Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut, cre],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifeng Geng [aut],
Yutian Li [aut],
XGBoost contributors [cph] (base XGBoost implementation)
Maintainer: Tong He <hetong007@gmail.com>
Diff between xgboost versions 0.81.0.1 dated 2019-01-31 and 0.82.1 dated 2019-03-11
xgboost-0.81.0.1/xgboost/src/rabit/include/dmlc/logging.h |only xgboost-0.82.1/xgboost/DESCRIPTION | 8 xgboost-0.82.1/xgboost/MD5 | 169 +-- xgboost-0.82.1/xgboost/build/vignette.rds |binary xgboost-0.82.1/xgboost/inst/doc/discoverYourData.html | 26 xgboost-0.82.1/xgboost/inst/doc/xgboost.pdf |binary xgboost-0.82.1/xgboost/inst/doc/xgboostPresentation.html | 30 xgboost-0.82.1/xgboost/src/include/xgboost/base.h | 18 xgboost-0.82.1/xgboost/src/include/xgboost/build_config.h | 12 xgboost-0.82.1/xgboost/src/include/xgboost/c_api.h | 9 xgboost-0.82.1/xgboost/src/include/xgboost/data.h | 39 xgboost-0.82.1/xgboost/src/include/xgboost/learner.h | 1 xgboost-0.82.1/xgboost/src/include/xgboost/logging.h | 12 xgboost-0.82.1/xgboost/src/include/xgboost/predictor.h | 3 xgboost-0.82.1/xgboost/src/include/xgboost/tree_model.h | 2 xgboost-0.82.1/xgboost/src/init.c | 6 xgboost-0.82.1/xgboost/src/rabit/include/dmlc/base.h | 92 +- xgboost-0.82.1/xgboost/src/rabit/include/dmlc/io.h | 3 xgboost-0.82.1/xgboost/src/rabit/include/dmlc/serializer.h | 1 xgboost-0.82.1/xgboost/src/rabit/include/dmlc/type_traits.h | 12 xgboost-0.82.1/xgboost/src/rabit/include/rabit/c_api.h | 9 xgboost-0.82.1/xgboost/src/rabit/include/rabit/internal/rabit-inl.h | 6 xgboost-0.82.1/xgboost/src/rabit/include/rabit/internal/timer.h | 16 xgboost-0.82.1/xgboost/src/rabit/include/rabit/internal/utils.h | 23 xgboost-0.82.1/xgboost/src/rabit/include/rabit/rabit.h | 10 xgboost-0.82.1/xgboost/src/rabit/include/rabit/serializable.h | 2 xgboost-0.82.1/xgboost/src/rabit/src/allreduce_base.cc | 6 xgboost-0.82.1/xgboost/src/rabit/src/allreduce_base.h | 2 xgboost-0.82.1/xgboost/src/rabit/src/allreduce_robust.cc | 6 xgboost-0.82.1/xgboost/src/rabit/src/c_api.cc | 10 xgboost-0.82.1/xgboost/src/rabit/src/engine.cc | 4 xgboost-0.82.1/xgboost/src/rabit/src/socket.h | 29 xgboost-0.82.1/xgboost/src/rabit/src/thread_local.h | 10 xgboost-0.82.1/xgboost/src/src/common/common.cc | 2 xgboost-0.82.1/xgboost/src/src/common/common.h | 4 xgboost-0.82.1/xgboost/src/src/common/compressed_iterator.h | 4 xgboost-0.82.1/xgboost/src/src/common/device_helpers.cuh | 76 + xgboost-0.82.1/xgboost/src/src/common/group_data.h | 26 xgboost-0.82.1/xgboost/src/src/common/hist_util.cc | 140 ++- xgboost-0.82.1/xgboost/src/src/common/hist_util.h | 95 -- xgboost-0.82.1/xgboost/src/src/common/host_device_vector.cc | 2 xgboost-0.82.1/xgboost/src/src/common/host_device_vector.cu | 6 xgboost-0.82.1/xgboost/src/src/common/host_device_vector.h | 11 xgboost-0.82.1/xgboost/src/src/common/math.h | 4 xgboost-0.82.1/xgboost/src/src/common/random.h | 4 xgboost-0.82.1/xgboost/src/src/common/span.h | 15 xgboost-0.82.1/xgboost/src/src/common/timer.h | 9 xgboost-0.82.1/xgboost/src/src/common/transform.h | 19 xgboost-0.82.1/xgboost/src/src/data/data.cc | 95 ++ xgboost-0.82.1/xgboost/src/src/data/simple_dmatrix.h | 4 xgboost-0.82.1/xgboost/src/src/data/sparse_page_dmatrix.cc | 2 xgboost-0.82.1/xgboost/src/src/data/sparse_page_dmatrix.h | 2 xgboost-0.82.1/xgboost/src/src/data/sparse_page_source.cc | 15 xgboost-0.82.1/xgboost/src/src/data/sparse_page_source.h | 5 xgboost-0.82.1/xgboost/src/src/data/sparse_page_writer.h | 2 xgboost-0.82.1/xgboost/src/src/gbm/gbtree_model.h | 2 xgboost-0.82.1/xgboost/src/src/learner.cc | 49 - xgboost-0.82.1/xgboost/src/src/linear/linear_updater.cc | 2 xgboost-0.82.1/xgboost/src/src/logging.cc | 2 xgboost-0.82.1/xgboost/src/src/metric/elementwise_metric.cc | 2 xgboost-0.82.1/xgboost/src/src/metric/elementwise_metric.cu | 4 xgboost-0.82.1/xgboost/src/src/objective/hinge.cc | 2 xgboost-0.82.1/xgboost/src/src/objective/hinge.cu | 2 xgboost-0.82.1/xgboost/src/src/objective/multiclass_obj.cc | 2 xgboost-0.82.1/xgboost/src/src/objective/multiclass_obj.cu | 2 xgboost-0.82.1/xgboost/src/src/objective/objective.cc | 2 xgboost-0.82.1/xgboost/src/src/objective/regression_obj.cc | 2 xgboost-0.82.1/xgboost/src/src/objective/regression_obj.cu | 2 xgboost-0.82.1/xgboost/src/src/predictor/predictor.cc | 2 xgboost-0.82.1/xgboost/src/src/tree/param.h | 117 +- xgboost-0.82.1/xgboost/src/src/tree/split_evaluator.cc | 2 xgboost-0.82.1/xgboost/src/src/tree/split_evaluator.h | 1 xgboost-0.82.1/xgboost/src/src/tree/tree_updater.cc | 2 xgboost-0.82.1/xgboost/src/src/tree/updater_basemaker-inl.h | 13 xgboost-0.82.1/xgboost/src/src/tree/updater_colmaker.cc | 46 - xgboost-0.82.1/xgboost/src/src/tree/updater_gpu.cu | 29 xgboost-0.82.1/xgboost/src/src/tree/updater_gpu_common.cuh | 47 - xgboost-0.82.1/xgboost/src/src/tree/updater_gpu_hist.cu | 72 + xgboost-0.82.1/xgboost/src/src/tree/updater_histmaker.cc | 134 +-- xgboost-0.82.1/xgboost/src/src/tree/updater_quantile_hist.cc | 423 ++++++---- xgboost-0.82.1/xgboost/src/src/tree/updater_quantile_hist.h | 172 +++- xgboost-0.82.1/xgboost/src/src/tree/updater_refresh.cc | 40 xgboost-0.82.1/xgboost/src/src/tree/updater_skmaker.cc | 25 xgboost-0.82.1/xgboost/src/xgboost_custom.cc | 2 xgboost-0.82.1/xgboost/tests/testthat/test_basic.R | 2 xgboost-0.82.1/xgboost/tests/testthat/test_callbacks.R | 2 86 files changed, 1390 insertions(+), 934 deletions(-)
Title: Sparse Additive Modelling
Description: Computationally efficient tools for high dimensional predictive
modeling (regression and classification). SAM is short for sparse
additive modeling, and adopts the computationally efficient basis
spline technique. We solve the optimization problems by various
computational algorithms including the block coordinate descent
algorithm, fast iterative soft-thresholding algorithm, and newton method.
The computation is further accelerated by warm-start and active-set tricks.
