Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.9 dated 2017-08-31 and 0.0.10 dated 2017-09-25
ChangeLog | 12 +++++++++ DESCRIPTION | 8 +++--- MD5 | 12 ++++----- inst/NEWS.Rd | 6 ++++ inst/tests/runit.index.R | 21 ++++++++++++++++- src/annoy.cpp | 2 - tests/runUnitTests.R | 58 +++++++++++++++++++++-------------------------- 7 files changed, 76 insertions(+), 43 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of subgroup
identification and personalized medicine models under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre],
Aaron Potvien [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.0.2 dated 2017-06-11 and 0.1.0 dated 2017-09-25
DESCRIPTION | 19 MD5 | 54 +- NAMESPACE | 26 + R/check_overlap.R | 123 +++++- R/data_prep_utils.R |only R/est_subgroup_effects.R | 307 ++++++++++++--- R/fit_losses.R | 482 ++++++++++++++++-------- R/fit_subgroup.R | 344 +++++++++++++---- R/multiple_treatment_utils.R |only R/plot_compare.R | 54 +- R/plot_subgroup_fitted.R | 26 - R/plot_subgroup_validated.R | 134 +++++- R/predict_subgroup.R | 40 + R/print_subgroup.R | 65 ++- R/summarize_subgroups.R | 148 +++++-- R/summary_subgroup.R | 54 ++ R/validate_subgroup.R | 456 +++++++++++++++++----- README.md | 167 ++++++++ build/vignette.rds |binary inst/doc/usage_of_the_personalized_package.html | 241 ++++++------ man/check.overlap.Rd | 55 ++ man/fit.subgroup.Rd | 40 + man/plot.Rd | 8 man/plotCompare.Rd | 3 man/print.Rd | 8 man/subgroup.effects.Rd | 7 man/summarize.subgroups.Rd | 6 man/validate.subgroup.Rd | 12 vignettes/usage_overview-1.png |only vignettes/vis_val-1.png |only 30 files changed, 2182 insertions(+), 697 deletions(-)
Title: Allows Interactive Visualization of Data Through a Web Browser
GUI
Description: Intended for both technical and non-technical users to create
interactive data visualizations through a web browser GUI without writing any
code.
Author: Eugene Dubossarsky [aut, cph, cre],
Julius Neggo [ctb] (Lead Developer),
Howard Song [aut] (Developer),
Susan Wang [ctb] (Project Manager),
Jason Widjaja [ctb] (Vignette),
Jose Magana [ctb] (Package Manager and Developer),
Sergey Skripko [ctb] (Developer)
Maintainer: Eugene Dubossarsky <eugene@presciient.com>
Diff between ggraptR versions 0.1 dated 2016-03-04 and 1.0 dated 2017-09-25
ggraptR-0.1/ggraptR/inst/ggraptR/functions/plot.R |only ggraptR-0.1/ggraptR/inst/ggraptR/global_constants.R |only ggraptR-0.1/ggraptR/inst/ggraptR/reactives/plotWidgetNames.R |only ggraptR-0.1/ggraptR/inst/ggraptR/reactives/plotWidgetOpts.R |only ggraptR-0.1/ggraptR/inst/ggraptR/reactives/plotWidgetSelectedVals.R |only ggraptR-0.1/ggraptR/inst/ggraptR/reactives/plotWidgetValsOLD.R |only ggraptR-0.1/ggraptR/inst/ggraptR/reactives/plotWidgetsLoadedCond.R |only ggraptR-0.1/ggraptR/inst/ggraptR/test.R |only ggraptR-0.1/ggraptR/inst/ggraptR/uiWidgets/fileWidgets.R |only ggraptR-0.1/ggraptR/inst/ggraptR/views/defunct |only ggraptR-0.1/ggraptR/inst/ggraptR/views/import |only ggraptR-0.1/ggraptR/inst/ggraptR/views/modals |only ggraptR-0.1/ggraptR/inst/ggraptR/views/plot |only ggraptR-0.1/ggraptR/inst/ggraptR/views/table |only ggraptR-1.0/ggraptR/DESCRIPTION | 47 ggraptR-1.0/ggraptR/MD5 | 118 +- ggraptR-1.0/ggraptR/NAMESPACE | 7 ggraptR-1.0/ggraptR/R/ggraptR.R | 95 + ggraptR-1.0/ggraptR/README.md | 4 ggraptR-1.0/ggraptR/build |only ggraptR-1.0/ggraptR/inst/doc |only ggraptR-1.0/ggraptR/inst/ggraptR/debug/debug.R | 32 ggraptR-1.0/ggraptR/inst/ggraptR/functions/aggregate.R | 62 - ggraptR-1.0/ggraptR/inst/ggraptR/functions/codeGen.R |only ggraptR-1.0/ggraptR/inst/ggraptR/functions/ggplots.R |only ggraptR-1.0/ggraptR/inst/ggraptR/functions/helper.R | 321 +++--- ggraptR-1.0/ggraptR/inst/ggraptR/globals.R |only ggraptR-1.0/ggraptR/inst/ggraptR/observeEvents.R | 167 +-- ggraptR-1.0/ggraptR/inst/ggraptR/reactives/dataset.R | 387 +++---- ggraptR-1.0/ggraptR/inst/ggraptR/reactives/download.R | 52 - ggraptR-1.0/ggraptR/inst/ggraptR/reactives/plot.R | 428 +------- ggraptR-1.0/ggraptR/inst/ggraptR/reactives/plotWidgetVals.R | 307 +---- ggraptR-1.0/ggraptR/inst/ggraptR/reactives/plotWidgetsDisplayCond.R | 198 --- ggraptR-1.0/ggraptR/inst/ggraptR/reactives/reactives.R | 230 +--- ggraptR-1.0/ggraptR/inst/ggraptR/server.R | 70 - ggraptR-1.0/ggraptR/inst/ggraptR/ui.R | 146 +- ggraptR-1.0/ggraptR/inst/ggraptR/uiWidgets/generalWidgets.R | 68 + ggraptR-1.0/ggraptR/inst/ggraptR/uiWidgets/ioWidgets.R |only ggraptR-1.0/ggraptR/inst/ggraptR/uiWidgets/manAggWidgets.R | 28 ggraptR-1.0/ggraptR/inst/ggraptR/uiWidgets/plotWidgets.R | 519 ++++------ ggraptR-1.0/ggraptR/inst/ggraptR/views/addDatasetCtrlsUI.R |only ggraptR-1.0/ggraptR/inst/ggraptR/views/codeCtrlsUI.R |only ggraptR-1.0/ggraptR/inst/ggraptR/views/modalPanels.R |only ggraptR-1.0/ggraptR/inst/ggraptR/views/plotBlock |only ggraptR-1.0/ggraptR/inst/ggraptR/views/plotCtrlsUI.R |only ggraptR-1.0/ggraptR/inst/ggraptR/views/tableCtrlsUI.R |only ggraptR-1.0/ggraptR/inst/ggraptR/www/demo.gif |only ggraptR-1.0/ggraptR/man/ggraptR.Rd | 13 ggraptR-1.0/ggraptR/tests |only ggraptR-1.0/ggraptR/vignettes |only 50 files changed, 1399 insertions(+), 1900 deletions(-)
Title: Fast Bayesian Methods for AB Testing
Description: A suite of functions that allow the user to analyze A/B test
data in a Bayesian framework. Intended to be a drop-in replacement for
common frequentist hypothesis test such as the t-test and chi-sq test.
