Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8 dated 2015-09-10 and 0.8.1 dated 2015-09-11
DESCRIPTION | 6 MD5 | 21 - R/reflist.r | 15 R/tax.r | 4 R/tv.home.r | 3 inst/ChangeLog | 3 inst/doc/vegdata.R | 17 inst/doc/vegdata.Rnw | 981 ++++++++++++++++++++++++------------------------- inst/doc/vegdata.pdf |binary tests/testthat/obs.rds |only tests/testthat/test.R | 98 ++-- vignettes/vegdata.Rnw | 981 ++++++++++++++++++++++++------------------------- 12 files changed, 1060 insertions(+), 1069 deletions(-)
Title: R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Description: This 'htmlwidget' provides pan and zoom
interactivity to R graphics, including 'base', 'lattice', and 'ggplot2'. The
interactivity is provided through the 'svg-pan-zoom.js' library. Various
options to the widget can tailor the pan and zoom experience to nearly any
user desire.
Author: Anders Riutta et. al. [aut, cph] (svg-pan-zoom.js BSD-licensed library
in htmlwidgets/lib, https://github.com/ariutta/svg-pan-zoom),
Jorik Tangelder [aut, cph] (hammer.js MIT-licensed touch library in
htmlwidgets/lib, https://github.com/hammerjs/hammer),
Kent Russell [aut, cre] (R interface to svg-pan-zoom.js)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between svgPanZoom versions 0.2.0 dated 2015-07-16 and 0.3.0 dated 2015-09-11
svgPanZoom-0.2.0/svgPanZoom/NEWS |only svgPanZoom-0.3.0/svgPanZoom/DESCRIPTION | 18 + svgPanZoom-0.3.0/svgPanZoom/MD5 | 18 + svgPanZoom-0.3.0/svgPanZoom/NEWS.md |only svgPanZoom-0.3.0/svgPanZoom/R/svgPanZoom.R | 7 svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/lib/hammer |only svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/lib/svg-pan-zoom/LICENSE_svg-pan-zoom | 46 ++-- svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/lib/svg-pan-zoom/dist/svg-pan-zoom.min.js | 6 svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/svgPanZoom.js | 94 +++++++++- svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/svgPanZoom.yaml | 12 - svgPanZoom-0.3.0/svgPanZoom/man/svgPanZoom.Rd | 2 11 files changed, 156 insertions(+), 47 deletions(-)
Title: Forecast Verification Routines for the SPECS FP7 Project
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between SpecsVerification versions 0.3-0 dated 2014-10-15 and 0.4-0 dated 2015-09-11
DESCRIPTION | 12 ++++---- MD5 | 60 +++++++++++++++++++++++------------------- NAMESPACE | 12 ++++++++ R/BrierScoreDecomposition.R | 4 +- R/ClimEns.R | 11 ++----- R/Corr.R |only R/CorrDiff.R |only R/Detrend.R | 17 +++++++++--- R/DressEnsemble.R | 6 ++-- R/EnsBrier.R | 27 +++++++++---------- R/EnsBrierDiff.R | 43 ++++++++++++++---------------- R/EnsBrierSs.R | 60 ++++++++++++++++++++++++------------------ R/EnsCrps.R | 45 +++++++++---------------------- R/EnsCrpsDiff.R | 43 +++++++++++++----------------- R/EnsCrpss.R | 61 +++++++++++++++++++++++++------------------ R/EnsRps.R | 18 ++---------- R/EnsRpsDiff.R | 23 ++++------------ R/EnsRpss.R | 21 ++++---------- R/FairBrier.R | 33 ++++++++++++++--------- R/FairBrierDiff.R | 45 +++++++++++++++---------------- R/FairBrierSs.R | 62 ++++++++++++++++++++++++-------------------- R/FairCrps.R | 46 +++++++++----------------------- R/FairCrpsDiff.R | 44 ++++++++++++++----------------- R/FairCrpss.R | 61 +++++++++++++++++++++++++------------------ R/FairRps.R | 18 ++---------- R/FairRpsDiff.R | 23 ++++------------ R/FairRpss.R | 21 ++++---------- R/FitAkdParameters.R | 11 ++----- R/Preprocess.R |only R/Rankhist.R | 12 ++++---- man/Corr.Rd |only man/CorrDiff.Rd |only man/Preprocess.Rd |only man/SpecsVerification.Rd | 3 +- 34 files changed, 404 insertions(+), 438 deletions(-)
More information about SpecsVerification at CRAN
Permanent link
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework for
quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of
financial assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.0 dated 2014-12-02 and 0.4.1 dated 2015-09-11
ChangeLog | 40 + DESCRIPTION | 16 MD5 | 21 NAMESPACE | 41 + R/arrays.R | 91 +-- README.md | 19 demo/00Index | 1 demo/ShinyDiscountCurves.R |only inst/NEWS.Rd | 21 inst/shiny |only src/Makevars.win | 33 - src/RcppExports.cpp | 1166 ++++++++++++++++++--------------------------- 12 files changed, 674 insertions(+), 775 deletions(-)
Title: Random Subspace Method (RSM) for Linear Regression
Description: Performs Random Subspace Method (RSM) for high-dimensional linear regression to obtain variable importance measures. The final model is chosen based on validation set or Generalized Information Criterion.