Author: Haoming Jiang, Yukun Ma, Xinyu Fei, Tuo Zhao, Xingguo Li, Han Liu, and Kathryn Roeder
Maintainer: Haoming Jiang <jianghm.ustc@gmail.com>
Diff between SAM versions 1.1.0 dated 2019-02-18 and 1.1.1 dated 2019-03-11
DESCRIPTION | 6 MD5 | 56 +++-- NAMESPACE | 54 ++--- R/SAM-package.R | 54 ++--- R/samEL.R | 462 ++++++++++++++++++++++++------------------------- R/samHL.R | 468 ++++++++++++++++++++++++------------------------- R/samLL.R | 480 +++++++++++++++++++++++++-------------------------- R/samQL.R | 444 +++++++++++++++++++++++------------------------ cleanup |only configure | 18 - configure.ac |only man/SAM-package.Rd | 60 +++--- man/plot.samEL.Rd | 44 ++-- man/plot.samHL.Rd | 44 ++-- man/plot.samLL.Rd | 44 ++-- man/plot.samQL.Rd | 44 ++-- man/predict.samEL.Rd | 58 +++--- man/predict.samHL.Rd | 66 +++---- man/predict.samLL.Rd | 66 +++---- man/predict.samQL.Rd | 58 +++--- man/print.samEL.Rd | 44 ++-- man/print.samHL.Rd | 44 ++-- man/print.samLL.Rd | 44 ++-- man/print.samQL.Rd | 44 ++-- man/samEL.Rd | 188 +++++++++---------- man/samHL.Rd | 192 ++++++++++---------- man/samLL.Rd | 198 ++++++++++----------- man/samQL.Rd | 198 ++++++++++----------- tests/test_linear.R | 160 ++++++++--------- tests/test_logis.R | 166 ++++++++--------- 30 files changed, 1903 insertions(+), 1901 deletions(-)
Title: Multiverse Analysis of Multinomial Processing Tree Models
Description: Statistical or cognitive modeling usually requires a number of more or less
arbitrary choices creating one specific path through a 'garden of forking paths'.
The multiverse approach (Steegen, Tuerlinckx, Gelman, & Vanpaemel, 2016,
<doi:10.1177/1745691616658637>) offers a principled alternative in which results
for all possible combinations of reasonable modeling choices are reported.
MPTmultiverse performs a multiverse analysis for multinomial processing tree
(MPT, Riefer & Batchelder, 1988, <doi:10.1037/0033-295X.95.3.318>) models combining
maximum-likelihood/frequentist and Bayesian estimation approaches with
different levels of pooling (i.e., data aggregation). For the
frequentist approaches, no pooling (with and without parametric or nonparametric
bootstrap) and complete pooling are implemented using
MPTinR <https://cran.r-project.org/package=MPTinR>.
For the Bayesian approaches, no pooling, complete pooling, and three different
variants of partial pooling are implemented using
TreeBUGS <https://cran.r-project.org/package=TreeBUGS>. The main function is
fit_mpt() who performs the multiverse analysis in one call.
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Daniel W. Heck [aut],
Marius Barth [aut],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between MPTmultiverse versions 0.1 dated 2018-11-19 and 0.2-0 dated 2019-03-11
DESCRIPTION | 11 +- MD5 | 28 +++--- NAMESPACE | 1 R/check_results.R | 32 ++++--- R/get_eqn_categories.R | 4 R/make_results_row.R | 21 +++- R/mpt_options.R | 4 R/mptinr.R | 18 ++-- R/plot_multiverseMPT.R | 9 +- R/treebugs.R | 7 + R/write_results.R |only build/vignette.rds |binary inst/doc/introduction-bayen_kuhlmann_2011.html | 111 +++++++++++++++---------- man/mpt_options.Rd | 2 man/write_results.Rd |only tests/testthat/test-mptinr.R | 21 ++-- 16 files changed, 169 insertions(+), 100 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Haoming Jiang, Xinyu Fei, Yukun Ma, Xingguo Li, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman, Tuo Zhao
Maintainer: Haoming Jiang <jianghm.ustc@gmail.com>
Diff between huge versions 1.3.0 dated 2019-02-22 and 1.3.1 dated 2019-03-11
DESCRIPTION | 6 MD5 | 79 +++--- NAMESPACE | 78 +++--- R/RcppExports.R | 46 +-- R/huge-package.R | 160 ++++++------ R/huge.R | 542 +++++++++++++++++++++---------------------- R/huge.ct.R | 182 +++++++------- R/huge.generator.R | 448 ++++++++++++++++++------------------ R/huge.glasso.R | 106 ++++---- R/huge.inference.R | 458 ++++++++++++++++++------------------- R/huge.mb.R | 278 +++++++++++----------- R/huge.npn.R | 164 ++++++------- R/huge.plot.R | 98 +++---- R/huge.roc.R | 234 +++++++++--------- R/huge.select.R | 604 ++++++++++++++++++++++++------------------------- R/huge.tiger.R | 188 +++++++-------- build/vignette.rds |binary configure | 18 - configure.ac |only data/datalist | 2 inst/doc/vignette.Rnw | 22 - inst/doc/vignette.pdf |binary man/huge-package.Rd | 104 ++++---- man/huge.Rd | 236 +++++++++---------- man/huge.generator.Rd | 164 ++++++------- man/huge.inference.Rd | 142 +++++------ man/huge.npn.Rd | 92 +++---- man/huge.plot.Rd | 94 +++---- man/huge.roc.Rd | 106 ++++---- man/huge.select.Rd | 176 +++++++------- man/plot.huge.Rd | 42 +-- man/plot.roc.Rd | 38 +-- man/plot.select.Rd | 38 +-- man/plot.sim.Rd | 38 +-- man/print.huge.Rd | 38 +-- man/print.roc.Rd | 38 +-- man/print.select.Rd | 38 +-- man/print.sim.Rd | 38 +-- man/stockdata.Rd | 60 ++-- tests/test.R | 52 ++-- vignettes/vignette.Rnw | 22 - 41 files changed, 2635 insertions(+), 2634 deletions(-)
Title: Statistical Hypothesis Testing Toolbox
Description: We provide a collection of statistical hypothesis testing procedures ranging from classical to modern methods for non-trivial settings such as high-dimensional scenario. For the general treatment of statistical hypothesis testing, see the book by Lehmann and Romano (2005) <doi:10.1007/0-387-27605-X>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [aut],
Hyungmin Park [aut],
Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <ksyou496@gmail.com>
Diff between SHT versions 0.1.0 dated 2019-03-05 and 0.1.1 dated 2019-03-11
SHT-0.1.0/SHT/README.md |only SHT-0.1.1/SHT/DESCRIPTION | 8 ++-- SHT-0.1.1/SHT/MD5 | 61 ++++++++++++++++++------------ SHT-0.1.1/SHT/NAMESPACE | 7 +++ SHT-0.1.1/SHT/NEWS.md | 6 ++- SHT-0.1.1/SHT/R/aux_etc.R | 19 +++++++++ SHT-0.1.1/SHT/R/cov1.2012Fisher.R |only SHT-0.1.1/SHT/R/cov1.2015WL.R |only SHT-0.1.1/SHT/R/cov2.2013CLX.R | 4 +- SHT-0.1.1/SHT/R/cov2.2015WL.R |only SHT-0.1.1/SHT/R/eqdist.2014BG.R | 5 +- SHT-0.1.1/SHT/R/mean1.1958Dempster.R | 4 +- SHT-0.1.1/SHT/R/mean1.1996BS.R | 4 +- SHT-0.1.1/SHT/R/mean1.2008SD.R | 4 +- SHT-0.1.1/SHT/R/mean2.2011LJW.R | 7 ++- SHT-0.1.1/SHT/R/meank.2007Schott.R |only SHT-0.1.1/SHT/R/meank.2009ZX.R | 6 +-- SHT-0.1.1/SHT/R/meank.2019CPH.R |only SHT-0.1.1/SHT/R/meank.anova.R | 4 +- SHT-0.1.1/SHT/R/package-SHT.R | 2 - SHT-0.1.1/SHT/R/unif.2017YMi.R |only SHT-0.1.1/SHT/R/unif.2017YMq.R |only SHT-0.1.1/SHT/build/partial.rdb |binary SHT-0.1.1/SHT/inst/REFERENCES.bib | 64 ++++++++++++++++++++++++++++++++ SHT-0.1.1/SHT/man/cov1.2012Fisher.Rd |only SHT-0.1.1/SHT/man/cov1.2015WL.Rd |only SHT-0.1.1/SHT/man/cov2.2013CLX.Rd | 2 - SHT-0.1.1/SHT/man/cov2.2015WL.Rd |only SHT-0.1.1/SHT/man/eqdist.2014BG.Rd | 4 +- SHT-0.1.1/SHT/man/mean1.1958Dempster.Rd | 2 - SHT-0.1.1/SHT/man/mean1.1996BS.Rd | 2 - SHT-0.1.1/SHT/man/mean1.2008SD.Rd | 2 - SHT-0.1.1/SHT/man/mean2.2011LJW.Rd | 4 +- SHT-0.1.1/SHT/man/meank.2007Schott.Rd |only SHT-0.1.1/SHT/man/meank.2009ZX.Rd | 4 +- SHT-0.1.1/SHT/man/meank.2019CPH.Rd |only SHT-0.1.1/SHT/man/meank.anova.Rd | 2 - SHT-0.1.1/SHT/man/unif.2017YMi.Rd |only SHT-0.1.1/SHT/man/unif.2017YMq.Rd |only 39 files changed, 168 insertions(+), 59 deletions(-)
Title: Interpolation Grids for Packages of the 'RobASt' - Family of
Packages
Description: Includes 'sysdata.rda' file for packages of the 'RobASt' - family of packages; is
currently used by package 'RobExtremes' only.