Author: Frank Portman [aut, cre]
Maintainer: Frank Portman <frank1214@gmail.com>
Diff between bayesAB versions 1.0.0 dated 2017-07-23 and 1.1.0 dated 2017-09-25
DESCRIPTION | 10 ++-- MD5 | 56 +++++++++++----------- NAMESPACE | 3 + NEWS.md | 16 ++++++ R/bayesAB.R | 2 R/bayesTest.R | 21 +++++--- R/checks.R | 3 - R/combine.R | 5 +- R/constructors.R | 14 ++++- R/dist-normal.R | 33 +++++-------- R/dists.R |only R/generics.R | 10 ++-- R/makePlots.R | 96 +++++++++++++++++--------------------- R/plotDists.R | 78 +++++++++++++++++++------------ R/posteriors.R | 30 ++++++------ R/util.R | 9 ++- inst/doc/introduction.html | 97 +++++++++++++++++++-------------------- man/bayesTest.Rd | 20 +++++--- man/combine.Rd | 4 - man/plot.bayesTest.Rd | 2 man/plotInvGamma.Rd | 4 + man/plotNormalInvGamma.Rd |only src/closedTests.cpp | 21 ++++---- tests/testthat/test-bernoulliC.R | 5 ++ tests/testthat/test-combine.R | 4 - tests/testthat/test-dists.R | 2 tests/testthat/test-generics.R | 5 +- tests/testthat/test-lognormal.R | 14 ++--- tests/testthat/test-normal.R | 15 +++--- tests/testthat/test-poissonC.R | 5 ++ 30 files changed, 330 insertions(+), 254 deletions(-)
Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications.
Author: Winston Chang [aut, cre],
Yihui Xie [ctb],
Francois Guillem [ctb],
Nicolas Perriault [ctb] (The CasperJS library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between webshot versions 0.4.1 dated 2017-05-31 and 0.4.2 dated 2017-09-25
DESCRIPTION | 6 - MD5 | 20 ++-- NEWS.md | 5 + R/webshot.R | 4 build/vignette.rds |binary inst/doc/intro.R | 6 - inst/doc/intro.Rmd | 4 inst/doc/intro.html | 245 ++++++++++++++++++++++++++++++---------------------- inst/webshot.js | 15 ++- man/webshot.Rd | 3 vignettes/intro.Rmd | 4 11 files changed, 183 insertions(+), 129 deletions(-)
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.4 dated 2016-02-11 and 0.4.1 dated 2017-09-25
DESCRIPTION | 7 +++---- MD5 | 15 ++++++++------- NAMESPACE | 2 +- R/extmat.R | 2 +- src/Makevars | 2 +- src/extmat.c | 9 --------- src/propack/dlansvd_irl.f | 3 --- src/propack/second.f | 1 + src/svd_init.c |only 9 files changed, 15 insertions(+), 26 deletions(-)
Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover
following the pattern-based metacommunity analysis of Leibold and Mikkelson
2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes
functions to visualize ecological networks, and to calculate modularity
as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas <tdallas@ucdavis.edu>
Diff between metacom versions 1.4.7 dated 2017-08-17 and 1.4.9 dated 2017-09-25
DESCRIPTION | 6 - MD5 | 30 +++--- NAMESPACE | 44 ++++----- NEWS.md |only R/BoundaryClump.R | 17 ++- R/Metacommunity.R | 75 ++++++++--------- README.md |only man/BoundaryClump.Rd | 155 +++++++++++++++++------------------ man/Coherence.Rd | 196 ++++++++++++++++++++++---------------------- man/Imagine.Rd | 132 ++++++++++++++--------------- man/Metacommunity.Rd | 216 ++++++++++++++++++++++++------------------------- man/Modularity.Rd | 184 ++++++++++++++++++++--------------------- man/NullMaker.Rd | 162 ++++++++++++++++++------------------ man/OrderMatrix.Rd | 138 +++++++++++++++---------------- man/TestMatrices.Rd | 100 +++++++++++----------- man/Turnover.Rd | 190 +++++++++++++++++++++---------------------- man/metacom-package.Rd | 176 +++++++++++++++++++-------------------- 17 files changed, 916 insertions(+), 905 deletions(-)
Title: Methods for Causal Inference with Interference
Description: Provides methods for estimating causal effects in the presence of
interference. Currently it implements the inverse-probability weighted (IPW)
estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele in "On causal
inference in the presence of interference" (Statistical Methods in Medical
Research (2012), 21(1) 55-75).
Author: Bradley Saul
Maintainer: Bradley Saul <bradleysaul@gmail.com>
Diff between inferference versions 0.4.62 dated 2015-06-08 and 0.5.4 dated 2017-09-25
inferference-0.4.62/inferference/R/score_matrix.R |only inferference-0.4.62/inferference/R/wght_calc.R |only inferference-0.4.62/inferference/R/wght_deriv_array.R |only inferference-0.4.62/inferference/R/wght_deriv_calc.R |only inferference-0.4.62/inferference/R/wght_matrix.R |only inferference-0.5.4/inferference/DESCRIPTION | 20 inferference-0.5.4/inferference/MD5 | 90 - inferference-0.5.4/inferference/NAMESPACE | 12 inferference-0.5.4/inferference/NEWS |only inferference-0.5.4/inferference/R/V_matrix_calc.R | 15 inferference-0.5.4/inferference/R/datasets.R | 34 inferference-0.5.4/inferference/R/effect_calc.R | 2 inferference-0.5.4/inferference/R/generics.R | 4 inferference-0.5.4/inferference/R/integrands.R | 85 inferference-0.5.4/inferference/R/interference.R | 81 inferference-0.5.4/inferference/R/ipw_interference.R | 50 inferference-0.5.4/inferference/R/score_functions.R | 149 + inferference-0.5.4/inferference/R/utilities.R | 86 inferference-0.5.4/inferference/R/wght_functions.R |only inferference-0.5.4/inferference/build/vignette.rds |binary inferference-0.5.4/inferference/data/vaccinesim.rdata |binary inferference-0.5.4/inferference/inst/CITATION |only inferference-0.5.4/inferference/inst/doc/inferference_intro.R | 265 +-- inferference-0.5.4/inferference/inst/doc/inferference_intro.Rmd | 548 ++++-- inferference-0.5.4/inferference/inst/doc/inferference_intro.html | 876 +++------- inferference-0.5.4/inferference/inst/doc/inferference_plots.R | 12 inferference-0.5.4/inferference/inst/doc/inferference_plots.Rmd | 2 inferference-0.5.4/inferference/inst/doc/inferference_plots.html | 113 - inferference-0.5.4/inferference/man/diagnose_weights.Rd |only inferference-0.5.4/inferference/man/direct_effect.Rd | 5 inferference-0.5.4/inferference/man/get_args.Rd |only inferference-0.5.4/inferference/man/indirect_effect.Rd | 7 inferference-0.5.4/inferference/man/inferference.Rd | 7 inferference-0.5.4/inferference/man/interference.Rd | 134 - inferference-0.5.4/inferference/man/log_likelihood.Rd |only inferference-0.5.4/inferference/man/logit_integrand.Rd | 39 inferference-0.5.4/inferference/man/overall_effect.Rd | 5 inferference-0.5.4/inferference/man/print.interference.Rd | 3 inferference-0.5.4/inferference/man/score_calc.Rd |only inferference-0.5.4/inferference/man/score_matrix.Rd |only inferference-0.5.4/inferference/man/total_effect.Rd | 5 inferference-0.5.4/inferference/man/vaccinesim.Rd | 15 inferference-0.5.4/inferference/man/voters.Rd | 23 inferference-0.5.4/inferference/man/wght_calc.Rd |only inferference-0.5.4/inferference/man/wght_deriv_array.Rd |only inferference-0.5.4/inferference/man/wght_deriv_calc.Rd |only inferference-0.5.4/inferference/man/wght_matrix.Rd |only inferference-0.5.4/inferference/tests/testthat/test_effects.R | 22 inferference-0.5.4/inferference/tests/testthat/test_interference.R | 69 inferference-0.5.4/inferference/tests/testthat/test_logit_integrand.R | 21 inferference-0.5.4/inferference/tests/testthat/test_scores.R | 17 inferference-0.5.4/inferference/tests/testthat/test_voter_example.R |only inferference-0.5.4/inferference/tests/testthat/test_wghts.R | 69 inferference-0.5.4/inferference/vignettes/inferference_intro.Rmd | 548 ++++-- inferference-0.5.4/inferference/vignettes/inferference_plots.Rmd | 2 55 files changed, 1906 insertions(+), 1529 deletions(-)
Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS), an efficient
and robust C library for convex problems. Conic and equality
constraints can be specified in addition to integer and
boolean variable constraints for mixed-integer problems. This
R interface is inspired by the python interface and has
similar calling conventions.