Author: Pawel Teisseyre, Robert A. Klopotek
Maintainer: Pawel Teisseyre <teisseyrep@ipipan.waw.pl>
Diff between regRSM versions 0.4 dated 2014-04-18 and 0.5 dated 2015-09-11
DESCRIPTION | 12 +-- MD5 | 8 +- NAMESPACE | 11 +++ R/parallelRSM.R | 94 +++++++++++++++--------------- R/regRSM.r | 174 ++++++++++++++++++++++++++++++++++++-------------------- 5 files changed, 181 insertions(+), 118 deletions(-)
Title: Local Time Space Kriging
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang <dliang@umces.edu>
Diff between ltsk versions 1.0.3 dated 2015-01-26 and 1.0.4 dated 2015-09-11
DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++++------ NAMESPACE | 5 +++++ R/check_input.R | 13 ++++++++++++- R/lnbk.R |only R/rowSplit_1.R |only R/tsbk.R |only R/vexpn.R | 14 ++++++++++++++ R/work.blk.kriging.R |only R/work.blk.kriging_2.R |only R/working.tsk.R | 2 +- man/ltsk-internal.Rd | 2 ++ man/tsbk.Rd |only 13 files changed, 51 insertions(+), 13 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl], Kathleen Gates [aut], Peter Molenaar
[aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-1 dated 2014-12-15 and 0.1-2 dated 2015-09-11
gimme-0.1-1/gimme/man/aggregate.Rd |only gimme-0.1-1/gimme/man/semigimme.Rd |only gimme-0.1-2/gimme/DESCRIPTION | 16 gimme-0.1-2/gimme/MD5 | 29 gimme-0.1-2/gimme/NAMESPACE | 24 gimme-0.1-2/gimme/R/aggSEM.R |only gimme-0.1-2/gimme/R/gimme-data.R |only gimme-0.1-2/gimme/R/gimme-pkg.R |only gimme-0.1-2/gimme/R/gimme.R | 2977 +++++++++++++++++++-------------- gimme-0.1-2/gimme/R/indSEM.R |only gimme-0.1-2/gimme/man/aggSEM.Rd |only gimme-0.1-2/gimme/man/gimme-package.Rd | 47 gimme-0.1-2/gimme/man/gimme.Rd | 119 - gimme-0.1-2/gimme/man/indSEM.Rd | 101 - gimme-0.1-2/gimme/man/ts1.Rd | 16 gimme-0.1-2/gimme/man/ts2.Rd | 16 gimme-0.1-2/gimme/man/ts3.Rd | 16 gimme-0.1-2/gimme/man/ts4.Rd | 16 gimme-0.1-2/gimme/man/ts5.Rd | 16 19 files changed, 2015 insertions(+), 1378 deletions(-)
Title: Automated Runs and Evaluations of Ecological Niche Models
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006).