Author: Matthias Kohl [aut, cph],
Bernhard Spangl [ctb] (contributed smoothed grid values of the Lagrange
multipliers),
Sascha Desmettre [ctb] (contributed smoothed grid values of the
Lagrange multipliers),
Eugen Massini [ctb] (contributed an interactive smoothing routine for
smoothing the Lagrange multipliers and smoothed grid values of the
Lagrange multipliers),
Mykhailo Pupashenko [ctb] (helped with manual smoothing of the
interpolators),
Daria Pupashenko [ctb] (helped with manual smoothing of the
interpolators),
Gerald Kroisandt [ctb] (helped with manual smoothing of the
interpolators),
Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between RobAStRDA versions 1.1.0 dated 2018-07-31 and 1.2.0 dated 2019-03-11
DESCRIPTION | 41 +++++++++++++++++++++-------------------- MD5 | 6 +++--- R/sysdata.rda |binary man/0RobRDA-package.Rd | 6 +++--- 4 files changed, 27 insertions(+), 26 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.5-1 dated 2018-09-11 and 2.5-2 dated 2019-03-11
DESCRIPTION | 8 MD5 | 32 NAMESPACE | 169 NEWS | 1170 +++--- R/commander.R | 2 R/data-menu.R | 5378 ++++++++++++++-------------- R/file-menu.R | 2136 +++++------ R/model-menu.R | 5 R/statistics-tables-menu.R | 5 build/vignette.rds |binary inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/po/ko/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 136 man/Rcmdr.Utilities.Rd | 1294 +++--- po/R-ko.po | 311 - po/R-zh.po | 80 17 files changed, 5402 insertions(+), 5324 deletions(-)
Title: Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School
Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary
school.
Author: Eleonora Feist [ctb] (contributed as student in the initial phase
--2008),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Anja Hueller [ctb] (contributed as student in the initial phase --2008)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTeach versions 2.6 dated 2016-04-23 and 2.8.0 dated 2019-03-11
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- R/illustLLN.R | 2 +- inst/CITATION | 3 ++- inst/NEWS | 22 ++++++++++++++++++++-- inst/TOBEDONE | 2 +- man/0distrTeach-package.Rd | 10 +++++----- man/IllustCLT.Rd | 6 +++--- 8 files changed, 47 insertions(+), 28 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports
the static site generator 'Hugo' (<https://gohugo.io>) best, and it also
supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Beilei Bian [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
JJ Allaire [ctb],
Kevin Ushey [ctb],
Leonardo Collado-Torres [ctb],
Xianying Tan [ctb],
Raniere Silva [ctb],
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 0.10 dated 2019-01-09 and 0.11 dated 2019-03-11
DESCRIPTION | 13 ++++++---- MD5 | 18 +++++++------- NEWS.md | 14 +++++++++++ R/hugo.R | 9 ++++++- R/install.R | 44 +++++++++++++++++------------------ R/serve.R | 1 R/site.R | 10 ++++++++ R/utils.R | 65 ++++++++++++++++++++++++++++++++++++---------------- README.md | 2 - man/install_hugo.Rd | 6 ++++ 10 files changed, 123 insertions(+), 59 deletions(-)
Title: Cluster High Dimensional Categorical Datasets
Description: Scalable Bayesian clustering of categorical datasets. The package implements a hierarchical Dirichlet
(Process) mixture of multinomial distributions. It is thus a probabilistic latent class model (LCM) and can be used
to reduce the dimensionality of hierarchical data and cluster individuals into latent classes. It can automatically
infer an appropriate number of latent classes or find k classes, as defined by the user. The model is based on a
paper by Dunson and Xing (2009) <doi:10.1198/jasa.2009.tm08439>, but implements a scalable variational inference algorithm so that it is
applicable to large datasets. It is described and tested in the accompanying paper by
Ahlmann-Eltze and Yau (2018) <doi:10.1109/DSAA.2018.00068>.
Author: Constantin Ahlmann-Eltze [aut, cre],
Christopher Yau [ths]
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Diff between mixdir versions 0.1.0 dated 2018-06-18 and 0.2.0 dated 2019-03-11
DESCRIPTION | 12 ++++++---- MD5 | 22 ++++++++++--------- NEWS.md |only R/mixdir.R | 8 ++++--- R/predict.R | 28 ++++++++++++++----------- README.md | 15 ++++++------- inst |only man/figures/README_plots/example-1.png |binary man/figures/README_plots/unnamed-chunk-3-1.png |binary man/find_defining_features.Rd | 8 ++++--- man/mixdir.Rd | 8 ++++--- man/plot_features.Rd | 18 ++++++++-------- man/predict.mixdir.Rd | 5 ++-- 13 files changed, 70 insertions(+), 54 deletions(-)
Title: The Multiple Filter Test for Change Point Detection
Description: Provides statistical tests and algorithms for the detection of change points in time series and point processes - particularly for changes in the mean in time series and for changes in the rate and in the variance in point processes. References - Michael Messer, Marietta Kirchner, Julia Schiemann, Jochen Roeper, Ralph Neininger and Gaby Schneider (2014), A multiple filter test for the detection of rate changes in renewal processes with varying variance <doi:10.1214/14-AOAS782>. Stefan Albert, Michael Messer, Julia Schiemann, Jochen Roeper, Gaby Schneider (2017), Multi-scale detection of variance changes in renewal processes in the presence of rate change points <doi:10.1111/jtsa.12254>. Michael Messer, Kaue M. Costa, Jochen Roeper and Gaby Schneider (2017), Multi-scale detection of rate changes in spike trains with weak dependencies <doi:10.1007/s10827-016-0635-3>. Michael Messer, Stefan Albert and Gaby Schneider (2018), The multiple filter test for change point detection in time series <doi:10.1007/s00184-018-0672-1>. Michael Messer, Hendrik Backhaus, Albrecht Stroh and Gaby Schneider (2019+) Peak detection in time series.
Author: Michael Messer, Stefan Albert, Solveig Plomer, Gaby Schneider
Maintainer: Michael Messer <messer@math.uni-frankfurt.de>
Diff between MFT versions 1.3 dated 2017-09-15 and 2.0 dated 2019-03-11
DESCRIPTION | 12 MD5 | 28 + NAMESPACE | 4 R/MFT.filterdata.R |only R/MFT.m_est.R | 221 +++++++------ R/MFT.mean.R | 245 ++++----------- R/MFT.peaks.R |only R/MFT.rate.R | 815 ++++++++++++++++++++++---------------------------- R/MFT.variance.R | 279 ++++------------- R/plot.MFT.R |only R/summary.MFT.R |only man/MFT.filterdata.Rd |only man/MFT.m_est.Rd | 55 +-- man/MFT.mean.Rd | 79 +--- man/MFT.peaks.Rd |only man/MFT.rate.Rd | 62 +-- man/MFT.variance.Rd | 56 +-- man/plot.MFT.Rd |only man/summary.MFT.Rd |only 19 files changed, 744 insertions(+), 1112 deletions(-)
Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre],
Ben Armstrong [aut],
Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between dlnm versions 2.3.8 dated 2019-02-04 and 2.3.9 dated 2019-03-11
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- NEWS.md | 12 +++++++++++ R/exphist.R | 49 ++++++++++++++++++++++----------------------- inst/NEWS | 12 +++++++++++ inst/doc/dlnmExtended.pdf |binary inst/doc/dlnmOverview.pdf |binary inst/doc/dlnmPenalized.pdf |binary inst/doc/dlnmTS.pdf |binary man/exphist.Rd | 2 - 10 files changed, 63 insertions(+), 38 deletions(-)
Title: Estimation and Testing Classes Based on Package 'distr'
Description: Evaluation (S4-)classes based on package distr for evaluating procedures
(estimators/tests) at data/simulation in a unified way.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTEst versions 2.7.0 dated 2018-07-23 and 2.8.0 dated 2019-03-11
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- R/plot-methods.R | 27 +++++++++++++++++++++------ inst/NEWS | 11 +++++++++++ man/0distrTEst-package.Rd | 6 +++--- man/plot-methods.Rd | 7 +++++++ 6 files changed, 55 insertions(+), 22 deletions(-)
Title: Simulation Classes Based on Package 'distr'
Description: S4-classes for setting up a coherent framework for simulation within the distr
family of packages.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrSim versions 2.7.0 dated 2018-07-23 and 2.8.0 dated 2019-03-11
DESCRIPTION | 16 +++++------ MD5 | 10 +++---- R/plot-methods.R | 66 ++++++++++++++++++++++++++++++++++++----------- inst/NEWS | 12 ++++++++ man/0distrSim-package.Rd | 6 ++-- man/plot-methods.Rd | 8 +++++ 6 files changed, 87 insertions(+), 31 deletions(-)
Title: Distribution Classes for Distributions from Rmetrics
Description: S4-distribution classes based on package distr for distributions from packages
'fBasics' and 'fGarch'.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrRmetrics versions 2.7.0 dated 2018-07-23 and 2.8.0 dated 2019-03-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 7 +++++++ man/0distrRmetrics-package.Rd | 6 +++--- 4 files changed, 18 insertions(+), 11 deletions(-)
Title: Documentation for 'distr' Family of R Packages
Description: Provides documentation in form of a common vignette to packages 'distr',
'distrEx', 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'.