Author: Anqi Fu [aut],
Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ECOSolveR versions 0.3-1 dated 2017-08-26 and 0.3-2 dated 2017-09-25
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/ecos.R | 6 +++--- README.md | 24 ++++++++++++++++-------- inst/INSTALL | 2 +- inst/doc/examples.html | 4 ++-- src/ecos/__.SYMDEF |binary 7 files changed, 32 insertions(+), 24 deletions(-)
Title: The Conditional Probability Function of a Competing Event
Description: Permits to estimate the conditional probability function of a competing event, and to fit, using the temporal process regression or the pseudo-value approach, a proportional-odds model to the conditional probability function (or other models by specifying another link function). See <doi:10.1111/j.1467-9876.2010.00729.x>.
Author: Arthur Allignol
Maintainer: Arthur Allignol <arthur.allignol@gmail.com>
Diff between Cprob versions 1.3 dated 2017-01-16 and 1.4 dated 2017-09-25
ChangeLog | 14 ++++++++++---- DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- man/Cprob-package.Rd | 2 +- man/cpf.Rd | 2 +- man/cpfpo.Rd | 2 +- man/lines.cpf.Rd | 2 +- man/plot.cpf.Rd | 2 +- man/predict.cpf.Rd | 2 +- man/print.cpf.Rd | 2 +- man/print.cpfpo.Rd | 2 +- man/pseudocpf.Rd | 2 +- man/summary.cpf.Rd | 2 +- man/summary.pseudocpf.Rd | 2 +- man/xyplot.cpfpo.Rd | 2 +- tests/tests.Cprob.Rout.save | 14 +++++++------- 16 files changed, 48 insertions(+), 42 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 [cre, aut],
Bernd Bischl [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.8.3 dated 2017-07-03 and 1.8.4 dated 2017-09-25
DESCRIPTION | 25 ++++----- MD5 | 78 +++++++++++++++------------- NAMESPACE | 14 +++++ NEWS.md | 12 ++++ R/checkBit.R |only R/checkClass.R | 1 R/checkDataTable.R | 42 +++++++++------ R/checkEnvironment.R | 2 R/checkList.R | 9 +++ R/checkLogical.R | 1 R/checkNames.R | 40 ++++++++------ R/checkR6.R |only R/checkTibble.R | 4 + R/zzz.R | 19 ++++--- README.md | 1 inst/doc/checkmate.R | 9 +-- inst/doc/checkmate.Rmd | 13 ++-- inst/doc/checkmate.html | 95 +++++++++++++++-------------------- inst/include/checkmate_stub.c | 4 - man/checkBit.Rd |only man/checkClass.Rd | 2 man/checkList.Rd | 9 +++ man/checkLogical.Rd | 2 man/checkNames.Rd | 53 +++++++++++-------- man/checkR6.Rd |only man/checkmate-package.Rd | 19 ++++--- src/checks.c | 85 +++++++++++++++---------------- src/helper.c | 33 +++++++++++- src/helper.h | 3 - src/is_integerish.c | 4 - src/which_first.c | 10 +-- tests/testthat/helper.R | 6 ++ tests/testthat/test_bit.R |only tests/testthat/test_checkDataFrame.R | 2 tests/testthat/test_checkDataTable.R | 21 ++++--- tests/testthat/test_checkMatrix.R | 4 - tests/testthat/test_checkNamed.R | 2 tests/testthat/test_checkNames.R | 19 ++++++- tests/testthat/test_checkOS.R | 6 +- tests/testthat/test_checkTibble.R | 9 ++- tests/testthat/test_include.R | 2 tests/testthat/test_r6.R |only vignettes/checkmate.Rmd | 13 ++-- 43 files changed, 404 insertions(+), 269 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 Generalized Linear Models (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 <fhui28@gmail.com>
Diff between boral versions 1.3.1 dated 2017-04-18 and 1.4 dated 2017-09-25
DESCRIPTION | 8 MD5 | 51 +- NAMESPACE | 2 R/auxilaryfunctions.R | 942 ++++++++++++++++++++++++++--------------- R/boral.jags.R | 370 +++++++++------- R/makejagsboralmodel.R | 36 + R/makejagsboralnullmodel.R | 29 - R/unseenfunctions.R | 199 ++++++-- inst/CITATION |only inst/NEWS.Rd | 34 - man/about.ssvs.Rd | 4 man/about.traits.Rd | 4 man/boral.Rd | 46 -- man/calc.condlogLik.Rd | 6 man/calc.logLik.lv0.Rd | 4 man/calc.marglogLik.Rd | 4 man/calc.varpart.Rd |only man/coefsplot.Rd | 1 man/get.enviro.cor.Rd | 3 man/get.hpdintervals.Rd | 2 man/get.mcmcsamples.Rd |only man/get.measures.Rd | 2 man/get.more.measures.Rd | 6 man/get.residual.cor.Rd | 33 - man/make.jagsboralmodel.Rd | 12 man/make.jagsboralnullmodel.Rd | 13 man/plot.boral.Rd | 2 man/predict.boral.Rd | 38 - 28 files changed, 1147 insertions(+), 704 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Implementations of functions which have been introduced in
R since version 3.0.0. The backports are conditionally exported which
results in R resolving the function names to the version shipped with R (if
available) and uses the implemented backports as fallback. This way package
developers can make use of the new functions without worrying about the
minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.1.0 dated 2017-05-22 and 1.1.1 dated 2017-09-25
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++++++++-------- NAMESPACE | 7 ++++++- NEWS.md | 11 ++++++++--- R/dotsElt.R |only R/dotsLength.R |only R/import.R | 4 ++-- R/isFALSE.R |only R/lengths.R | 2 +- R/trimws.R | 11 ++++++----- R/zzz.R | 4 ++++ man/dotsElt.Rd |only man/dotsLength.Rd |only man/isFALSE.Rd |only src |only tests/helper/helper.R | 8 ++++++++ tests/test_dotsElt.R |only tests/test_dotsLength.R |only tests/test_isFALSE.R |only 19 files changed, 59 insertions(+), 24 deletions(-)
Title: Simulating Phylogenetic Trees under General Bellman Harris and
Lineage Shift Model
Description: Provides a flexible simulation tool for phylogenetic trees under a general model for speciation and extinction. Trees with a user-specified number of extant tips, or a user-specified stem age are simulated. It is possible to assume any probability distribution for the waiting time until speciation and extinction. Furthermore, the waiting times to speciation / extinction may be scaled in different parts of the tree, meaning we can simulate trees with clade-dependent diversification processes. At a speciation event, one species splits into two. We allow for two different modes at these splits: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. The symmetric mode can be seen as an vicariant or allopatric process where divided populations suffer equal evolutionary forces while the asymmetric mode could be seen as a peripatric speciation where a mother lineage continues to exist.