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella <bob.muscarella@gmail.com>
Diff between ENMeval versions 0.1.1 dated 2014-10-05 and 0.2.0 dated 2015-09-11
DESCRIPTION | 14 +- MD5 | 52 +++---- NAMESPACE | 6 NEWS | 10 + R/ENMevaluate.R | 89 ++++++------- R/all.classes.R | 2 R/calc.aicc.R | 2 R/get.block.R | 1 R/get.checkerboard1.R | 25 ++- R/get.checkerboard2.R | 16 ++ R/get.jackknife.R | 2 R/get.randomkfold.R | 3 R/get.user.R | 3 R/make.args.R | 2 R/tuning.R | 301 +++++++++++++++++++++++++-------------------- data/enmeval_results.rda |binary inst/CITATION | 6 man/ENMeval-package.Rd | 12 + man/ENMevaluate.Rd | 19 ++ man/ENMevaluation-class.Rd | 17 +- man/calc.aicc.Rd | 2 man/calc.niche.overlap.Rd | 2 man/corrected.var.Rd | 2 man/enmeval_results.Rd | 5 man/eval.plot.Rd | 2 man/get.evaluation.bins.Rd | 6 man/make.args.Rd | 2 27 files changed, 347 insertions(+), 256 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between devtools versions 1.8.0 dated 2015-05-09 and 1.9.1 dated 2015-09-11
devtools-1.8.0/devtools/R/install-gitorious.r |only devtools-1.8.0/devtools/man/cran_env_vars.Rd |only devtools-1.8.0/devtools/man/install_gitorious.Rd |only devtools-1.8.0/devtools/tests/testthat/test-load-dir.r |only devtools-1.9.1/devtools/DESCRIPTION | 19 devtools-1.9.1/devtools/MD5 | 191 +++++----- devtools-1.9.1/devtools/NAMESPACE | 22 - devtools-1.9.1/devtools/R/build.r | 2 devtools-1.9.1/devtools/R/check-cran.r | 50 +- devtools-1.9.1/devtools/R/check-devtools.r | 6 devtools-1.9.1/devtools/R/check.r | 120 ++---- devtools-1.9.1/devtools/R/cran.r | 4 devtools-1.9.1/devtools/R/create.r | 4 devtools-1.9.1/devtools/R/deps.R | 87 ++++ devtools-1.9.1/devtools/R/dev-help.r | 2 devtools-1.9.1/devtools/R/dev-mode.r | 2 devtools-1.9.1/devtools/R/doctor.R | 40 +- devtools-1.9.1/devtools/R/document.r | 10 devtools-1.9.1/devtools/R/git.R | 46 +- devtools-1.9.1/devtools/R/imports-env.r | 27 - devtools-1.9.1/devtools/R/infrastructure-git.R | 135 ++++++- devtools-1.9.1/devtools/R/infrastructure.R | 74 ++- devtools-1.9.1/devtools/R/install-bitbucket.r | 2 devtools-1.9.1/devtools/R/install-github.r | 8 devtools-1.9.1/devtools/R/install.r | 31 + devtools-1.9.1/devtools/R/load-dll.r | 10 devtools-1.9.1/devtools/R/load.r | 19 devtools-1.9.1/devtools/R/package.r | 23 - devtools-1.9.1/devtools/R/release.r | 23 - devtools-1.9.1/devtools/R/remove-s4-class.r | 67 +++ devtools-1.9.1/devtools/R/revdep-summarise.R | 22 + devtools-1.9.1/devtools/R/revdep.R | 16 devtools-1.9.1/devtools/R/rtools.r | 5 devtools-1.9.1/devtools/R/run-source.r | 5 devtools-1.9.1/devtools/R/session-info.r | 3 devtools-1.9.1/devtools/R/show-news.r | 2 devtools-1.9.1/devtools/R/test.r | 13 devtools-1.9.1/devtools/R/uninstall.r |only devtools-1.9.1/devtools/R/upload-ftp.r |only devtools-1.9.1/devtools/R/utils.r | 8 devtools-1.9.1/devtools/R/vignettes.r | 5 devtools-1.9.1/devtools/R/with-debug.r | 5 devtools-1.9.1/devtools/R/with.r | 64 +++ devtools-1.9.1/devtools/R/zzz.r | 13 devtools-1.9.1/devtools/README.md | 5 devtools-1.9.1/devtools/build |only devtools-1.9.1/devtools/inst/doc |only devtools-1.9.1/devtools/inst/templates/travis.yml | 9 devtools-1.9.1/devtools/man/as.package.Rd | 6 devtools-1.9.1/devtools/man/build_vignettes.Rd | 6 devtools-1.9.1/devtools/man/check.Rd | 31 - devtools-1.9.1/devtools/man/check_failures.Rd |only devtools-1.9.1/devtools/man/devtools-deprecated.Rd |only devtools-1.9.1/devtools/man/dr_github.Rd | 4 devtools-1.9.1/devtools/man/infrastructure.Rd | 10 devtools-1.9.1/devtools/man/install.Rd | 14 devtools-1.9.1/devtools/man/install_bitbucket.Rd | 5 devtools-1.9.1/devtools/man/install_deps.Rd | 13 devtools-1.9.1/devtools/man/install_git.Rd | 7 devtools-1.9.1/devtools/man/install_github.Rd | 7 devtools-1.9.1/devtools/man/install_svn.Rd | 7 devtools-1.9.1/devtools/man/install_url.Rd | 7 devtools-1.9.1/devtools/man/install_version.Rd | 7 devtools-1.9.1/devtools/man/load_all.Rd | 9 devtools-1.9.1/devtools/man/package_deps.Rd | 6 devtools-1.9.1/devtools/man/release.Rd | 2 devtools-1.9.1/devtools/man/revdep.Rd | 2 devtools-1.9.1/devtools/man/revdep_check.Rd | 8 devtools-1.9.1/devtools/man/source_url.Rd | 6 devtools-1.9.1/devtools/man/submit_cran.Rd | 2 devtools-1.9.1/devtools/man/test.Rd | 6 devtools-1.9.1/devtools/man/uninstall.Rd |only devtools-1.9.1/devtools/man/use_build_ignore.Rd | 3 devtools-1.9.1/devtools/man/use_data.Rd | 3 devtools-1.9.1/devtools/man/use_data_raw.Rd | 3 devtools-1.9.1/devtools/man/use_git.Rd | 2 devtools-1.9.1/devtools/man/use_git_hook.Rd | 4 devtools-1.9.1/devtools/man/use_github.Rd | 45 ++ devtools-1.9.1/devtools/man/use_github_links.Rd |only devtools-1.9.1/devtools/man/use_package.Rd | 3 devtools-1.9.1/devtools/man/use_readme_rmd.Rd | 3 devtools-1.9.1/devtools/man/with_debug.Rd | 6 devtools-1.9.1/devtools/man/with_something.Rd | 12 devtools-1.9.1/devtools/tests/test-that.R | 6 devtools-1.9.1/devtools/tests/testthat/test-check.r | 26 - devtools-1.9.1/devtools/tests/testthat/test-dll.r | 7 devtools-1.9.1/devtools/tests/testthat/test-github-connections.R |only devtools-1.9.1/devtools/tests/testthat/test-infrastructure.r |only devtools-1.9.1/devtools/tests/testthat/test-load.r |only devtools-1.9.1/devtools/tests/testthat/test-package.R | 4 devtools-1.9.1/devtools/tests/testthat/test-remotes.r |only devtools-1.9.1/devtools/tests/testthat/test-s4-sort.r |only devtools-1.9.1/devtools/tests/testthat/test-s4-unload.r | 4 devtools-1.9.1/devtools/tests/testthat/test-test.r |only devtools-1.9.1/devtools/tests/testthat/test-uninstall.r |only devtools-1.9.1/devtools/tests/testthat/test-vignettes.r | 30 + devtools-1.9.1/devtools/tests/testthat/test-with.r | 38 + devtools-1.9.1/devtools/tests/testthat/testHelp/DESCRIPTION | 2 devtools-1.9.1/devtools/tests/testthat/testS4sort |only devtools-1.9.1/devtools/tests/testthat/testTest |only devtools-1.9.1/devtools/tests/testthat/testTestWithDepends |only devtools-1.9.1/devtools/tests/testthat/testUseData |only devtools-1.9.1/devtools/vignettes |only 103 files changed, 1087 insertions(+), 478 deletions(-)
Title: Correspondence Analysis Variants
Description: Provides six variants of two-way correspondence analysis (ca):
simple ca, singly ordered ca, doubly ordered ca, non-symmetrical ca,
singly ordered non symmetrical ca, and doubly ordered non symmetrical
ca.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unina2.it>
Diff between CAvariants versions 2.1 dated 2014-07-23 and 3.0 dated 2015-09-11
CAvariants-2.1/CAvariants/R/plotcacorporateplus.R |only CAvariants-2.1/CAvariants/R/printcacorporateplus.R |only CAvariants-2.1/CAvariants/man/plotcacorporateplus.Rd |only CAvariants-2.1/CAvariants/man/printcacorporateplus.Rd |only CAvariants-3.0/CAvariants/DESCRIPTION | 21 ++---- CAvariants-3.0/CAvariants/MD5 | 34 +++++----- CAvariants-3.0/CAvariants/NAMESPACE | 18 ++++- CAvariants-3.0/CAvariants/R/CAvariants.R | 20 +++--- CAvariants-3.0/CAvariants/R/caellipse.R | 34 +++++----- CAvariants-3.0/CAvariants/R/nsca.ellipse.R | 32 +++++----- CAvariants-3.0/CAvariants/R/plot.CAvariants.R |only CAvariants-3.0/CAvariants/R/plotone.R | 4 - CAvariants-3.0/CAvariants/R/print.CAvariants.R |only CAvariants-3.0/CAvariants/R/summary.CAvariants.R |only CAvariants-3.0/CAvariants/data/asbestos.rda |binary CAvariants-3.0/CAvariants/data/shopdataM.rda |binary CAvariants-3.0/CAvariants/man/CAvariants.Rd | 56 +++++------------- CAvariants-3.0/CAvariants/man/caellipse.Rd | 12 +-- CAvariants-3.0/CAvariants/man/nsca.ellipse.Rd | 13 ++-- CAvariants-3.0/CAvariants/man/plot.CAvariants.Rd |only CAvariants-3.0/CAvariants/man/plotone.Rd | 2 CAvariants-3.0/CAvariants/man/print.CAvariants.Rd |only CAvariants-3.0/CAvariants/man/summary.CAvariants.Rd |only 23 files changed, 116 insertions(+), 130 deletions(-)
Title: Regularization Paths for Huber Loss Regression and Quantile
Regression Penalized by Lasso or Elastic-Net
Description: Efficient algorithms for fitting entire regularization paths for Huber loss regression and quantile regression penalized by lasso or elastic-net.