Author: Florian Camphausen [ctb] (contributed as student to the documented
packages in the initial phase --2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student to the documented packages
in the initial phase --2005)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrDoc versions 2.7.1 dated 2018-07-23 and 2.8.0 dated 2019-03-11
DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS | 8 ++++++++ inst/doc/distr.Rnw | 16 +++++++++++----- inst/doc/distr.pdf |binary man/0distrDoc-package.Rd | 6 +++--- vignettes/distr.Rnw | 16 +++++++++++----- 8 files changed, 50 insertions(+), 30 deletions(-)
Title: Object Oriented Implementation of Distributions
Description: S4-classes and methods for distributions.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005),
R Core Team [ctb, cph] (for source file ks.c/ routines 'pKS2' and
'pKolmogorov2x')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distr versions 2.7.0 dated 2018-07-11 and 2.8.0 dated 2019-03-11
distr-2.7.0/distr/man/GeomParameter-class.Rd |only distr-2.8.0/distr/DESCRIPTION | 16 - distr-2.8.0/distr/MD5 | 92 ++++---- distr-2.8.0/distr/NAMESPACE | 4 distr-2.8.0/distr/R/0pre270.R | 27 ++ distr-2.8.0/distr/R/AllClasses.R | 40 ++- distr-2.8.0/distr/R/AllGenerics.R | 2 distr-2.8.0/distr/R/AllInitialize.R | 68 +++--- distr-2.8.0/distr/R/ContDistribution.R | 11 - distr-2.8.0/distr/R/DiscreteDistribution.R | 60 ++++- distr-2.8.0/distr/R/GeometricDistribution.R | 57 ++--- distr-2.8.0/distr/R/LatticeDistribution.R | 80 +++++-- distr-2.8.0/distr/R/MinMaximum.R | 11 - distr-2.8.0/distr/R/Truncate.R | 13 + distr-2.8.0/distr/R/UnivarLebDecDistribution.R | 2 distr-2.8.0/distr/R/UnivarMixingDistribution.R | 2 distr-2.8.0/distr/R/UtilitiesDistributions.R | 5 distr-2.8.0/distr/R/bAcDcLcDistribution.R | 106 ++++++++- distr-2.8.0/distr/R/decomposePM.R | 3 distr-2.8.0/distr/R/flat.R | 9 distr-2.8.0/distr/R/internalUtils.R | 148 ++++++++++++- distr-2.8.0/distr/R/internalUtils_LCD.R | 6 distr-2.8.0/distr/R/liesInSupport.R | 127 ++++++++++- distr-2.8.0/distr/R/plot-methods.R | 182 ++++++++++++++--- distr-2.8.0/distr/R/plot-methods_LebDec.R | 147 ++++++++++--- distr-2.8.0/distr/R/qqplot.R | 33 ++- distr-2.8.0/distr/R/solve.R | 37 +-- distr-2.8.0/distr/build/vignette.rds |binary distr-2.8.0/distr/demo/ConvolutionNormalDistr.R | 14 - distr-2.8.0/distr/demo/Expectation.R | 4 distr-2.8.0/distr/demo/StationaryRegressorDistr.R | 8 distr-2.8.0/distr/demo/nFoldConvolution.R | 24 +- distr-2.8.0/distr/demo/range.R | 10 distr-2.8.0/distr/inst/NEWS | 44 ++++ distr-2.8.0/distr/inst/doc/newDistributions-knitr.Rnw | 10 distr-2.8.0/distr/inst/doc/newDistributions-knitr.pdf |binary distr-2.8.0/distr/man/0distr-package.Rd | 6 distr-2.8.0/distr/man/DiscreteDistribution-class.Rd | 3 distr-2.8.0/distr/man/MinMaximum-methods.Rd | 2 distr-2.8.0/distr/man/distr-defunct.Rd |only distr-2.8.0/distr/man/internals.Rd | 6 distr-2.8.0/distr/man/liesInSupport.Rd | 127 ++++++++++- distr-2.8.0/distr/man/operators-methods.Rd | 2 distr-2.8.0/distr/man/options.Rd | 4 distr-2.8.0/distr/man/plot-methods.Rd | 11 - distr-2.8.0/distr/man/qqplot.Rd | 4 distr-2.8.0/distr/tests/Examples |only distr-2.8.0/distr/vignettes/newDistributions-knitr.Rnw | 10 48 files changed, 1223 insertions(+), 354 deletions(-)
Title: Construct Reproducible Analytic Data Sets as R Packages
Description: A framework to help construct R data packages in a
reproducible manner. Potentially time consuming processing of
raw data sets into analysis ready data sets is done in a reproducible
manner and decoupled from the usual R CMD build process so that
data sets can be processed into R objects in the data package and
the data package can then be shared, built, and installed by others
without the need to repeat computationally costly data processing.
The package maintains data provenance by turning the data processing
scripts into package vignettes, as well as enforcing documentation
and version checking of included data objects. Data packages can be
version controlled in github, and used to share data for manuscripts,
collaboration and general reproducibility.
Author: Greg Finak [aut, cre, cph],
Paul Obrecht [ctb],
Ellis Hughes [ctb],
Kara Woo [rev] (Kara reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/230>),
William Landau [rev] (William reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/230>)
Maintainer: Greg Finak <gfinak@fredhutch.org>
Diff between DataPackageR versions 0.15.4 dated 2018-10-24 and 0.15.5 dated 2019-03-11
DESCRIPTION | 10 + MD5 | 39 +++---- NEWS.md | 12 +- R/01.R | 1 R/autodoc.R | 4 R/build.R | 6 - R/environments.R | 40 +++++++ R/processData.R | 16 ++- R/prompt.R | 6 - README.md | 18 +-- inst/doc/YAML_CONFIG.html | 44 ++++++-- inst/doc/usingDataPackageR.R | 4 inst/doc/usingDataPackageR.Rmd | 4 inst/doc/usingDataPackageR.html | 103 +++++++++++--------- man/DataPackageR-package.Rd | 2 man/document.Rd | 6 - man/package_build.Rd | 4 tests/testthat/test-datapackager-object-read.R | 33 ++++++ tests/testthat/test-r-processing.R | 16 +-- tests/testthat/test-updating-datapackager-version.R |only vignettes/usingDataPackageR.Rmd | 4 21 files changed, 258 insertions(+), 114 deletions(-)
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement
for the 'zip' function, that does not require any additional
external tools on any platform.
Author: Gábor Csárdi, Kuba Podgórski, Rich Geldreich
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between zip versions 2.0.0 dated 2019-02-25 and 2.0.1 dated 2019-03-11
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/utils.R | 9 +++++++++ R/zip.R | 4 ++++ src/miniz.c | 2 ++ tests/testthat/helper.R | 8 ++++++++ tests/testthat/test-zip.R | 28 ++++++++++++++-------------- 8 files changed, 52 insertions(+), 24 deletions(-)
Title: Utilities for Start-Up Messages
Description: Provides utilities to create or suppress start-up messages.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between startupmsg versions 0.9.5 dated 2018-07-11 and 0.9.6 dated 2019-03-11
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- inst/NEWS | 7 +++++++ 3 files changed, 17 insertions(+), 10 deletions(-)
Title: Tools for Spell Checking in R
Description: Spell checking common document formats including latex, markdown, manual pages,
and description files. Includes utilities to automate checking of documentation and
vignettes as a unit test during 'R CMD check'. Both British and American English are
supported out of the box and other languages can be added. In addition, packages may
define a 'wordlist' to allow custom terminology without having to abuse punctuation.
Author: Jeroen Ooms [cre, aut] (<https://orcid.org/0000-0002-4035-0289>),
Jim Hester [aut]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between spelling versions 2.0 dated 2018-12-17 and 2.1 dated 2019-03-11
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS | 6 ++++++ R/check-files.R | 31 +++++++++++++++++++++++++++---- R/spell-check.R | 3 ++- 5 files changed, 45 insertions(+), 14 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.7 dated 2019-02-13 and 1.7.1 dated 2019-03-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/gwa_description.pdf |binary inst/doc/vignette1.html | 4 ++-- inst/doc/vignette2.html | 4 ++-- man/NAM-package.Rd | 4 ++-- src/Functions.cpp | 14 ++++++++------ 7 files changed, 24 insertions(+), 22 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional kernel term and sampling techniques as described
by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.6 dated 2019-02-13 and 1.6.1 dated 2019-03-11
DESCRIPTION | 8 - MD5 | 10 +- R/RcppExports.R | 238 ++++++++++++++++++++++++++-------------------------- man/bWGR.Rd | 4 man/mvr.Rd | 18 +++ src/wgr20190212.cpp | 14 +-- 6 files changed, 152 insertions(+), 140 deletions(-)
Title: Lightweight R Interface to the Alpha Vantage API
Description: Alpha Vantage has free historical financial information.