Author: Oskar Hagen, Tanja Stadler
Maintainer: Oskar Hagen <oskar.hagen@outlook.com>
Diff between TreeSimGM versions 2.2 dated 2017-08-10 and 2.3 dated 2017-09-25
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/mytree.asymmetric.age.R | 30 +++++++++++++++--------------- R/mytree.asymmetric.taxa.R | 28 ++++++++++++++-------------- R/mytree.symmetric.age.R | 24 ++++++++++++------------ R/mytree.symmetric.taxa.R | 24 ++++++++++++------------ R/track.shift.R | 4 +++- man/TreeSimGM-package.Rd | 6 +++--- man/sim.age.Rd | 2 +- man/sim.taxa.Rd | 2 +- man/track.shift.Rd | 5 ++++- 11 files changed, 79 insertions(+), 74 deletions(-)
Title: Read, Write, Visualize and Manipulate PDB Files
Description: Provides tools to read, write, visualize PDB files and perform some
structural manipulations.
Author: Julien Idé
Maintainer: Julien Idé <julien.ide.fr@gmail.com>
Diff between Rpdb versions 2.2 dated 2014-04-26 and 2.3 dated 2017-09-25
Rpdb-2.2/Rpdb/man/subset.pdb.Rd |only Rpdb-2.3/Rpdb/DESCRIPTION | 14 +- Rpdb-2.3/Rpdb/MD5 | 159 +++++++++++----------- Rpdb-2.3/Rpdb/NAMESPACE | 217 +++++++++++++++++++++++++++++-- Rpdb-2.3/Rpdb/R/Rpdb-package.R |only Rpdb-2.3/Rpdb/R/addAxes.R | 49 ++++++- Rpdb-2.3/Rpdb/R/addLabels.R | 83 ++++++++++- Rpdb-2.3/Rpdb/R/atoms.R | 75 ++++++++++ Rpdb-2.3/Rpdb/R/basis.R | 46 ++++++ Rpdb-2.3/Rpdb/R/bond-angle-dihedral.R | 56 ++++++++ Rpdb-2.3/Rpdb/R/cellProperties.R | 73 +++++++++- Rpdb-2.3/Rpdb/R/centres.R | 93 +++++++++++++ Rpdb-2.3/Rpdb/R/conect.R | 71 +++++++++- Rpdb-2.3/Rpdb/R/coords.R | 86 ++++++++++++ Rpdb-2.3/Rpdb/R/cryst1.R | 51 ++++++- Rpdb-2.3/Rpdb/R/distances.R | 79 +++++++++++ Rpdb-2.3/Rpdb/R/elements.R |only Rpdb-2.3/Rpdb/R/inertia.R | 40 +++++ Rpdb-2.3/Rpdb/R/masses.R | 39 +++++ Rpdb-2.3/Rpdb/R/measure.R | 62 +++++--- Rpdb-2.3/Rpdb/R/merge.coords.R | 57 +++++++- Rpdb-2.3/Rpdb/R/mirror.R | 55 +++++++ Rpdb-2.3/Rpdb/R/mirrorHelpers.R | 78 +++++++++-- Rpdb-2.3/Rpdb/R/natom.R | 54 +++++++ Rpdb-2.3/Rpdb/R/pdb.R | 56 +++++++- Rpdb-2.3/Rpdb/R/range.coords.R | 30 ++++ Rpdb-2.3/Rpdb/R/read.pdb.R | 52 +++++++ Rpdb-2.3/Rpdb/R/reindex.R | 35 ++++- Rpdb-2.3/Rpdb/R/replicate.R | 44 ++++++ Rpdb-2.3/Rpdb/R/rotation.R | 53 +++++++ Rpdb-2.3/Rpdb/R/rotationHelpers.R | 62 ++++++++ Rpdb-2.3/Rpdb/R/split.pdb.R | 51 +++++++ Rpdb-2.3/Rpdb/R/subset.atoms.R | 41 +++++ Rpdb-2.3/Rpdb/R/toSymbols.R | 45 ++++++ Rpdb-2.3/Rpdb/R/translation.R | 76 ++++++++++ Rpdb-2.3/Rpdb/R/translationHelpers.R | 91 ++++++++++++- Rpdb-2.3/Rpdb/R/universalConstants.R |only Rpdb-2.3/Rpdb/R/unsplit.R | 175 +++++++++++-------------- Rpdb-2.3/Rpdb/R/vectorialOperations.R | 39 +++++ Rpdb-2.3/Rpdb/R/viewAxis.R | 64 ++++++++- Rpdb-2.3/Rpdb/R/visualize.R | 104 +++++++++++++- Rpdb-2.3/Rpdb/R/wrap.R | 44 ++++++ Rpdb-2.3/Rpdb/R/write.pdb.R | 28 ++++ Rpdb-2.3/Rpdb/R/xyz2abc.R | 64 ++++++++- Rpdb-2.3/Rpdb/man/Rpdb-package.Rd | 23 +-- Rpdb-2.3/Rpdb/man/addAxes.Rd | 50 ++++--- Rpdb-2.3/Rpdb/man/addLabels.Rd | 88 ++++++++---- Rpdb-2.3/Rpdb/man/atoms.Rd | 126 ++++++++++-------- Rpdb-2.3/Rpdb/man/basis.Rd | 60 ++++---- Rpdb-2.3/Rpdb/man/bond-angle-dihedral.Rd | 74 +++++++--- Rpdb-2.3/Rpdb/man/cellProperties.Rd | 77 +++++++---- Rpdb-2.3/Rpdb/man/centres.Rd | 88 +++++++----- Rpdb-2.3/Rpdb/man/conect.Rd | 92 ++++++++----- Rpdb-2.3/Rpdb/man/coords.Rd | 128 ++++++++++-------- Rpdb-2.3/Rpdb/man/cryst1.Rd | 75 ++++++---- Rpdb-2.3/Rpdb/man/distances.Rd | 105 +++++++++------ Rpdb-2.3/Rpdb/man/elements.Rd | 61 ++++---- Rpdb-2.3/Rpdb/man/inertia.Rd | 47 ++++-- Rpdb-2.3/Rpdb/man/masses.Rd | 39 +++-- Rpdb-2.3/Rpdb/man/merge.coords.Rd | 60 ++++---- Rpdb-2.3/Rpdb/man/mirror.Rd | 71 +++++++--- Rpdb-2.3/Rpdb/man/mirrorHelpers.Rd | 102 +++++++++----- Rpdb-2.3/Rpdb/man/natom.Rd | 64 +++++---- Rpdb-2.3/Rpdb/man/pdb.Rd | 82 ++++++----- Rpdb-2.3/Rpdb/man/range.coords.Rd | 33 ++-- Rpdb-2.3/Rpdb/man/read.pdb.Rd | 77 ++++++----- Rpdb-2.3/Rpdb/man/reindex.Rd | 45 +++--- Rpdb-2.3/Rpdb/man/replicate.Rd | 49 ++++--- Rpdb-2.3/Rpdb/man/rotation.Rd | 67 ++++++--- Rpdb-2.3/Rpdb/man/rotationHelpers.Rd | 61 ++++++-- Rpdb-2.3/Rpdb/man/split.pdb.Rd | 62 +++++--- Rpdb-2.3/Rpdb/man/subset.atoms.Rd |only Rpdb-2.3/Rpdb/man/toSymbols.Rd | 41 +++-- Rpdb-2.3/Rpdb/man/translation.Rd | 102 ++++++++++---- Rpdb-2.3/Rpdb/man/translationHelpers.Rd | 129 +++++++++++------- Rpdb-2.3/Rpdb/man/universalConstants.Rd | 28 ++-- Rpdb-2.3/Rpdb/man/unsplit.Rd | 75 +++++----- Rpdb-2.3/Rpdb/man/vectorialOperations.Rd | 31 ++-- Rpdb-2.3/Rpdb/man/viewAxis.Rd | 57 ++++++-- Rpdb-2.3/Rpdb/man/visualize.Rd | 174 ++++++++++++++---------- Rpdb-2.3/Rpdb/man/wrap.Rd | 52 ++++--- Rpdb-2.3/Rpdb/man/write.pdb.Rd | 36 ++--- Rpdb-2.3/Rpdb/man/xyz2abc.Rd | 98 +++++++------- 83 files changed, 4029 insertions(+), 1391 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-24 dated 2017-09-19 and 0.3-25 dated 2017-09-25