Author: Congrui Yi
Maintainer: Congrui Yi <congrui-yi@uiowa.edu>
Diff between hqreg versions 0.9 dated 2015-06-20 and 1.0 dated 2015-09-11
hqreg-0.9/hqreg/R/setupPsi.R |only hqreg-1.0/hqreg/DESCRIPTION | 8 hqreg-1.0/hqreg/MD5 | 23 - hqreg-1.0/hqreg/NAMESPACE | 4 hqreg-1.0/hqreg/NEWS |only hqreg-1.0/hqreg/R/cv.hqreg.R | 21 - hqreg-1.0/hqreg/R/hqreg.R | 110 ++++--- hqreg-1.0/hqreg/R/init.R |only hqreg-1.0/hqreg/R/loss.hqreg.R | 6 hqreg-1.0/hqreg/man/cv.hqreg.Rd | 2 hqreg-1.0/hqreg/man/hqreg-package.Rd | 4 hqreg-1.0/hqreg/man/hqreg.Rd | 40 +- hqreg-1.0/hqreg/man/predict.hqreg.Rd | 2 hqreg-1.0/hqreg/src/hqreg.c | 547 ++++++++++++++++++++++++++++++----- 14 files changed, 599 insertions(+), 168 deletions(-)
More information about hindexcalculator at CRAN
Permanent link
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.2 dated 2014-11-18 and 2.3 dated 2015-09-11
DESCRIPTION | 20 LICENSE |only MD5 | 32 - NAMESPACE | 33 + R/OUshifts.R | 287 +++++------ R/phyloglm.R | 1242 +++++++++++++++++++++++++----------------------- R/phylolm.R | 648 ++++++++++++------------- R/phylostep.R |only README.md |only man/OUshifts.Rd | 142 ++--- man/flowerTree.Rd | 20 man/phyloglm-methods.Rd | 74 +- man/phyloglm.Rd | 198 ++++--- man/phylolm-methods.Rd | 107 ++-- man/phylolm-package.Rd | 40 - man/phylolm.Rd | 252 ++++----- man/phylostep.Rd |only man/rbinTrait.Rd | 86 +-- src/Makevars | 3 19 files changed, 1662 insertions(+), 1522 deletions(-)
Title: Fitting Structural Equation Mixture Models
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach <nora.umbach@web.de>
Diff between nlsem versions 0.4.1 dated 2015-07-29 and 0.5 dated 2015-09-11
ChangeLog | 10 DESCRIPTION | 13 MD5 | 46 - NAMESPACE | 16 R/em.R | 440 ++++++++--------- R/lms.R | 49 - R/model.R | 1085 ++++++++++++++++++++++++------------------- R/nsemm.R | 84 +-- R/qml.R | 2 R/s3generics.R | 454 +++++++++++++---- R/semm.R | 288 +++++------ man/anova.Rd | 18 man/as.data.frame.Rd | 16 man/count_free_parameters.Rd | 11 man/create_sem.Rd | 26 - man/em.Rd | 4 man/fill_model.Rd | 21 man/get_factor_scores.Rd | 7 man/nlsem-package.Rd | 36 - man/qml.Rd | 79 +-- man/simulate.Rd | 29 - man/specify_sem.Rd | 200 ++++--- tests/tests_for_model.R | 33 - tests/tests_for_semm.R | 15 24 files changed, 1674 insertions(+), 1308 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>
Diff between Rdsdp versions 1.0.3 dated 2015-07-12 and 1.0.4 dated 2015-09-11
DESCRIPTION | 6 - MD5 | 12 +- R/Rdsdp.R | 313 ++++++++++++++++++++++++++++---------------------------- src/Rreadsdpa.c | 2 tests/test1.R | 6 - tests/test2.R | 41 ++----- tests/test3.R | 4 7 files changed, 189 insertions(+), 195 deletions(-)
Title: Iterated Racing Procedures
Description: Iterated racing for automatic algorithm configuration.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@ulb.ac.be>
Diff between irace versions 1.06 dated 2014-11-26 and 1.07 dated 2015-09-11
irace-1.06/irace/README |only irace-1.07/irace/DESCRIPTION | 11 irace-1.07/irace/MD5 | 43 + irace-1.07/irace/NAMESPACE | 5 irace-1.07/irace/NEWS | 29 + irace-1.07/irace/R/cluster.R | 13 irace-1.07/irace/R/irace.R | 149 ++++-- irace-1.07/irace/R/main.R | 76 +++ irace-1.07/irace/R/race-wrapper.R | 325 ++++++++------- irace-1.07/irace/R/race.R | 286 ++++++------- irace-1.07/irace/R/readConfiguration.R | 184 ++++++-- irace-1.07/irace/R/readParameters.R | 19 irace-1.07/irace/R/testing.R |only irace-1.07/irace/R/utils.R | 66 ++- irace-1.07/irace/R/version.R | 2 