All you need to do is get a free API key at <https://www.alphavantage.co>.
Then you can use the R interface to retrieve free equity information.
Refer to the Alpha Vantage website for more information.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between alphavantager versions 0.1.0 dated 2017-09-03 and 0.1.1 dated 2019-03-11
alphavantager-0.1.0/alphavantager/tests/testthat/api_key.txt |only alphavantager-0.1.1/alphavantager/DESCRIPTION | 22 alphavantager-0.1.1/alphavantager/MD5 | 31 - alphavantager-0.1.1/alphavantager/NAMESPACE | 10 alphavantager-0.1.1/alphavantager/NEWS.md | 24 alphavantager-0.1.1/alphavantager/R/alphavantager-package.R | 34 - alphavantager-0.1.1/alphavantager/R/av_api_key.R | 54 +- alphavantager-0.1.1/alphavantager/R/av_get.R | 250 +++++----- alphavantager-0.1.1/alphavantager/R/global_vars.R | 2 alphavantager-0.1.1/alphavantager/README.md | 166 +++--- alphavantager-0.1.1/alphavantager/man/alphavantager.Rd | 36 - alphavantager-0.1.1/alphavantager/man/av_api_key.Rd | 62 +- alphavantager-0.1.1/alphavantager/man/av_get.Rd | 70 +- alphavantager-0.1.1/alphavantager/tests/testthat.R | 8 alphavantager-0.1.1/alphavantager/tests/testthat/helpers_auth.R | 43 - alphavantager-0.1.1/alphavantager/tests/testthat/test_av_api_key.R | 32 - alphavantager-0.1.1/alphavantager/tests/testthat/test_av_get.R | 221 ++++---- 17 files changed, 550 insertions(+), 515 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-28 0.7
2017-10-22 0.6
2017-09-30 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-27 0.0.1
Title: Just a Rather Bayesian Evidence Synthesis
Description: Provides a new class of Bayesian meta-analysis models that we called "The Hierarchical Meta-Regression" (HMR). The aim of HMR is to incorporate into the meta-analysis, the data collection process, which results in a model for the internal and external validity bias. In this way, it is possible to combine studies of different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS). The statistical methods and their applications are described in Verde (2019) <doi:10.1002/bimj.201700266> and in Verde (2017) <doi:10.5772/intechopen.70231>.
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between jarbes versions 1.7.0 dated 2018-07-31 and 1.7.2 dated 2019-03-11
ChangeLog | 63 ++-- DESCRIPTION | 15 - MD5 | 32 +- NAMESPACE | 10 R/ges.R |only R/gesmix.R |only R/hmr.R | 681 +++++++++++++++++++++++++++--------------------- R/jarbes-package.R | 34 +- R/metarisk.R | 325 +++++++++++----------- man/ges.Rd |only man/gesmix.Rd |only man/hmr.Rd | 243 ++++++++++------- man/metarisk.Rd | 124 ++++---- man/plot.ges.Rd |only man/plot.gesmix.Rd |only man/print.ges.Rd |only man/print.gesmix.Rd |only man/print.hmr.Rd | 4 man/summary.ges.Rd |only man/summary.gesmix.Rd |only man/summary.hmr.Rd | 4 man/summary.metarisk.Rd | 4 22 files changed, 868 insertions(+), 671 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <jasson@toulouse.inra.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.5-13.4 dated 2019-03-01 and 0.5-13.5 dated 2019-03-11
DESCRIPTION | 6 - MD5 | 48 ++++++------ NAMESPACE | 1 R/zzz.R | 3 man/base-copies.Rd |only man/bigrational.Rd | 2 src/Makevars.in | 1 src/Rgmp.h | 17 ---- src/biginteger.h | 5 + src/bigintegerR.cc | 81 +++++++++++---------- src/bigintegerR.h | 2 src/bigmod.cc | 158 ++++++++++++++++++++--------------------- src/bigmod.h | 181 +++++++++++++++++++++++++++++++++++++++-------- src/bigrationalR.cc | 11 ++ src/bigvec.cc | 146 +++++++++++++++++++++---------------- src/bigvec.h | 40 ++++++---- src/bigvec_q.cc | 48 +++++------- src/bigvec_q.h | 27 +++---- src/factor.cc | 2 src/factorize.cc | 10 +- src/matrix.cc | 13 ++- src/matrixq.cc | 16 ++-- src/solve.h | 19 +--- src/templateMatrix.h |only tests/gmp-test.R | 1 tests/gmp-test.Rout.save | 3 26 files changed, 500 insertions(+), 341 deletions(-)
Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using
state space models. The first implemented model is described in Fahrmeir
(1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the
Extended Kalman filter is replaced by an unscented Kalman filter and other
options including particle filters. The implemented particle filters support
more general state space models.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [cph],
Anthony Williams [cph],
Boost developers [cph],
R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.6.3 dated 2019-01-11 and 0.6.4 dated 2019-03-11
dynamichazard-0.6.3/dynamichazard/src/PF/taylor_normal_approx.cpp |only dynamichazard-0.6.3/dynamichazard/tests/testthat/previous_results/cloglog-PF-RW.RDS |only dynamichazard-0.6.4/dynamichazard/DESCRIPTION | 10 dynamichazard-0.6.4/dynamichazard/MD5 | 155 +- dynamichazard-0.6.4/dynamichazard/NAMESPACE | 2 dynamichazard-0.6.4/dynamichazard/NEWS.md | 13 dynamichazard-0.6.4/dynamichazard/R/HDs.R | 2 dynamichazard-0.6.4/dynamichazard/R/PF.R | 442 +++++-- dynamichazard-0.6.4/dynamichazard/R/RcppExports.R | 60 dynamichazard-0.6.4/dynamichazard/R/roxygen_tags.R | 1 dynamichazard-0.6.4/dynamichazard/inst/doc/Bootstrap_illustration.pdf |binary dynamichazard-0.6.4/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.pdf |binary dynamichazard-0.6.4/dynamichazard/inst/doc/Diagnostics.pdf |binary dynamichazard-0.6.4/dynamichazard/inst/doc/Particle_filtering.pdf |binary dynamichazard-0.6.4/dynamichazard/inst/doc/ddhazard.pdf |binary dynamichazard-0.6.4/dynamichazard/man/PF_EM.Rd | 8 dynamichazard-0.6.4/dynamichazard/man/PF_control.Rd | 12 dynamichazard-0.6.4/dynamichazard/man/PF_forward_filter.Rd | 5 dynamichazard-0.6.4/dynamichazard/man/PF_get_score_n_hess.Rd |only dynamichazard-0.6.4/dynamichazard/man/get_Q_0.Rd | 12 dynamichazard-0.6.4/dynamichazard/man/hds.Rd | 2 dynamichazard-0.6.4/dynamichazard/src/BLAS_LAPACK/arma_BLAS_LAPACK.cpp | 20 dynamichazard-0.6.4/dynamichazard/src/Makevars | 2 dynamichazard-0.6.4/dynamichazard/src/Makevars.win | 3 dynamichazard-0.6.4/dynamichazard/src/PF.cpp | 212 +-- dynamichazard-0.6.4/dynamichazard/src/PF/PF_data.h | 391 +----- dynamichazard-0.6.4/dynamichazard/src/PF/PF_logger.cpp | 80 + dynamichazard-0.6.4/dynamichazard/src/PF/PF_score_n_Hess.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/PF_utils.cpp | 171 ++ dynamichazard-0.6.4/dynamichazard/src/PF/PF_utils.h | 200 +-- dynamichazard-0.6.4/dynamichazard/src/PF/PFs.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/PFs.h | 436 ------ dynamichazard-0.6.4/dynamichazard/src/PF/cond_approx.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/cond_approx.h |only dynamichazard-0.6.4/dynamichazard/src/PF/covarmat.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/covarmat.h |only dynamichazard-0.6.4/dynamichazard/src/PF/densities.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/densities.h | 162 -- dynamichazard-0.6.4/dynamichazard/src/PF/dists.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/dists.h |only dynamichazard-0.6.4/dynamichazard/src/PF/est_params_dens.cpp | 6 dynamichazard-0.6.4/dynamichazard/src/PF/importance_samplers.cpp | 479 +++++++ dynamichazard-0.6.4/dynamichazard/src/PF/importance_samplers.h | 448 ------- dynamichazard-0.6.4/dynamichazard/src/PF/particles.cpp | 5 dynamichazard-0.6.4/dynamichazard/src/PF/particles.h | 63 - dynamichazard-0.6.4/dynamichazard/src/PF/r_to_cpp_clouds_n_reverse.cpp | 11 dynamichazard-0.6.4/dynamichazard/src/PF/resamplers.cpp |only dynamichazard-0.6.4/dynamichazard/src/PF/resamplers.h | 194 --- dynamichazard-0.6.4/dynamichazard/src/PF_fixed_effects.cpp | 335 +---- dynamichazard-0.6.4/dynamichazard/src/RcppExports.cpp | 265 +++- dynamichazard-0.6.4/dynamichazard/src/arma_BLAS_LAPACK.h | 4 dynamichazard-0.6.4/dynamichazard/src/ddhazard.h | 2 dynamichazard-0.6.4/dynamichazard/src/ddhazard/EKF_solver.cpp | 6 dynamichazard-0.6.4/dynamichazard/src/ddhazard_fit.cpp | 7 dynamichazard-0.6.4/dynamichazard/src/family.cpp | 20 dynamichazard-0.6.4/dynamichazard/src/family.h | 12 dynamichazard-0.6.4/dynamichazard/src/for_tests.cpp | 300 ++++ dynamichazard-0.6.4/dynamichazard/src/thread_pool.h | 44 dynamichazard-0.6.4/dynamichazard/src/utils.h | 22 dynamichazard-0.6.4/dynamichazard/tests/testthat.R | 1 dynamichazard-0.6.4/dynamichazard/tests/testthat/VAR_data.