pdf |binary nplr-0.1-5/nplr/man/convertToProp.Rd | 3 + nplr-0.1-5/nplr/man/getEstimates.Rd | 3 + nplr-0.1-5/nplr/man/nplr.Rd | 13 ++++--- nplr-0.1-5/nplr/man/plot.nplr.Rd | 3 + nplr-0.1-5/nplr/man/summary.nplr.Rd |only nplr-0.1-5/nplr/vignettes/nplr.Rnw | 18 ++++++---- nplr-0.1-5/nplr/vignettes/nplrApp.pdf |only 19 files changed, 123 insertions(+), 73 deletions(-)
Title: Easy Authentication with Google OAuth2 API
Description: Create R functions that interact with OAuth2 Google APIs easily,
with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre],
Jennifer Bryan [ctb],
Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAuthR versions 0.3.1 dated 2016-06-25 and 0.4.0 dated 2016-09-04
googleAuthR-0.3.1/googleAuthR/vignettes/googleAuthR.md |only googleAuthR-0.4.0/googleAuthR/DESCRIPTION | 12 googleAuthR-0.4.0/googleAuthR/MD5 | 67 googleAuthR-0.4.0/googleAuthR/NAMESPACE | 12 googleAuthR-0.4.0/googleAuthR/NEWS.md | 18 googleAuthR-0.4.0/googleAuthR/R/googleAuthR.R | 5 googleAuthR-0.4.0/googleAuthR/R/googleAuthR_auth.R | 39 googleAuthR-0.4.0/googleAuthR/R/googleAuthR_auto_auth.R |only googleAuthR-0.4.0/googleAuthR/R/googleAuthR_batch.R | 18 googleAuthR-0.4.0/googleAuthR/R/googleAuthR_discovery.R |only googleAuthR-0.4.0/googleAuthR/R/googleAuthR_discovery_build.R |only googleAuthR-0.4.0/googleAuthR/R/googleAuthR_discovery_utilities.R |only googleAuthR-0.4.0/googleAuthR/R/googleAuthR_generator.R | 20 googleAuthR-0.4.0/googleAuthR/R/googleAuthR_options.R | 8 googleAuthR-0.4.0/googleAuthR/R/googleAuthR_shiny.R | 141 + googleAuthR-0.4.0/googleAuthR/README.md | 272 +- googleAuthR-0.4.0/googleAuthR/build/vignette.rds |binary googleAuthR-0.4.0/googleAuthR/inst/doc/googleAuthR.Rmd | 279 +- googleAuthR-0.4.0/googleAuthR/inst/doc/googleAuthR.html | 1156 ++++------ googleAuthR-0.4.0/googleAuthR/inst/embed |only googleAuthR-0.4.0/googleAuthR/inst/flexdashbord |only googleAuthR-0.4.0/googleAuthR/inst/shiny/ui.R | 2 googleAuthR-0.4.0/googleAuthR/man/gar_attach_auto_auth.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_auth.Rd | 4 googleAuthR-0.4.0/googleAuthR/man/gar_auth_js.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_auth_jsUI.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_auth_service.Rd | 3 googleAuthR-0.4.0/googleAuthR/man/gar_auto_auth.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_create_api_objects.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_create_api_skeleton.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_create_package.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_discovery_api.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_discovery_apis_list.Rd |only googleAuthR-0.4.0/googleAuthR/man/gar_js_getToken.Rd |only googleAuthR-0.4.0/googleAuthR/man/get_google_token.Rd | 7 googleAuthR-0.4.0/googleAuthR/man/googleAuthR.Rd | 5 googleAuthR-0.4.0/googleAuthR/man/is_legit_token.Rd | 6 googleAuthR-0.4.0/googleAuthR/man/token_exists.Rd | 6 googleAuthR-0.4.0/googleAuthR/tests |only googleAuthR-0.4.0/googleAuthR/vignettes/googleAuthR.Rmd | 279 +- 40 files changed, 1318 insertions(+), 1041 deletions(-)