irace-1.07/irace/README.md |only irace-1.07/irace/inst/bin/irace | 2 irace-1.07/irace/inst/examples/acotsp/default.txt |only irace-1.07/irace/inst/examples/acotsp/forbidden.txt |only irace-1.07/irace/inst/examples/acotsp/hook-run | 14 irace-1.07/irace/inst/examples/mpi/tune-main-cluster-mpi | 4 irace-1.07/irace/inst/templates/tune-conf.tmpl | 101 ++-- irace-1.07/irace/man/hook.evaluate.default.Rd | 12 irace-1.07/irace/man/hook.run.default.Rd | 10 irace-1.07/irace/man/irace-package.Rd | 13 25 files changed, 847 insertions(+), 517 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfcomb versions 2.1-3 dated 2015-04-29 and 2.1-4 dated 2015-09-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 18 +++++++++--------- src/logistic.cpp | 10 +++++----- 4 files changed, 21 insertions(+), 21 deletions(-)
Title: Assessing Functional Impact on Gene Expression of Mutations in
Cancer
Description: A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer. Given a patient-gene matrix encoding the presence/absence of a mutation, a patient-gene expression matrix encoding continuous value expression data, and a graph structure encoding whether two genes are known to be functionally related, xseq outputs: a) the probability that a recurrently mutated gene g influences gene expression across the population of patients;
and b) the probability that an individual mutation in gene g in an individual patient m influences expression within that patient.
Author: Jiarui Ding, Sohrab Shah
Maintainer: Jiarui Ding <jiaruid@cs.ubc.ca>
Diff between xseq versions 0.2.0 dated 2015-08-29 and 0.2.1 dated 2015-09-11
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/xseq-package.Rmd | 4 ++-- inst/doc/xseq-package.pdf |binary src/register.c | 2 +- vignettes/xseq-package.Rmd | 4 ++-- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: Basic Wireless Communications
Description: A basic wireless communications simulation package in R. The package includes
modulation functions for BPSK, QPSK, 8-PSK, 16-PSK, 16-QAM and 64-QAM. Also included is
an AWGN noise generation function. Additionally, the package includes functions to plot
an I (in-phase) and Q (quadrature) scatter diagram, or density plot. Together these functions
enable the evaluation of respective bit error and symbol rates in an AWGN channel and for
easily viewing the respective signals and noise in a scatter plot or density plot.
Author: Alberto Gutierrez [aut, cre]
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Diff between rwirelesscom versions 1.0.1 dated 2015-08-17 and 1.3 dated 2015-09-11
DESCRIPTION | 8 - MD5 | 38 ++++---- NAMESPACE | 2 R/rwirelesscom.R | 215 +++++++++++++++++++++++++++++++++++++++++-------- man/f16pskdemod.Rd |only man/f16pskmod.Rd |only man/f16qamdemod.Rd | 7 - man/f16qammod.Rd | 13 +- man/f64qamdemod.Rd | 7 - man/f64qammod.Rd | 8 - man/f8pskdemod.Rd | 5 - man/f8pskmod.Rd | 5 - man/fNo.Rd | 5 - man/fbpskdemod.Rd | 7 - man/fbpskmod.Rd | 3 man/fqpskdemod.Rd | 5 - man/fqpskmod.Rd | 3 man/iqdensityplot.Rd | 9 +- man/iqscatterplot.Rd | 5 - man/rwirelesscom.Rd | 3 tests/testthat/test1.R | 28 ++++++ 21 files changed, 287 insertions(+), 89 deletions(-)
Title: Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
Description: Rapid, simulation-based exact (restricted) likelihood ratio tests
for testing the presence of variance components/nonparametric terms for
models fit with nlme::lme(),lme4::lmer(), gamm4::gamm4(), mgcv::gamm() and
SemiPar::spm().