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/AUX_normal_approx_w_cloud_mean_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/AUX_normal_approx_w_particles_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/Brier_AUX_normal_w_particles_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_EM_print | 2 dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_VARS.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_VARS_non_zero_mean_inter.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_VARS_non_zero_mean_slope.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_get_score_n_hess-help-res-O_N_sq.RDS |only dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_get_score_n_hess-help-res.RDS |only dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_head_neck_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_head_neck_w_Brier_method_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_mean_2D.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_normal_approx_w_cloud_mean_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_normal_approx_w_particles_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/PF_quantile_2D.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/bootstrap_filter_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/n_smooth_final_RW.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/n_smooth_final_VAR.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/pf_t_dist_proposal.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/previous_results/survival_lung_example_cloud_means.RDS |binary dynamichazard-0.6.4/dynamichazard/tests/testthat/test_LAPACK_BLAS.R | 9 dynamichazard-0.6.4/dynamichazard/tests/testthat/test_PF.R | 627 +++++++++- dynamichazard-0.6.4/dynamichazard/tests/testthat/test_cloglog.R | 6 dynamichazard-0.6.4/dynamichazard/tests/testthat/test_cpp_utils.R | 27 dynamichazard-0.6.4/dynamichazard/tests/testthat/test_help_page_examples.R | 110 + 86 files changed, 3107 insertions(+), 2299 deletions(-)
Title: Fast Pseudo Random Number Generators
Description: Several fast random number generators are provided as C++
header only libraries: The PCG family by O'Neill (2014
<https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as
Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018
<arXiv:1805.01407>). In addition fast functions for generating random
numbers according to a uniform, normal and exponential distribution
are included. The latter two use the Ziggurat algorithm originally
proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>).
These functions are exported to R and as a C++ interface and are
enabled for use with the default 64 bit generator from the PCG family,
Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds
Threefry engine (Salmon et al., 2011 <doi:10.1145/2063384.2063405>) as
provided by the package 'sitmo'.
Author: Ralf Stubner [aut, cre],
daqana GmbH [cph],
David Blackman [ctb],
Melissa O'Neill [ctb],
Sebastiano Vigna [ctb],
Aaron Lun [ctb]
Maintainer: Ralf Stubner <ralf.stubner@daqana.com>
Diff between dqrng versions 0.1.0 dated 2019-03-04 and 0.1.1 dated 2019-03-11
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ NEWS.md | 5 +++ inst/doc/dqrng.Rmd | 7 ++--- inst/doc/dqrng.html | 53 ++++++++++++++++++++---------------------- inst/doc/parallel.html | 4 +-- inst/include/convert_seed.h | 38 ++++++++++++++++++++++++++---- tests/testthat/test-convert.R | 24 ++++++++++++++----- vignettes/dqrng.Rmd | 7 ++--- 9 files changed, 101 insertions(+), 59 deletions(-)
Title: Inference and Design for Predictive Values in Diagnostic Tests
Description: Computation of asymptotic confidence intervals for negative and positive predictive values in binary diagnostic tests in case-control studies. Experimental design for hypothesis tests on predictive values.
Author: Frank Schaarschmidt [aut, cre]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between bdpv versions 1.1 dated 2014-03-06 and 1.3 dated 2019-03-11
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 +++ man/bdpv-package.Rd | 6 +++--- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Bitcoin API
Description: Implementation of the RPC-JSON API for Bitcoin and utility functions for address creation and content analysis of the blockchain.
Author: Bernhard Pfaff [aut, cre]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between rbtc versions 0.1-5 dated 2018-09-12 and 0.1-6 dated 2019-03-11
DESCRIPTION | 10 MD5 | 180 ++++----- NAMESPACE | 186 ++++----- R/BtcAddresses.R | 843 +++++++++++++++++++++---------------------- man/ANSRPC-class.Rd | 68 +-- man/BTCADR-class.Rd | 88 ++-- man/CONRPC-class.Rd | 46 +- man/ECPARAM-class.Rd | 72 +-- man/ECPOINT-class.Rd | 74 +-- man/EcparamOrNull-class.Rd | 44 +- man/NullOrCharacter-class.Rd | 34 - man/NullOrInteger-class.Rd | 34 - man/PrivKey2PubKey.Rd | 78 +-- man/PrivKey2Wif.Rd | 89 ++-- man/PubHash2BtcAdr.Rd | 72 +-- man/PubKey2PubHash.Rd | 78 +-- man/Wif2PrivKey.Rd | 87 ++-- man/addnode.Rd | 82 ++-- man/base58CheckDecode.Rd | 80 ++-- man/base58CheckEncode.Rd | 82 ++-- man/bkfee.Rd | 74 +-- man/blockattime.Rd | 72 +-- man/blockstats.Rd | 78 +-- man/clearbanned.Rd | 68 +-- man/concatHex.Rd | 93 ++-- man/conrpc.Rd | 60 +-- man/containsPoint-methods.Rd | 108 ++--- man/createBtcAdr.Rd | 74 +-- man/createPrivateKey.Rd | 73 +-- man/date2int.Rd | 74 +-- man/decodeHex.Rd | 85 ++-- man/decoderawtransaction.Rd | 62 +-- man/decodescript.Rd | 90 ++-- man/disconnectnode.Rd | 84 ++-- man/ecoperators-methods.Rd | 140 +++---- man/ecparam.Rd | 86 ++-- man/ecpoint.Rd | 98 ++-- man/getaddednodeinfo.Rd | 76 +-- man/getbestblockhash.Rd | 86 ++-- man/getblock.Rd | 114 ++--- man/getblockchaininfo.Rd | 86 ++-- man/getblockcount.Rd | 86 ++-- man/getblockhash.Rd | 92 ++-- man/getblockheader.Rd | 110 ++--- man/getchaintips.Rd | 88 ++-- man/getchaintxstats.Rd | 98 ++-- man/getconnectioncount.Rd | 66 +-- man/getdifficulty.Rd | 86 ++-- man/gethelp.Rd | 62 +-- man/getinfo.Rd | 68 +-- man/getmempoolancestors.Rd | 96 ++-- man/getmempooldescendants.Rd | 96 ++-- man/getmempoolentry.Rd | 90 ++-- man/getmempoolinfo.Rd | 86 ++-- man/getnettotals.Rd | 70 +-- man/getnetworkinfo.Rd | 68 +-- man/getpeerinfo.Rd | 68 +-- man/getrawmempool.Rd | 100 ++--- man/getrawtransaction.Rd | 84 ++-- man/gettxout.Rd | 106 ++--- man/gettxoutproof.Rd | 112 ++--- man/gettxoutsetinfo.Rd | 88 ++-- man/getwalletinfo.Rd | 58 +- man/hash160.Rd | 74 +-- man/hash256.Rd | 72 +-- man/int2date.Rd | 80 ++-- man/intMaxDay.Rd | 80 ++-- man/intMinDay.Rd | 80 ++-- man/intRangeDay.Rd | 78 +-- man/intRangePeriod.Rd | 84 ++-- man/isNull-methods.Rd | 70 +-- man/listbanned.Rd | 68 +-- man/ping.Rd | 74 +-- man/preciousblock.Rd | 94 ++-- man/pruneblockchain.Rd | 102 ++--- man/rpcpost.Rd | 64 +-- man/setnetworkactive.Rd | 72 +-- man/show-methods.Rd | 44 +- man/startbtc.Rd | 70 +-- man/stopbtc.Rd | 54 +- man/timeofblock.Rd | 68 +-- man/txfee.Rd | 72 +-- man/txids.Rd | 74 +-- man/txinids.Rd | 72 +-- man/txstats.Rd | 70 +-- man/utxoage.Rd | 78 +-- man/utxotype.Rd | 68 +-- man/utxovalue.Rd | 68 +-- man/validBtcAdr.Rd | 72 +-- man/verifychain.Rd | 100 ++--- man/verifytxoutproof.Rd | 96 ++-- 91 files changed, 4047 insertions(+), 4037 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling for both dichotomous and polytomous responses. Various cognitive diagnosis models can be estimated, include the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7>, the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070>, and many other models they subsume. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between GDINA versions 2.3.2 dated 2019-01-04 and 2.4.0 dated 2019-03-11
DESCRIPTION | 8 +-- MD5 | 47 +++++++++-------- NEWS.md | 7 ++ R/GDI.R | 23 ++++++-- R/M2.R | 2 R/RcppExports.R | 4 - R/itemfit.R | 30 +++++------ R/plotIRF.GDINA.R | 22 ++++---- R/utils.R | 9 +-- README.md | 2 build/vignette.rds |binary inst/CITATION | 8 +-- inst/doc/GDINA.R |only inst/doc/GDINA.Rmd | 86 ++++++++++++++++++++++++++++++-- inst/doc/GDINA.html | 136 ++++++++++++++++++++++++++++++++++++++++++++++++---- inst/shiny/server.R | 19 ++++--- inst/shiny/ui.R | 4 - man/Qval.Rd | 11 ++-- man/itemfit.Rd | 8 +-- man/modelfit.Rd | 2 src/LouisC.cpp | 6 +- src/RcppExports.cpp | 20 +++---- src/fitstats.cpp | 77 ++++++++++++++++++++++++++++- src/util.cpp | 1 vignettes/GDINA.Rmd | 86 ++++++++++++++++++++++++++++++-- 25 files changed, 490 insertions(+), 128 deletions(-)
Title: Near-Isotonic Regression
Description: Implements a path algorithm for Near-Isotonic
Regression. For more details see the help files.