ChangeLog | 24 DESCRIPTION | 8 MD5 | 12 configure | 1545 +------------------------------------------------------ configure.ac | 29 - inst/ChangeLog | 24 inst/SVN_VERSION | 2 7 files changed, 116 insertions(+), 1528 deletions(-)
Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between MPSEM versions 0.3-2 dated 2017-08-22 and 0.3-3 dated 2017-09-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/MPSEM.pdf |binary man/PEM.Rd | 11 ++++++----- src/MPSEM.c | 5 ++--- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.4 dated 2017-06-02 and 1.5 dated 2017-09-25
ChangeLog | 11 DESCRIPTION | 10 MD5 | 65 +- NAMESPACE | 13 R/blhs.R |only R/gp.R | 228 +++++++++ R/gp_sep.R | 226 +++++++++ R/laGP.R | 165 ++++--- R/laGP_sep.R | 488 +++++++++++--------- build/vignette.rds |binary inst/doc/laGP.Rnw | 2 inst/doc/laGP.pdf |binary man/aGP.Rd | 6 man/alcGP.Rd | 111 +++- man/blhs.Rd |only man/fcalib.Rd | 2 man/laGP.Rd | 295 +++++++----- man/newGP.Rd | 2 man/optim.auglag.Rd | 2 src/gp.c | 1224 ++++++++++++++++++++++++++++++++++++++-------------- src/gp.h | 100 ++-- src/gp_sep.c | 1142 +++++++++++++++++++++++++++++++++++------------- src/gp_sep.h | 76 +-- src/ieci.c | 39 + src/init.c | 32 + src/laGP.c | 138 ++++- src/laGP.h | 30 - src/laGP_sep.c | 96 ++-- src/laGP_sep.h | 26 - src/matrix.c | 24 - src/symbols.rds |only src/util.c | 9 src/util.h | 2 vignettes/laGP.Rnw | 2 vignettes/laGP.bib | 6 35 files changed, 3277 insertions(+), 1295 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph],
Mitchell O'Hara-Wild [aut],
Christoph Bergmeir [aut],
Slava Razbash [aut],
Earo Wang [aut]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.1 dated 2017-06-17 and 8.2 dated 2017-09-25
forecast-8.1/forecast/ChangeLog |only forecast-8.2/forecast/DESCRIPTION | 11 - forecast-8.2/forecast/MD5 | 94 ++++++------ forecast-8.2/forecast/NEWS.md |only forecast-8.2/forecast/R/HoltWintersNew.R | 56 +++---- forecast-8.2/forecast/R/acf.R | 45 +++--- forecast-8.2/forecast/R/arfima.R | 36 ++-- forecast-8.2/forecast/R/arima.R | 18 +- forecast-8.2/forecast/R/armaroots.R | 26 +-- forecast-8.2/forecast/R/bootstrap.R | 33 ++-- forecast-8.2/forecast/R/checkresiduals.R | 20 +- forecast-8.2/forecast/R/clean.R | 9 - forecast-8.2/forecast/R/dshw.r | 57 ++++--- forecast-8.2/forecast/R/errors.R | 6 forecast-8.2/forecast/R/ets.R | 42 +++-- forecast-8.2/forecast/R/fitBATS.R | 20 +- forecast-8.2/forecast/R/fitTBATS.R | 21 +- forecast-8.2/forecast/R/forecast-package.R | 20 +- forecast-8.2/forecast/R/forecast.R | 16 +- forecast-8.2/forecast/R/forecast2.R | 74 ++++----- forecast-8.2/forecast/R/ggplot.R | 150 ++++++++++---------- forecast-8.2/forecast/R/graph.R | 16 +- forecast-8.2/forecast/R/mforecast.R | 62 ++++---- forecast-8.2/forecast/R/newarima2.R | 29 +++ forecast-8.2/forecast/R/nnetar.R | 46 +++--- forecast-8.2/forecast/R/simulate.R | 20 +- forecast-8.2/forecast/R/subset.R | 14 - forecast-8.2/forecast/R/tscv.R | 13 + forecast-8.2/forecast/R/wrangle.R | 2 forecast-8.2/forecast/README.md | 10 - forecast-8.2/forecast/build/vignette.rds |binary forecast-8.2/forecast/inst/CITATION | 11 + forecast-8.2/forecast/inst/doc/JSS2008.pdf |binary forecast-8.2/forecast/man/auto.arima.Rd | 2 forecast-8.2/forecast/man/bld.mbb.bootstrap.Rd | 3 forecast-8.2/forecast/man/dshw.Rd | 12 - forecast-8.2/forecast/man/forecast.nnetar.Rd | 24 +-- forecast-8.2/forecast/man/geom_forecast.Rd | 2 forecast-8.2/forecast/man/na.interp.Rd | 1 forecast-8.2/forecast/man/nnetar.Rd | 14 + forecast-8.2/forecast/man/plot.Arima.Rd | 2 forecast-8.2/forecast/man/plot.ets.Rd | 2 forecast-8.2/forecast/man/plot.mforecast.Rd | 2 forecast-8.2/forecast/man/tsCV.Rd | 11 + forecast-8.2/forecast/man/tsclean.Rd | 2 forecast-8.2/forecast/man/tsdisplay.Rd | 2 forecast-8.2/forecast/man/tsoutliers.Rd | 2 forecast-8.2/forecast/tests/testthat/test-refit.R | 16 +- forecast-8.2/forecast/tests/testthat/test-wrangle.R | 8 - 49 files changed, 589 insertions(+), 493 deletions(-)
Title: Sensory and Consumer Data Mapping
Description: External preference mapping technique is commonly used in sensory analysis
field to explain consumer preferences in function of sensory attributes of products
Danzart (1998) (<https://www.lavoisier.fr/livre/agro-alimentaire/evaluation-
sensorielle-3e-ed/depledt/descriptif-9782743009977>). The package provides map
visualization with options in dimension reduction methods and prediction models
from linear and non linear regressions. A smoothed version of the map performed using
LOESS algorithm is available. A comparison approach of maps stability from different
features before and after smoothing is provided. A 'shiny' application is included.