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph] (for source file 'format.perc')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.5.3 dated 2014-11-25 and 2.6.1 dated 2016-09-04
distrMod-2.5.3/distrMod/tests |only distrMod-2.6.1/distrMod/DESCRIPTION | 32 distrMod-2.6.1/distrMod/MD5 | 165 distrMod-2.6.1/distrMod/NAMESPACE | 13 distrMod-2.6.1/distrMod/R/0distrModUtils.R | 446 + distrMod-2.6.1/distrMod/R/AllGeneric.R | 7 distrMod-2.6.1/distrMod/R/AllPlot.R | 41 distrMod-2.6.1/distrMod/R/Estimate.R | 216 distrMod-2.6.1/distrMod/R/Estimator.R | 298 - distrMod-2.6.1/distrMod/R/MCEstimate.R | 44 distrMod-2.6.1/distrMod/R/MCEstimator.R | 9 distrMod-2.6.1/distrMod/R/MDEstimator.R | 10 distrMod-2.6.1/distrMod/R/MLEstimator.R | 14 distrMod-2.6.1/distrMod/R/ParamFamParameter.R | 7 distrMod-2.6.1/distrMod/R/checkEstClassForParamFamilyMethods.R |only distrMod-2.6.1/distrMod/R/confint.R | 2 distrMod-2.6.1/distrMod/R/existsPIC.R | 6 distrMod-2.6.1/distrMod/R/internalMleCalc.R | 11 distrMod-2.6.1/distrMod/R/mleCalc-methods.R | 17 distrMod-2.6.1/distrMod/R/modifyModel.R | 4 distrMod-2.6.1/distrMod/R/qqplot.R | 153 distrMod-2.6.1/distrMod/R/returnlevelplot.R |only distrMod-2.6.1/distrMod/R/validParameter.R | 2 distrMod-2.6.1/distrMod/build/vignette.rds |binary distrMod-2.6.1/distrMod/inst/NEWS | 60 distrMod-2.6.1/distrMod/inst/doc/distrMod.R | 1 distrMod-2.6.1/distrMod/inst/doc/distrMod.Rnw | 2280 +++++----- distrMod-2.6.1/distrMod/inst/doc/distrMod.pdf |binary distrMod-2.6.1/distrMod/inst/scripts/distrModExample.R | 276 - distrMod-2.6.1/distrMod/inst/scripts/distrModExample1.R | 262 - distrMod-2.6.1/distrMod/man/0distrMod-package.Rd | 102 distrMod-2.6.1/distrMod/man/BetaFamily.Rd | 2 distrMod-2.6.1/distrMod/man/BiasType-class.Rd | 2 distrMod-2.6.1/distrMod/man/Confint-class.Rd | 2 distrMod-2.6.1/distrMod/man/Estimate-class.Rd | 2 distrMod-2.6.1/distrMod/man/Estimator.Rd | 120 distrMod-2.6.1/distrMod/man/InternalReturnClasses-class.Rd | 2 distrMod-2.6.1/distrMod/man/L2GroupFamily-class.Rd | 2 distrMod-2.6.1/distrMod/man/L2LocationFamily-class.Rd | 2 distrMod-2.6.1/distrMod/man/L2LocationFamily.Rd | 2 distrMod-2.6.1/distrMod/man/L2LocationScaleFamily-class.Rd | 2 distrMod-2.6.1/distrMod/man/L2LocationScaleFamily.Rd | 2 distrMod-2.6.1/distrMod/man/L2LocationUnknownScaleFamily.Rd | 2 distrMod-2.6.1/distrMod/man/L2ParamFamily-class.Rd | 23 distrMod-2.6.1/distrMod/man/L2ParamFamily.Rd | 2 distrMod-2.6.1/distrMod/man/L2ScaleFamily-class.Rd | 2 distrMod-2.6.1/distrMod/man/L2ScaleFamily.Rd | 2 distrMod-2.6.1/distrMod/man/L2ScaleUnknownLocationFamily.Rd | 2 distrMod-2.6.1/distrMod/man/MCEstimate-class.Rd | 262 - distrMod-2.6.1/distrMod/man/MCEstimator.Rd | 2 distrMod-2.6.1/distrMod/man/MDEstimator.Rd | 8 distrMod-2.6.1/distrMod/man/MLEstimator.Rd | 7 distrMod-2.6.1/distrMod/man/NBinomFamily.Rd | 2 distrMod-2.6.1/distrMod/man/NormType-class.Rd | 2 distrMod-2.6.1/distrMod/man/NormType.Rd | 2 distrMod-2.6.1/distrMod/man/ParamFamParameter-class.Rd | 2 distrMod-2.6.1/distrMod/man/ParamFamParameter.Rd | 2 distrMod-2.6.1/distrMod/man/ParamFamily.Rd | 2 distrMod-2.6.1/distrMod/man/QFNorm.Rd | 2 distrMod-2.6.1/distrMod/man/QFnorm-class.Rd | 2 distrMod-2.6.1/distrMod/man/addAlphTrsp2col.Rd | 2 distrMod-2.6.1/distrMod/man/asRiskwithBias-class.Rd | 2 distrMod-2.6.1/distrMod/man/asSemivar-class.Rd | 2 distrMod-2.6.1/distrMod/man/asSemivar.Rd | 2 distrMod-2.6.1/distrMod/man/asymmetricBias-class.Rd | 2 distrMod-2.6.1/distrMod/man/asymmetricBias.Rd | 2 distrMod-2.6.1/distrMod/man/distrModMASK.Rd | 2 distrMod-2.6.1/distrMod/man/distrModOptions.Rd | 2 distrMod-2.6.1/distrMod/man/existsPIC.Rd | 6 distrMod-2.6.1/distrMod/man/internal-methods.Rd |only distrMod-2.6.1/distrMod/man/internalClassUnions-class.Rd | 2 distrMod-2.6.1/distrMod/man/internalmleHelpers.Rd | 7 distrMod-2.6.1/distrMod/man/internals-qqplot.Rd | 11 distrMod-2.6.1/distrMod/man/internals.Rd | 39 distrMod-2.6.1/distrMod/man/isKerAinKerB.Rd | 2 distrMod-2.6.1/distrMod/man/meRes.Rd | 2 distrMod-2.6.1/distrMod/man/mleCalc-methods.Rd | 5 distrMod-2.6.1/distrMod/man/negativeBias.Rd | 2 distrMod-2.6.1/distrMod/man/norms.Rd | 2 distrMod-2.6.1/distrMod/man/onesidedBias-class.Rd | 2 distrMod-2.6.1/distrMod/man/positiveBias.Rd | 2 distrMod-2.6.1/distrMod/man/qqplot.Rd | 410 + distrMod-2.6.1/distrMod/man/returnlevelplot.Rd |only distrMod-2.6.1/distrMod/man/symmetricBias-class.Rd | 2 distrMod-2.6.1/distrMod/man/symmetricBias.Rd | 2 distrMod-2.6.1/distrMod/vignettes/distrMod.Rnw | 2280 +++++----- 86 files changed, 4210 insertions(+), 3528 deletions(-)
Title: S4 Classes for Elliptically Contoured Distributions
Description: Distribution (S4-)classes for elliptically contoured distributions (based on
package 'distr').
Author: Peter Ruckdeschel [cre, aut, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrEllipse versions 2.5 dated 2013-09-13 and 2.6.2 dated 2016-09-04
DESCRIPTION | 23 ++++++----- MD5 | 59 ++++++++++++++-------------- NAMESPACE | 4 + R/01.R | 34 ++++++++++++++++ R/AllClasses.R | 2 R/AllGenerics.R | 11 +++++ R/AllShow.R | 2 R/EllipticalDistribution.R | 13 +++++- R/MVMixingDistribution.R | 66 ++++++++++++++++---------------- R/MVNorm.R | 4 - R/SphericalDistribution.R | 30 +++++++++++--- inst/NEWS | 19 +++++++++ man/0distrEllipse-package.Rd | 20 +++++---- man/EllipticalDistribution-class.Rd | 6 ++ man/EllipticalDistribution.Rd | 2 man/EllipticalParameter-class.Rd | 2 man/MVnormDistribution-class.Rd | 2 man/MVnormDistribution.Rd | 2 man/MVnormParameter-class.Rd | 2 man/MVtDistribution-class.Rd | 2 man/MVtDistribution.Rd | 2 man/MVtParameter-class.Rd | 2 man/MultivarDistrList-class.Rd | 3 - man/MultivarDistrList.Rd | 2 man/MultivarMixingDistribution-class.Rd | 10 +++- man/MultivarMixingDistribution.Rd | 2 man/SphericalDistribution-class.Rd | 45 +++++++++++++-------- man/SphericalDistribution.Rd | 2 man/distrEllipse-deprecated.Rd |only man/distrEllipseMASK.Rd | 2 man/distrEllipseoptions.Rd | 2 31 files changed, 250 insertions(+), 127 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.26 dated 2016-06-13 and 5.29 dated 2016-09-04