Author: Holger Hoefling, Ryan Tibshirani, Robert Tibshirani
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between neariso versions 1.0 dated 2011-01-03 and 1.0.1 dated 2019-03-11
DESCRIPTION | 13 +++++++------ MD5 |only NAMESPACE | 2 +- src/NIR.cc | 6 +++--- src/neariso_init.c |only 5 files changed, 11 insertions(+), 10 deletions(-)
Title: Multivariate Interpolation
Description: Contains methods for creating multivariate/multidimensional
interpolations of functions on a hypercube. If available through fftw3, the DCT-II/FFT
is used to compute coefficients for a Chebyshev interpolation.
Other interpolation methods for arbitrary Cartesian grids are also provided, a piecewise multilinear,
and the Floater-Hormann barycenter method. For scattered data polyharmonic splines with a linear term
is provided. The time-critical parts are written in C for speed. All interpolants are parallelized if
used to evaluate more than one point.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>)
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between chebpol versions 2.0 dated 2018-09-15 and 2.1 dated 2019-03-11
chebpol-2.0/chebpol/src/rbfalglib.cpp |only chebpol-2.1/chebpol/DESCRIPTION | 18 ++++++------ chebpol-2.1/chebpol/MD5 | 41 +++++++++++++--------------- chebpol-2.1/chebpol/R/chebpol-package.R | 6 +++- chebpol-2.1/chebpol/R/ipol.R | 8 ++++- chebpol-2.1/chebpol/R/simplexlinear.R | 6 ++-- chebpol-2.1/chebpol/configure | 30 +++++++++++++++----- chebpol-2.1/chebpol/configure.ac | 20 ++++++++----- chebpol-2.1/chebpol/inst/doc/chebpol.pdf |binary chebpol-2.1/chebpol/inst/doc/chebusage.Rnw | 3 ++ chebpol-2.1/chebpol/inst/doc/chebusage.pdf |binary chebpol-2.1/chebpol/inst/doc/stalker.R | 13 ++++++-- chebpol-2.1/chebpol/inst/doc/stalker.Rnw | 33 +++++++++++++--------- chebpol-2.1/chebpol/inst/doc/stalker.pdf |binary chebpol-2.1/chebpol/man/chebpol-package.Rd | 6 +++- chebpol-2.1/chebpol/man/ipol.Rd | 3 +- chebpol-2.1/chebpol/src/Makevars.in | 4 +- chebpol-2.1/chebpol/src/chebpol.c | 36 +++++++++++++++++++----- chebpol-2.1/chebpol/src/config.h | 2 - chebpol-2.1/chebpol/src/stalker.c | 27 ++++++++++++++++-- chebpol-2.1/chebpol/vignettes/chebusage.Rnw | 3 ++ chebpol-2.1/chebpol/vignettes/stalker.Rnw | 33 +++++++++++++--------- 22 files changed, 198 insertions(+), 94 deletions(-)
Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions
based on R base graphics, interval management functions and svg importation
functions among others. Also include stereographic projection functions,
and other functions made to deal with large datasets while keeping options
to get into the details of the data.
The palaeomagnetism functions are based on:
Tauxe, L., 2010. Essentials of Paleomagnetism. University of California
Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>;
Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural
Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge
University Press, 289 pp.;
Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections
with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205,
<doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>
Diff between StratigrapheR versions 0.0.1 dated 2018-12-31 and 0.0.2 dated 2019-03-11
DESCRIPTION | 6 MD5 | 48 +- NAMESPACE | 1 R/StratigrapheR.R | 1142 +++++++++++++++++++++++++-------------------------- R/centresvg.R | 122 ----- R/framesvg.R | 9 R/ignore.R | 9 R/infobar.R | 6 R/minorAxis.R | 188 +++++--- R/neatPick.R | 53 +- R/neatPicked.R | 40 - R/nlegend.R |only R/pdfDisplay.R | 115 +++-- R/whiteSet.R | 57 +- R/ylink.R | 4 R/zijderveld.R | 4 man/StratigrapheR.Rd | 1140 +++++++++++++++++++++++++------------------------- man/ignore.Rd | 5 man/infobar.Rd | 8 man/minorAxis.Rd | 14 man/neatPick.Rd | 53 +- man/neatPicked.Rd | 37 - man/nlegend.Rd |only man/pdfDisplay.Rd | 63 +- man/ylink.Rd | 4 man/zijderveld.Rd | 4 26 files changed, 1595 insertions(+), 1537 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. From 'rgdal' 1.4.1, provision is made for 'PROJ6' accommodation, with 'PROJ6' functionality to follow; from 1.4.1 'rgdal' will build and function when 'PROJ' >= 6. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.3-9 dated 2019-02-21 and 1.4-2 dated 2019-03-11
ChangeLog | 82 +++++++++++++++++++++++++++++++ DESCRIPTION | 12 ++-- MD5 | 37 +++++++------- NAMESPACE | 1 R/AAA.R | 2 R/Class-CRSx.R | 2 R/make_EPSG.R | 12 ++++ R/project.R | 6 ++ R/wrappers.R | 2 configure | 103 ++++++++++++++++++++++++++++++++++------ configure.ac | 78 ++++++++++++++++++++++++++++-- inst/ChangeLog | 82 +++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary man/make_EPSG.Rd | 22 ++++---- src/Makevars.win | 1 src/gdal-bindings.cpp | 7 +- src/inverser.c | 1 src/proj_info6.cpp |only src/projectit.cpp | 41 ++++++++++----- 20 files changed, 421 insertions(+), 72 deletions(-)
Title: Fast Reader for 'Wavefront' OBJ 3D Scene Files
Description: Wraps 'tiny_obj_loader' C++ library for reading the 'Wavefront' OBJ
3D file format including both mesh objects and materials files. The
resultant R objects are either structured to match the 'tiny_obj_loader'
internal data representation or in a form directly compatible with the 'rgl'
package.
Author: Gregory Jefferis [aut, cph, cre]
(<https://orcid.org/0000-0002-0587-9355>),
Syoyo Fujita [aut, cph] (tiny_obj_loader.* are copyright Syoyo Fujita)
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between readobj versions 0.3.1 dated 2018-10-03 and 0.3.2 dated 2019-03-11
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NEWS.md | 5 +++++ tests/testthat/test-loadobj.R | 6 ++++++ 4 files changed, 21 insertions(+), 9 deletions(-)
Title: Confidence Intervals for Two Sample Comparisons
Description: Calculation of the parametric, nonparametric confidence intervals
for the difference or ratio of location parameters, nonparametric confidence interval
for the Behrens-Fisher problem and for the difference, ratio and odds-ratio of binomial
proportions for comparison of independent samples. Common wrapper functions to split
data sets and apply confidence intervals or tests to these subsets.
A by-statement allows calculation of CI separately for the levels of further factors.
CI are not adjusted for multiplicity.