It presents an easy GUI for the implemented functions as well as a comparative tool
of fit models using several criteria. Basic analysis such as characterization of
products, panelists and sessions likewise consumer segmentation are available.
Author: Ibtihel Rebhi [aut, cre], Rihab Boubakri [ctb], Dhafer Malouche [ctb]
Maintainer: Ibtihel Rebhi <ibtihel.rebhi@enit.utm.tn>
Diff between SensMap versions 0.1 dated 2017-09-23 and 0.2 dated 2017-09-25
DESCRIPTION | 28 +++++++++++++++------------- MD5 | 12 ++++++------ man/PrefMap.Rd | 29 ++++++++++++----------------- man/SensMapUI.Rd | 2 +- man/SmoothMap.Rd | 21 ++++++--------------- man/StabMap.Rd | 14 ++++++++------ tests/testthat/Rplots.pdf |binary 7 files changed, 48 insertions(+), 58 deletions(-)
Title: Panel Smooth Transition Regression Modelling
Description: Provides the Panel Smooth Transition Regression (PSTR) modelling.
The modelling procedure consists of three stages: Specification, Estimation and Evaluation.
The package offers sharp tools helping the package user(s) to conduct model specification tests,
to do PSTR model estimation, and to do model evaluation.
The tests implemented in the package allow for cluster-dependency and are heteroskedasticity-consistent.
The wild bootstrap and wild cluster bootstrap tests are also implemented.
Parallel computation (as an option) is implemented in some functions for bootstrap tests.
The package suits tasks running many cores on super-computation servers.
Author: Yukai Yang [aut, cre]
Maintainer: Yukai Yang <yukai.yang@statistik.uu.se>
Diff between PSTR versions 1.0.1 dated 2017-09-13 and 1.1.0 dated 2017-09-25
DESCRIPTION | 10 MD5 | 25 - NAMESPACE | 7 NEWS.md |only R/PSTR.R | 920 ------------------------------------------------- R/estimation.R |only R/evaluation.R |only R/specification.R |only R/utils.R | 104 +++++ README.md | 113 +++++- man/EstPSTR.Rd | 27 + man/EvalTest.Rd | 6 man/LinTest.Rd | 2 man/PSTR.Rd | 7 man/plot_transition.Rd |only man/print.PSTR.Rd | 4 16 files changed, 272 insertions(+), 953 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Diff between PRIMsrc versions 0.7.3 dated 2017-08-07 and 0.7.4 dated 2017-09-25
PRIMsrc-0.7.3/PRIMsrc/inst/doc/PRIMsrc_0.7.3.pdf |only PRIMsrc-0.7.4/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.7.4/PRIMsrc/MD5 | 28 PRIMsrc-0.7.4/PRIMsrc/R/PRIMsrc.internal.r | 913 ++++++++++++----------- PRIMsrc-0.7.4/PRIMsrc/R/PRIMsrc.r | 396 +++++---- PRIMsrc-0.7.4/PRIMsrc/README.md | 12 PRIMsrc-0.7.4/PRIMsrc/inst/NEWS | 55 + PRIMsrc-0.7.4/PRIMsrc/inst/doc/PRIMsrc_0.7.4.pdf |only PRIMsrc-0.7.4/PRIMsrc/man/PRIMsrc-package.Rd | 16 PRIMsrc-0.7.4/PRIMsrc/man/plot.sbh.Rd | 6 PRIMsrc-0.7.4/PRIMsrc/man/plot_boxkm.Rd | 6 PRIMsrc-0.7.4/PRIMsrc/man/plot_boxtrace.Rd | 6 PRIMsrc-0.7.4/PRIMsrc/man/plot_boxtraj.Rd | 2 PRIMsrc-0.7.4/PRIMsrc/man/plot_profile.Rd | 2 PRIMsrc-0.7.4/PRIMsrc/man/predict.sbh.Rd | 4 PRIMsrc-0.7.4/PRIMsrc/man/sbh.Rd | 230 +++-- 16 files changed, 929 insertions(+), 755 deletions(-)
Title: Benchmark and Correctness Data for Weighted Random Sampling
Without Replacement
Description: Includes performance measurements and results of repeated
experiment runs (for correctness checks) for code in the
'wrswoR' package.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between wrswoR.benchmark versions 0.1-1 dated 2016-02-12 and 0.2 dated 2017-09-25
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 6 +++--- R/aaa-rextdata.R | 4 ++-- R/timings.R | 8 ++++++++ man/p_values_7.Rd | 1 - man/p_values_agg.Rd | 1 - man/timings.Rd | 34 +++++++++++----------------------- 9 files changed, 40 insertions(+), 44 deletions(-)
More information about wrswoR.benchmark at CRAN
Permanent link
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between ManlyMix versions 0.1.8 dated 2017-09-05 and 0.1.9 dated 2017-09-25
DESCRIPTION | 8 ++-- MD5 | 12 +++--- NEWS | 4 ++ R/main.R | 2 + R/other.R | 114 ++++++++++++++++++++++++++++----------------------------- demo/acidity.R | 27 ++++++++++--- demo/ais.R | 25 ------------ 7 files changed, 94 insertions(+), 98 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) and transforms to the appropriate formats of
the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization
for the structure of RDML object and GUI for RDML editing.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut],
Andrej-Nikolai Spiess [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>
Diff between RDML versions 0.9-8 dated 2017-09-05 and 0.9-9 dated 2017-09-25
CHANGELOG | 4 DESCRIPTION | 12 MD5 | 37 - R/RDML.AsTable.R | 7 R/RDML.types.R | 3 README.md | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/CreateRDML.R | 19 inst/doc/CreateRDML.Rmd | 37 - inst/doc/CreateRDML.html | 585 ++++++++++++++------------ inst/doc/RDML.R | 27 - inst/doc/RDML.Rmd | 10 inst/doc/RDML.html | 357 ++++++++------- inst/doc/usingRDML_with_other_R_packages.R |only inst/doc/usingRDML_with_other_R_packages.Rmd |only inst/doc/usingRDML_with_other_R_packages.html |only man/astable-method.Rd | 2 vignettes/CreateRDML.Rmd | 37 - vignettes/RDML.Rmd | 10 vignettes/usingRDML_with_other_R_packages.Rmd | 7 21 files changed, 626 insertions(+), 532 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut],
Nicolas Lambert [aut],
Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.1.0 dated 2017-03-06 and 0.1.1 dated 2017-09-25