Author: Fabian Scheipl [aut, cre],
Ben Bolker [aut]
Maintainer: Fabian Scheipl <fabian.scheipl@stat.uni-muenchen.de>
Diff between RLRsim versions 3.0 dated 2014-08-12 and 3.1-2 dated 2015-09-11
DESCRIPTION | 19 +- MD5 | 34 +-- NAMESPACE | 23 ++ NEWS | 5 R/LRTSim.R | 252 ++++++++++++++--------------- R/RLRTSim.R | 395 +++++++++++++++++++++++----------------------- R/RLRsim-package.R | 36 +++- R/exactLRT.R | 131 +++++++-------- R/exactRLRT.R | 180 +++++++++++--------- R/extract.lmeDesign.R | 125 +++++++------- R/extract.lmerModDesign.R | 60 +++--- man/LRTSim.Rd | 3 man/RLRsim-package.Rd | 40 +++- man/exactLRT.Rd | 5 man/exactRLRT.Rd | 12 - man/extract.lmeDesign.Rd | 7 src/RLRsim.cpp | 141 ++++++++-------- src/RcppExports.cpp | 34 +-- 18 files changed, 792 insertions(+), 710 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.44.0 dated 2015-02-22 and 0.45.0 dated 2015-09-11
PSCBS-0.44.0/PSCBS/.Rinstignore |only PSCBS-0.45.0/PSCBS/DESCRIPTION | 22 +- PSCBS-0.45.0/PSCBS/MD5 | 105 +++++---- PSCBS-0.45.0/PSCBS/NAMESPACE | 108 +++------- PSCBS-0.45.0/PSCBS/NEWS | 26 ++ PSCBS-0.45.0/PSCBS/R/AbstractCBS.HCLUST.R | 5 PSCBS-0.45.0/PSCBS/R/AbstractCBS.PRUNE.R | 2 PSCBS-0.45.0/PSCBS/R/AbstractCBS.R | 14 - PSCBS-0.45.0/PSCBS/R/AbstractCBS.REPORT.R | 34 ++- PSCBS-0.45.0/PSCBS/R/CBS.CALL.R | 10 PSCBS-0.45.0/PSCBS/R/CBS.EXTS.R | 8 PSCBS-0.45.0/PSCBS/R/CBS.IO.R | 16 - PSCBS-0.45.0/PSCBS/R/CBS.PLOT,many.R | 4 PSCBS-0.45.0/PSCBS/R/CBS.PLOT.R | 2 PSCBS-0.45.0/PSCBS/R/CBS.PRUNE.R | 2 PSCBS-0.45.0/PSCBS/R/CBS.R | 4 PSCBS-0.45.0/PSCBS/R/CBS.joinSegments.R | 53 +++- PSCBS-0.45.0/PSCBS/R/DNAcopy.EXTS.R | 14 - PSCBS-0.45.0/PSCBS/R/NonPairedPSCBS.R | 2 PSCBS-0.45.0/PSCBS/R/PSCBS.R | 4 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.PLOT.R | 2 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.applyByRegion.R | 2 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.callGNL.R | 2 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.updateMeansTogether.R | 28 +- PSCBS-0.45.0/PSCBS/R/findLargeGaps.R | 45 ++-- PSCBS-0.45.0/PSCBS/R/gapsToSegments.R | 20 + PSCBS-0.45.0/PSCBS/R/segmentByCBS.R | 45 +++- PSCBS-0.45.0/PSCBS/R/segmentByNonPairedPSCBS.R | 2 PSCBS-0.45.0/PSCBS/R/segmentByPairedPSCBS.R | 19 + PSCBS-0.45.0/PSCBS/R/writeWIG.R |only PSCBS-0.45.0/PSCBS/R/zzz.R | 1 PSCBS-0.45.0/PSCBS/build/vignette.rds |binary PSCBS-0.45.0/PSCBS/inst/doc/CBS.pdf |binary PSCBS-0.45.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary PSCBS-0.45.0/PSCBS/inst/templates/rsp/CBS,report.tex.rsp | 2 PSCBS-0.45.0/PSCBS/inst/templates/rsp/PairedPSCBS,report.tex.rsp | 2 PSCBS-0.45.0/PSCBS/man/AbstractCBS.Rd | 27 +- PSCBS-0.45.0/PSCBS/man/CBS.Rd | 12 - PSCBS-0.45.0/PSCBS/man/Non-documented_objects.Rd | 4 PSCBS-0.45.0/PSCBS/man/NonPairedPSCBS.Rd | 4 PSCBS-0.45.0/PSCBS/man/PSCBS.Rd | 6 PSCBS-0.45.0/PSCBS/man/PairedPSCBS.Rd | 22 +- PSCBS-0.45.0/PSCBS/man/findLargeGaps.Rd | 5 PSCBS-0.45.0/PSCBS/man/gapsToSegments.data.frame.Rd | 4 PSCBS-0.45.0/PSCBS/man/hclustCNs.AbstractCBS.Rd | 2 PSCBS-0.45.0/PSCBS/man/pruneByHClust.AbstractCBS.Rd | 2 PSCBS-0.45.0/PSCBS/man/report.AbstractCBS.Rd | 2 PSCBS-0.45.0/PSCBS/man/segmentByCBS.Rd | 8 PSCBS-0.45.0/PSCBS/man/segmentByPairedPSCBS.Rd | 3 PSCBS-0.45.0/PSCBS/man/writeSegments.CBS.Rd | 58 ++--- PSCBS-0.45.0/PSCBS/tests/PairedPSCBS,plot.R.HIDE |only PSCBS-0.45.0/PSCBS/tests/findLargeGaps.