/tmp/cranberry36285aacec72/quantreg-5.29/quantreg/DESCRIPTION | 6 - /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/MD5 | 33 ++++---- /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/R/khmal.R | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/R/nlrq.R | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/inst/ChangeLog | 15 +++ /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/inst/TODO | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/man/rq.Rd | 13 ++- /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/akj.f | 8 +- /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/cholesky.f | 40 +++++----- /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/combos.f | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/crq.f | 4 - /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/mcmb.c | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/ratfor/combos.r | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/ratfor/rq0.f |only /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/rq1.f | 2 /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/sparskit2.f | 14 +-- /tmp/cranberry36285aacec72/quantreg-5.29/quantreg/src/srqfn.f | 2 quantreg/src/rq0.f | 2 18 files changed, 87 insertions(+), 64 deletions(-)
Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 6.0.0 dated 2016-06-14 and 6.1.0 dated 2016-09-04
mixOmics-6.0.0/mixOmics/R/multilevel.R |only mixOmics-6.0.0/mixOmics/man/multilevel.Rd |only mixOmics-6.1.0/mixOmics/DESCRIPTION | 8 mixOmics-6.1.0/mixOmics/MD5 | 202 +++--- mixOmics-6.1.0/mixOmics/NAMESPACE | 33 - mixOmics-6.1.0/mixOmics/NEWS | 39 + mixOmics-6.1.0/mixOmics/R/AUC_ROC.R |only mixOmics-6.1.0/mixOmics/R/LOGOCV.R | 47 + mixOmics-6.1.0/mixOmics/R/MCVfold.R | 136 ++-- mixOmics-6.1.0/mixOmics/R/block.pls.R | 2 mixOmics-6.1.0/mixOmics/R/block.plsda.R | 2 mixOmics-6.1.0/mixOmics/R/block.spls.R | 2 mixOmics-6.1.0/mixOmics/R/block.splsda.R | 2 mixOmics-6.1.0/mixOmics/R/check_entry.R | 4 mixOmics-6.1.0/mixOmics/R/cimDiablo.R | 12 mixOmics-6.1.0/mixOmics/R/circosPlot.R | 83 ++ mixOmics-6.1.0/mixOmics/R/internal_graphic.perf.R |only mixOmics-6.1.0/mixOmics/R/internal_graphicModule.R | 120 ++- mixOmics-6.1.0/mixOmics/R/internal_mint.block.R | 6 mixOmics-6.1.0/mixOmics/R/internal_wrapper.mint.R | 37 - mixOmics-6.1.0/mixOmics/R/internal_wrapper.mint.block.R | 2 mixOmics-6.1.0/mixOmics/R/mint.block.pls.R | 2 mixOmics-6.1.0/mixOmics/R/mint.block.plsda.R | 4 mixOmics-6.1.0/mixOmics/R/mint.block.spls.R | 2 mixOmics-6.1.0/mixOmics/R/mint.block.splsda.R | 5 mixOmics-6.1.0/mixOmics/R/mint.pls.R | 2 mixOmics-6.1.0/mixOmics/R/mint.plsda.R | 2 mixOmics-6.1.0/mixOmics/R/mint.spls.R | 2 mixOmics-6.1.0/mixOmics/R/mint.splsda.R | 2 mixOmics-6.1.0/mixOmics/R/mixOmics.R | 2 mixOmics-6.1.0/mixOmics/R/network.R | 31 - mixOmics-6.1.0/mixOmics/R/pca.R | 49 - mixOmics-6.1.0/mixOmics/R/perf.R | 129 +++- mixOmics-6.1.0/mixOmics/R/perf.diablo.R | 26 mixOmics-6.1.0/mixOmics/R/perf.mint.splsda.R | 79 ++ mixOmics-6.1.0/mixOmics/R/plot.pca.R | 11 mixOmics-6.1.0/mixOmics/R/plot.perf.R | 487 ++++++++++++---- mixOmics-6.1.0/mixOmics/R/plot.tune.R |only mixOmics-6.1.0/mixOmics/R/plotDiablo.R | 16 mixOmics-6.1.0/mixOmics/R/plotIndiv.R | 50 + mixOmics-6.1.0/mixOmics/R/plotIndiv.mint.R | 8 mixOmics-6.1.0/mixOmics/R/plotIndiv.pca.R | 9 mixOmics-6.1.0/mixOmics/R/plotIndiv.pls.R | 5 mixOmics-6.1.0/mixOmics/R/plotIndiv.sgcca.R | 9 mixOmics-6.1.0/mixOmics/R/plotVar.R | 97 +-- mixOmics-6.1.0/mixOmics/R/pls.R | 2 mixOmics-6.1.0/mixOmics/R/plsda.R | 2 mixOmics-6.1.0/mixOmics/R/predict.mint.block.pls.R | 13 