DESCRIPTION | 8 +-- MD5 | 98 +++++++++++++++++++++++++++++++++++++------ R/gdev.R | 13 +++-- R/sdev.R | 13 +++-- R/tdev.R | 12 +++-- build/vignette.rds |binary inst/doc/MTA.html | 8 +-- inst/doc/MTA_Scenario.Rmd | 6 +- inst/doc/MTA_Scenario.html | 34 +++++++------- man/gdev.Rd | 13 +++-- man/sdev.Rd | 13 +++-- man/tdev.Rd | 12 +++-- vignettes/MTA_Scenario.Rmd | 6 +- vignettes/MTA_Scenario_cache |only vignettes/MTA_Scenario_files |only 15 files changed, 160 insertions(+), 76 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows
various cartographic representations such as proportional symbols, chroropleth,
typology, flows or discontinuities maps. It also offers several features enhancing
the graphic presentation of maps like cartographic palettes, layout
elements (scale, north arrow, title...), labels, legends or access to some
cartographic APIs. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut],
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.0.0 dated 2017-09-19 and 2.0.1 dated 2017-09-25
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 10 +++++++++- R/getOuterBorders.R | 2 +- R/utils.R | 2 ++ README.md | 6 +----- inst/doc/cartography.html | 6 +++--- man/getOuterBorders.Rd | 2 +- 8 files changed, 27 insertions(+), 21 deletions(-)
Title: Estimate Growth Rates from Experimental Data
Description: A collection of methods to determine growth rates from
experimental data, in particular from batch experiments and
plate reader trials.
Author: Thomas Petzoldt
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between growthrates versions 0.6.5 dated 2016-03-14 and 0.7.0 dated 2017-09-25
growthrates-0.6.5/growthrates/inst/doc/Introduction.pdf |only growthrates-0.6.5/growthrates/inst/doc/User_models.pdf |only growthrates-0.7.0/growthrates/DESCRIPTION | 26 +- growthrates-0.7.0/growthrates/MD5 | 114 +++++----- growthrates-0.7.0/growthrates/NAMESPACE | 2 growthrates-0.7.0/growthrates/R/all_easylinear.R | 6 growthrates-0.7.0/growthrates/R/all_growthmodels.R | 2 growthrates-0.7.0/growthrates/R/all_splines.R | 2 growthrates-0.7.0/growthrates/R/antibiotic.R |only growthrates-0.7.0/growthrates/R/cost.R | 12 - growthrates-0.7.0/growthrates/R/fit_easylinear.R | 33 ++ growthrates-0.7.0/growthrates/R/fit_growthmodel.R | 4 growthrates-0.7.0/growthrates/R/grow_exponential.R | 9 growthrates-0.7.0/growthrates/R/grow_richards.R | 2 growthrates-0.7.0/growthrates/R/grow_twostep.R | 4 growthrates-0.7.0/growthrates/R/growthrates-package.R | 10 growthrates-0.7.0/growthrates/R/methods.R | 2 growthrates-0.7.0/growthrates/R/plot.R | 18 + growthrates-0.7.0/growthrates/R/predict.R |only growthrates-0.7.0/growthrates/build/vignette.rds |binary growthrates-0.7.0/growthrates/data/antibiotic.txt.gz |only growthrates-0.7.0/growthrates/inst/doc/Introduction.R | 2 growthrates-0.7.0/growthrates/inst/doc/Introduction.Rmd | 53 ++-- growthrates-0.7.0/growthrates/inst/doc/Introduction.html |only growthrates-0.7.0/growthrates/inst/doc/User_models.R | 2 growthrates-0.7.0/growthrates/inst/doc/User_models.Rmd | 14 - growthrates-0.7.0/growthrates/inst/doc/User_models.html |only growthrates-0.7.0/growthrates/man/all_easylinear.Rd | 11 growthrates-0.7.0/growthrates/man/all_growthmodels.Rd | 5 growthrates-0.7.0/growthrates/man/all_splines.Rd | 7 growthrates-0.7.0/growthrates/man/antibiotic.Rd |only growthrates-0.7.0/growthrates/man/bactgrowth.Rd | 1 growthrates-0.7.0/growthrates/man/cost.Rd | 1 growthrates-0.7.0/growthrates/man/extract.Rd | 5 growthrates-0.7.0/growthrates/man/fit_easylinear.Rd | 15 - growthrates-0.7.0/growthrates/man/fit_growthmodel.Rd | 3 growthrates-0.7.0/growthrates/man/fit_spline.Rd | 1 growthrates-0.7.0/growthrates/man/function_growthmodel-class.Rd | 2 growthrates-0.7.0/growthrates/man/generics.Rd | 3 growthrates-0.7.0/growthrates/man/grow_baranyi.Rd | 1 growthrates-0.7.0/growthrates/man/grow_exponential.Rd | 1 growthrates-0.7.0/growthrates/man/grow_genlogistic.Rd | 3 growthrates-0.7.0/growthrates/man/grow_gompertz.Rd | 1 growthrates-0.7.0/growthrates/man/grow_huang.Rd | 1 growthrates-0.7.0/growthrates/man/grow_logistic.Rd | 1 growthrates-0.7.0/growthrates/man/grow_richards.Rd | 3 growthrates-0.7.0/growthrates/man/grow_twostep.Rd | 9 growthrates-0.7.0/growthrates/man/growthmodel-class.Rd | 1 growthrates-0.7.0/growthrates/man/growthmodel-constructor.Rd | 3 growthrates-0.7.0/growthrates/man/growthrates-classes.Rd | 10 growthrates-0.7.0/growthrates/man/growthrates-package.Rd | 19 - growthrates-0.7.0/growthrates/man/lm_window.Rd | 3 growthrates-0.7.0/growthrates/man/methods.Rd | 31 +- growthrates-0.7.0/growthrates/man/multisplit.Rd | 5 growthrates-0.7.0/growthrates/man/names.Rd | 4 growthrates-0.7.0/growthrates/man/parse_formula.Rd | 1 growthrates-0.7.0/growthrates/man/parse_formula_nonlin.Rd | 1 growthrates-0.7.0/growthrates/man/plot.Rd | 9 growthrates-0.7.0/growthrates/man/predict.Rd |only growthrates-0.7.0/growthrates/src/R_init_growthrates.c |only growthrates-0.7.0/growthrates/vignettes/Introduction.Rmd | 53 ++-- growthrates-0.7.0/growthrates/vignettes/User_models.Rmd | 14 - growthrates-0.7.0/growthrates/vignettes/growthrates.bib | 16 - 63 files changed, 300 insertions(+), 261 deletions(-)
Title: A Hybrid Filter-Wrapper Feature Selection Method
Description: A hybrid method of feature selection which combines both filter and wrapper methods. The first level involves feature reduction based on some of the important filter methods while the second level involves feature subset selection as in a wrapper method. Comparative analysis with the existing feature selection packages shows this package results in higher classification accuracy, reduced processing time and improved data handling capacity.