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,flavors.R.HIDE |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,median.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,prune.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,weights.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS.R | 44 +++- PSCBS-0.45.0/PSCBS/tests/segmentByNonPairedPSCBS,medianDH.R | 12 - 58 files changed, 486 insertions(+), 334 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa <minato-nakazawa@umin.net>
Maintainer: Minato Nakazawa <minato-nakazawa@umin.net>
Diff between fmsb versions 0.5.1 dated 2014-09-15 and 0.5.2 dated 2015-09-11
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 8 +++++++- NEWS | 5 +++++ R/demogjpn.R | 38 ++++++++++++++++++++------------------ man/Jvital.Rd | 6 ++++-- man/lifetable.Rd | 6 +++--- 7 files changed, 50 insertions(+), 35 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-7 dated 2015-08-19 and 0.1-9 dated 2015-09-11
DESCRIPTION | 8 +-- MD5 | 30 ++++++------ NAMESPACE | 2 R/AncestralStates.R | 2 R/BootstrapRep.R | 95 +++++++++++++++++++++++++++++++++------ R/CalcR2CvCorrected.R | 2 R/MantelCor.R | 12 ++-- R/MonteCarloStat.R | 21 +++++++- R/MultivDriftTest.R |only R/TestModularity.R | 10 ++-- inst/CITATION |only inst/tests/test.TestModularity.r | 6 +- man/AncestralStates.Rd | 2 man/BootstrapRep.Rd | 8 +-- man/BootstrapStat.Rd |only man/MantelCor.Rd | 6 +- man/MultivDriftTest.Rd |only man/TestModularity.Rd | 8 +-- 18 files changed, 151 insertions(+), 61 deletions(-)
Title: Censored Linear Mixture Regression Models
Description: Fit censored linear regression models where the random errors follow a finite mixture of Normal or Student-t distributions.
Author: Luis Benites Sanchez, Victor Hugo Lachos
Maintainer: Luis Benites Sanchez <lbenitesanchez@gmail.com>
Diff between CensMixReg versions 0.5 dated 2015-08-27 and 0.7 dated 2015-09-11
DESCRIPTION | 12 - MD5 | 13 - R/CensMixReg.R | 394 ++++------------------------------------------ R/CensMixRegEM.R |only R/UtilityFunctions.R | 10 - man/CensMixReg-package.Rd | 6 man/CensMixReg.Rd | 4 man/wage.rates.Rd | 62 +++++-- 8 files changed, 112 insertions(+), 389 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.0.5 dated 2015-03-23 and 2.0.6 dated 2015-09-11
DESCRIPTION | 9 +++-- MD5 | 29 +++++++++-------- NAMESPACE | 8 ++++ R/addBAMMlegend.R | 18 +++++++++-- R/colorMap.R | 75 +++++++++++++++++++++++++++++++--------------- R/plot.bammdata.R | 18 ++++++----- R/samplingProbs.R | 4 ++ R/setBAMMpriors.R | 8 ++++ R/traitDependentBAMM.R | 42 +++++++++++++++++++------ R/writeEventData.R | 4 +- inst |only man/BAMMtools-package.Rd | 14 +++++--- man/addBAMMlegend.Rd | 7 +++- man/getTipRates.Rd | 2 - man/plot.bammdata.Rd | 4 +- man/traitDependentBAMM.Rd | 19 +++++++---- 16 files changed, 180 insertions(+), 81 deletions(-)