mixOmics-6.1.0/mixOmics/R/print.methods.R | 249 ++++---- mixOmics-6.1.0/mixOmics/R/roc_utils.R |only mixOmics-6.1.0/mixOmics/R/spca.R | 148 ++++ mixOmics-6.1.0/mixOmics/R/spls.R | 2 mixOmics-6.1.0/mixOmics/R/splsda.R | 2 mixOmics-6.1.0/mixOmics/R/tune.R | 32 - mixOmics-6.1.0/mixOmics/R/tune.diablo.R |only mixOmics-6.1.0/mixOmics/R/tune.mint.splsda.R | 77 +- mixOmics-6.1.0/mixOmics/R/tune.multilevel.R | 7 mixOmics-6.1.0/mixOmics/R/tune.splsda.R | 131 +++- mixOmics-6.1.0/mixOmics/R/vip.R | 14 mixOmics-6.1.0/mixOmics/R/wrapper.ilr.R | 365 ----------- mixOmics-6.1.0/mixOmics/data/Koren.16S.rda |binary mixOmics-6.1.0/mixOmics/data/diverse.16S.rda |binary mixOmics-6.1.0/mixOmics/data/vac18.simulated.rda |binary mixOmics-6.1.0/mixOmics/man/Koren.16S.Rd | 9 mixOmics-6.1.0/mixOmics/man/auroc.Rd |only mixOmics-6.1.0/mixOmics/man/block.pls.Rd | 2 mixOmics-6.1.0/mixOmics/man/block.plsda.Rd | 7 mixOmics-6.1.0/mixOmics/man/block.spls.Rd | 2 mixOmics-6.1.0/mixOmics/man/block.splsda.Rd | 8 mixOmics-6.1.0/mixOmics/man/cimDiablo.Rd | 14 mixOmics-6.1.0/mixOmics/man/circosPlot.Rd | 35 - mixOmics-6.1.0/mixOmics/man/diverse.16S.Rd | 12 mixOmics-6.1.0/mixOmics/man/explained_variance.Rd | 2 mixOmics-6.1.0/mixOmics/man/logratio.transfo.Rd | 5 mixOmics-6.1.0/mixOmics/man/mint.block.pls.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.block.plsda.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.block.spls.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.block.splsda.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.pls.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.plsda.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.spls.Rd | 2 mixOmics-6.1.0/mixOmics/man/mint.splsda.Rd | 2 mixOmics-6.1.0/mixOmics/man/mixOmics.Rd | 2 mixOmics-6.1.0/mixOmics/man/pca.Rd | 11 mixOmics-6.1.0/mixOmics/man/perf.Rd | 37 - mixOmics-6.1.0/mixOmics/man/plot.perf.Rd | 63 +- mixOmics-6.1.0/mixOmics/man/plot.tune.Rd |only mixOmics-6.1.0/mixOmics/man/plotContrib.Rd | 2 mixOmics-6.1.0/mixOmics/man/plotDiablo.Rd | 3 mixOmics-6.1.0/mixOmics/man/plotIndiv.Rd | 13 mixOmics-6.1.0/mixOmics/man/plotLoadings.Rd | 2 mixOmics-6.1.0/mixOmics/man/plotVar.Rd | 5 mixOmics-6.1.0/mixOmics/man/pls.Rd | 5 mixOmics-6.1.0/mixOmics/man/plsda.Rd | 13 mixOmics-6.1.0/mixOmics/man/predict.Rd | 6 mixOmics-6.1.0/mixOmics/man/spca.Rd | 26 mixOmics-6.1.0/mixOmics/man/spls.Rd | 47 + mixOmics-6.1.0/mixOmics/man/splsda.Rd | 19 mixOmics-6.1.0/mixOmics/man/stemcells.Rd | 6 mixOmics-6.1.0/mixOmics/man/tune.Rd | 22 mixOmics-6.1.0/mixOmics/man/tune.block.splsda.Rd |only mixOmics-6.1.0/mixOmics/man/tune.mint.splsda.Rd | 18 mixOmics-6.1.0/mixOmics/man/tune.multilevel.Rd | 36 - mixOmics-6.1.0/mixOmics/man/tune.splsda.Rd | 58 + mixOmics-6.1.0/mixOmics/man/vac18.simulated.Rd | 8 mixOmics-6.1.0/mixOmics/man/vip.Rd | 2 mixOmics-6.1.0/mixOmics/man/withinVariation.Rd | 4 107 files changed, 2088 insertions(+), 1242 deletions(-)
Title: Evidential Clustering
Description: Various clustering algorithms that produce a credal partition,
i.e., a set of Dempster-Shafer mass functions representing the membership of objects
to clusters. The mass functions quantify the cluster-membership uncertainty of the objects.