Author: Yamini Pandari [aut, cre]
Maintainer: Yamini Pandari <yamseee@gmail.com>
Diff between HybridFS versions 0.1.0 dated 2017-09-25 and 0.1.1 dated 2017-09-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/HybridFS.R | 10 ++++++---- man/HybridFS.Rd | 8 +++++--- 4 files changed, 18 insertions(+), 14 deletions(-)
Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between BIGL versions 1.0.1 dated 2017-06-30 and 1.1.0 dated 2017-09-25
DESCRIPTION | 10 +- MD5 | 38 ++++---- NAMESPACE | 3 R/MarginalFit-methods.R | 6 - R/bootstrap.R | 15 ++- R/fitMarginals.R | 18 +++- R/isobologram.R |only R/maxR-functions.R | 8 - build/vignette.rds |binary inst/NEWS | 10 ++ inst/doc/analysis.R | 3 inst/doc/analysis.Rmd | 7 + inst/doc/analysis.html | 169 ++++++++++++++++++---------------------- inst/doc/methodology.html | 50 +++++------ inst/ui/server.R | 46 ++++++++-- inst/ui/ui.R | 13 ++- man/fitMarginals.Rd | 4 man/isobologram.Rd |only man/marginalNLS.Rd | 4 tests/testthat/test_marginals.R | 18 ++++ vignettes/analysis.Rmd | 7 + 21 files changed, 261 insertions(+), 168 deletions(-)
Title: Analyzing Multiple Omics Data with an Offset Approach
Description: Fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block.
Author: Simon Klau, Roman Hornung
Maintainer: Simon Klau <simonklau@ibe.med.uni-muenchen.de>
Diff between prioritylasso versions 0.2.0 dated 2017-07-17 and 0.2.1 dated 2017-09-25
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + R/cvm_prioritylasso.R | 2 +- R/prioritylasso.R | 23 ++++++++++++++--------- inst/doc/prioritylasso_vignette.html | 4 ++-- man/cvm_prioritylasso.Rd | 2 +- man/prioritylasso.Rd | 2 +- 8 files changed, 32 insertions(+), 26 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random Forest. The
Weighted Subspace Random Forest algorithm was proposed in the
International Journal of Data Warehousing and Mining by Baoxun Xu,
Joshua Zhexue Huang, Graham Williams, Qiang Wang, and Yunming Ye
(2012) <DOI:10.4018/jdwm.2012040103>. The algorithm can classify
very high-dimensional data with random forests built using small
subspaces. A novel variable weighting method is used for variable
subspace selection in place of the traditional random variable
sampling.This new approach is particularly useful in building
models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham J. Williams [aut],
Junchao Lv [aut],
Baoxun Xu [aut],
Joshua Zhexue Huang [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.7.13 dated 2017-04-17 and 1.7.17 dated 2017-09-25
DESCRIPTION | 82 +++++++++++++++-------------- MD5 | 34 ++++++------ R/print.wsrf.R | 1 R/wsrf.default.R | 3 - build/vignette.rds |binary inst/NEWS.Rd | 26 ++++++--- inst/doc/wsrf-guide.R | 2 inst/doc/wsrf-guide.Rmd | 8 +- inst/doc/wsrf-guide.html | 130 ++++++++++++++++------------------------------- man/combine.wsrf.Rd | 2 man/correlation.wsrf.Rd | 5 + man/print.wsrf.Rd | 2 man/strength.wsrf.Rd | 5 + man/subset.wsrf.Rd | 2 man/wsrf.Rd | 23 ++++---- tests/wsrftest.R | 9 +-- tests/wsrftest.Rout.save | 9 +-- vignettes/wsrf-guide.Rmd | 8 +- 18 files changed, 165 insertions(+), 186 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-65 dated 2017-09-18 and 0.8-67 dated 2017-09-25
DESCRIPTION | 11 ++-- MD5 | 24 ++++----- R/margLogLik2.R | 2 R/mvJointModelBayes.R | 2 R/survfitJM.mvJMbayes.R | 35 ++++++++++--- inst/NEWS | 18 ++++++ inst/doc/Multivariate_Joint_Models.html | 28 ++++++++-- inst/shiny_app_JM/server.R | 83 +++++++++++++++++++++++--------- inst/shiny_app_JM/ui.R | 4 + man/JMbayes.Rd | 4 - man/mvJointModelBayes.Rd | 4 - man/plot-survfitJM.Rd | 78 ++++++++++++++++++++---------- src/fast_LAPRWM.cpp | 16 +++--- 13 files changed, 217 insertions(+), 92 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearization of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.9.8 dated 2017-08-21 and 0.9.10 dated 2017-09-25
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ R/domain.R | 5 +++-- R/vardannual.R | 22 ++++++++++++---------- R/vardchanges.R | 18 +++++++++--------- R/vardchangespoor.R | 17 +++++++++-------- R/vardcros.R | 18 ++++++++++-------- R/vardcrospoor.R | 14 +++++++------- R/vardom.R | 14 ++++++++------ R/vardom_othstr.R | 6 +++--- R/vardomh.R | 22 +++++++++++----------- R/varpoord.R | 12 ++++++------ inst/NEWS | 4 ++++ man/vardannual.Rd | 5 ++++- man/vardcros.Rd | 3 ++- man/vardom.Rd | 1 + man/vardom_othstr.Rd | 1 + man/vardomh.Rd | 1 + man/varpoord.Rd | 3 ++- 19 files changed, 115 insertions(+), 95 deletions(-)
Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially balanced designs from a set of (contiguous) potential sampling locations in a study region. Accommodates , without detrimental effects on spatial balance, sites that the researcher wishes to include in the survey for reasons other than the current randomisation (legacy sites).
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>
Diff between MBHdesign versions 1.0.70 dated 2017-07-12 and 1.0.76 dated 2017-09-25
DESCRIPTION | 6 - MD5 | 18 ++-- R/MBHdesign.R | 179 +++++++++++++++++++----------------------------- R/sysdata.rda |binary inst/doc/MBHdesign.Rnw | 4 - inst/doc/MBHdesign.pdf |binary man/alterInclProbs.Rd | 2 man/modEsti.Rd | 2 man/quasiSamp.Rd | 2 vignettes/MBHdesign.Rnw | 4 - 10 files changed, 91 insertions(+), 126 deletions(-)