The algorithms are: Evidential c-Means (ECM), Relational Evidential c-Means (RECM),
Constrained Evidential c-Means (CECM), EVCLUS and EK-NNclus.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evclust versions 1.0.2 dated 2016-05-29 and 1.0.3 dated 2016-09-04
DESCRIPTION | 8 +-- MD5 | 49 ++++++++++++----------- NAMESPACE | 2 R/cecm.R | 16 ++++--- R/createD.R | 2 R/createPairs.R | 2 R/ecm.R | 2 R/evclust.R | 3 - R/kevclus.R | 83 +++++++++++++++++++++++++++++----------- R/plaus_dist.R |only R/plot.credpart.R | 9 +--- R/recm.R | 2 build/vignette.rds |binary inst/doc/Introduction.R | 6 +- inst/doc/Introduction.Rmd | 12 ++--- inst/doc/Introduction.html | 92 ++++++++++++++++++++++----------------------- man/cecm.Rd | 8 +-- man/createD.Rd | 2 man/createPairs.Rd | 2 man/ecm.Rd | 2 man/evclust.Rd | 3 - man/kevclus.Rd | 16 ++++--- man/plot.credpart.Rd | 7 +-- man/recm.Rd | 2 vignettes/Introduction.Rmd | 12 ++--- vignettes/tdenoeux.bib | 7 +-- 26 files changed, 196 insertions(+), 153 deletions(-)
More information about RcmdrPlugin.FuzzyClust at CRAN
Permanent link
More information about fontBitstreamVera at CRAN
Permanent link
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 2.2.0 dated 2016-09-02 and 2.2.1 dated 2016-09-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/NEWS.Rd | 2 +- inst/doc/dtwclust.R | 18 +++++++++--------- inst/doc/dtwclust.Rnw | 22 +++++++++++----------- inst/doc/dtwclust.pdf |binary vignettes/dtwclust-concordance.tex | 4 ++-- vignettes/dtwclust.Rnw | 22 +++++++++++----------- 8 files changed, 45 insertions(+), 45 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures
and centrality indices. Allows for flexible specification of any undirected network
estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler',
'glasso', 'huge' and 'parcor' packages.
Author: Sacha Epskamp and Eiko I. Fried
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 0.2 dated 2016-01-19 and 0.3 dated 2016-09-04
bootnet-0.2/bootnet/R/bootstrapIncreasesEdges.R |only bootnet-0.2/bootnet/R/evenMoreTests.R |only bootnet-0.3/bootnet/DESCRIPTION | 16 bootnet-0.3/bootnet/MD5 | 32 - bootnet-0.3/bootnet/NAMESPACE | 11 bootnet-0.3/bootnet/NEWS |only bootnet-0.3/bootnet/R/Smetric.R |only bootnet-0.3/bootnet/R/bootTable.R | 78 ++- bootnet-0.3/bootnet/R/bootnet.R | 623 +++++++++++++----------- bootnet-0.3/bootnet/R/bootnetResultsMethods.R | 6 bootnet-0.3/bootnet/R/centralityCompare.R |only bootnet-0.3/bootnet/R/checkDefault.R |only bootnet-0.3/bootnet/R/checkInput.R |only bootnet-0.3/bootnet/R/estimateNetwork.R | 105 +++- bootnet-0.3/bootnet/R/plotMethod.R | 537 +++++++++++++++----- bootnet-0.3/bootnet/R/printMethod.R | 50 + bootnet-0.3/bootnet/R/zzz.R |only bootnet-0.3/bootnet/inst |only bootnet-0.3/bootnet/man/bootnet.Rd | 177 ++---- bootnet-0.3/bootnet/man/corStability.Rd |only bootnet-0.3/bootnet/man/differenceTest.Rd |only bootnet-0.3/bootnet/man/estimateNetwork.Rd |only bootnet-0.3/bootnet/man/plot.bootnet.Rd | 16 23 files changed, 1075 insertions(+), 576 deletions(-)