Author: Frank Schaarschmidt [aut, cre],
Daniel Gerhard [aut]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between pairwiseCI versions 0.1-26 dated 2018-05-07 and 0.1-27 dated 2019-03-11
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Testing for Partial Copulas and the Simplifying Assumption in
Vine Copulas
Description: Routines for two different test types, the Constant Conditional Correlation (CCC) test and the Vectorial Independence (VI) test are provided (Kurz and Spanhel (2017) <arXiv:1706.02338>). The tests can be applied to check whether a conditional copula coincides with its partial copula. Functions to test whether a regular vine copula satisfies the so-called simplifying assumption or to test a single copula within a regular vine copula to be a (j-1)-th order partial copula are available. The CCC test comes with a decision tree approach to allow testing in high-dimensional settings.
Author: Malte S. Kurz [aut, cre]
Maintainer: Malte S. Kurz <malte.kurz@stat.uni-muenchen.de>
Diff between pacotest versions 0.3 dated 2018-03-12 and 0.3.1 dated 2019-03-11
DESCRIPTION | 8 ++--- MD5 | 9 ++++-- NEWS.md | 4 ++ tests/testthat/hardCodedResEcorr_rversion_gt3_6_0.csv |only tests/testthat/hardCodedResPacotestRvineSeq_rversion_gt3_6_0.csv |only tests/testthat/hardCodedResPacotestRvineSingleCopula_rversion_gt3_6_0.csv |only tests/testthat/helper-pacotestRegressionTests.R | 15 +++++++--- 7 files changed, 25 insertions(+), 11 deletions(-)
Title: Package Management Tool
Description: Tools to more conveniently perform tasks associated with
add-on packages. pacman conveniently wraps library and package
related functions and names them in an intuitive and consistent
fashion. It seeks to combine functionality from lower level
functions which can speed up workflow.
Author: Tyler Rinker [aut, cre, ctb],
Dason Kurkiewicz [aut, ctb],
Keith Hughitt [ctb],
Albert Wang [ctb],
Garrick Aden-Buie [ctb],
Albert Wang [ctb],
Lukas Burk [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between pacman versions 0.5.0 dated 2018-10-22 and 0.5.1 dated 2019-03-11
pacman-0.5.0/pacman/build |only pacman-0.5.0/pacman/inst/doc |only pacman-0.5.0/pacman/tests |only pacman-0.5.0/pacman/vignettes |only pacman-0.5.1/pacman/DESCRIPTION | 9 +- pacman-0.5.1/pacman/MD5 | 87 +++++++++++------------- pacman-0.5.1/pacman/NEWS | 8 ++ pacman-0.5.1/pacman/R/p_data.R | 4 - pacman-0.5.1/pacman/R/p_install.R | 4 - pacman-0.5.1/pacman/R/p_install_version.R | 2 pacman-0.5.1/pacman/R/p_install_version_gh.R | 2 pacman-0.5.1/pacman/R/p_library.R | 4 - pacman-0.5.1/pacman/R/p_loaded.R | 7 + pacman-0.5.1/pacman/inst/removed |only pacman-0.5.1/pacman/man/p_data.Rd | 4 - pacman-0.5.1/pacman/man/p_install.Rd | 4 - pacman-0.5.1/pacman/man/p_install_version.Rd | 2 pacman-0.5.1/pacman/man/p_install_version_gh.Rd | 2 pacman-0.5.1/pacman/man/p_library.Rd | 4 - pacman-0.5.1/pacman/man/p_loaded.Rd | 7 + 20 files changed, 89 insertions(+), 61 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.16 dated 2017-04-01 and 1.16.1 dated 2019-03-11
ncdf4-1.16.1/ncdf4/DESCRIPTION | 6 +++--- ncdf4-1.16.1/ncdf4/MD5 | 8 +++----- ncdf4-1.16.1/ncdf4/R/ncdf4.R | 2 +- ncdf4-1.16.1/ncdf4/configure.ac |only ncdf4-1.16/ncdf4/tools/aclocal.m4 |only ncdf4-1.16/ncdf4/tools/configure.ac |only ncdf4-1.16/ncdf4/tools/regenerate |only 7 files changed, 7 insertions(+), 9 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [aut] (<https://orcid.org/0000-0002-3603-2691>),
Sydney E. Everhart [ctb, dtc] (<https://orcid.org/0000-0002-5773-1280>),
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb]
(<https://orcid.org/0000-0002-7324-7448>),
Erik Sotka [ctb],
Brian J. Knaus [ctb] (<https://orcid.org/0000-0003-1665-4343>),
Patrick G. Meirmans [ctb] (<https://orcid.org/0000-0002-6395-8107>),
Niklaus J. Grunwald [ths] (<https://orcid.org/0000-0003-1656-7602>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.8.1 dated 2018-08-22 and 2.8.2 dated 2019-03-11
poppr-2.8.1/poppr/vignettes/small_logo.png |only poppr-2.8.2/poppr/DESCRIPTION | 10 poppr-2.8.2/poppr/MD5 | 48 +- poppr-2.8.2/poppr/NEWS | 10 poppr-2.8.2/poppr/R/imsn.R | 42 +- poppr-2.8.2/poppr/R/internal.r | 3 poppr-2.8.2/poppr/R/poppr.R | 315 ++++++++++--------- poppr-2.8.2/poppr/README.md | 6 poppr-2.8.2/poppr/build/vignette.rds |binary poppr-2.8.2/poppr/inst/doc/algo.pdf |binary poppr-2.8.2/poppr/inst/doc/mlg.html | 233 +++++++------- poppr-2.8.2/poppr/inst/doc/poppr_manual.html | 90 +++-- poppr-2.8.2/poppr/man/Aeut.Rd | 10 poppr-2.8.2/poppr/man/Pinf.Rd | 4 poppr-2.8.2/poppr/man/Pram.Rd | 8 poppr-2.8.2/poppr/man/figures |only poppr-2.8.2/poppr/man/imsn.Rd | 41 +- poppr-2.8.2/poppr/man/monpop.Rd | 8 poppr-2.8.2/poppr/man/partial_clone.Rd | 4 poppr-2.8.2/poppr/man/poppr-package.Rd | 322 ++++++++++---------- poppr-2.8.2/poppr/tests/testthat/test-filter.R | 4 poppr-2.8.2/poppr/tests/testthat/test-jackia.R | 4 poppr-2.8.2/poppr/tests/testthat/test-round-robin.R | 6 poppr-2.8.2/poppr/tests/testthat/test-snpclone.R | 4 poppr-2.8.2/poppr/tests/testthat/test-values.R | 4 poppr-2.8.2/poppr/vignettes/the_bibliography.bib | 5 26 files changed, 642 insertions(+), 539 deletions(-)
Title: Wilcoxon-Mann-Whitney Sample Size Planning
Description: Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test
that is needed for a given power and two sided type I error rate. The method works for metric data with and without
ties, count data, ordered categorical data, and even dichotomous data.
But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect.
For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Arne C. Bathke [aut],
Edgar Brunner [aut],
Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Frank Konietschke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between WMWssp versions 0.3.6 dated 2019-03-07 and 0.3.7 dated 2019-03-11
DESCRIPTION | 9 ++++----- MD5 | 12 ++++++------ NAMESPACE | 1 - R/utility.R | 23 +++++++++++++++++++---- README.md | 2 +- tests/testthat/test_MinMax.R | 8 ++++---- tests/testthat/test_WMWssp.R | 10 +++++----- 7 files changed, 39 insertions(+), 26 deletions(-)
Title: Functions for Spatial Thinning of Species Occurrence Records for
Use in Ecological Models
Description: spThin is a set of functions that can be used to spatially thin
species occurrence data. The resulting thinned data can be used in ecological
modeling, such as ecological niche modeling.
Author: Matthew E. Aiello-Lammens, Robert A. Boria, Aleksandar Radosavljevic,
Bruno Vilela, and Robert P. Anderson
Maintainer: Matthew E. Aiello-Lammens <matt.lammens@gmail.com>
Diff between spThin versions 0.1.0 dated 2014-11-17 and 0.1.0.1 dated 2019-03-11
DESCRIPTION | 6 - MD5 | 14 ++-- build/vignette.rds |binary data/Heteromys_anomalus_South_America.rda |binary inst/doc/spThin_vignette.R | 2 inst/doc/spThin_vignette.Rmd | 6 - inst/doc/spThin_vignette.html | 102 +++++++++++++++++------------- vignettes/spThin_vignette.Rmd | 6 - 8 files changed, 70 insertions(+), 66 deletions(-)
Title: Prediction Intervals for Random-Effects Meta-Analysis
Description: An implementation of prediction intervals for random-effects meta-analysis:
Higgins et al. (2009) <doi:10.1111/j.1467-985X.2008.00552.x>, Partlett and Riley (2017)
<doi:10.1002/sim.7140>, and Nagashima et al. (2018) <doi:10.1177/0962280218773520>,
<arXiv:1804.01054>.
Author: Kengo Nagashima [aut, cre] (<https://orcid.org/0000-0003-4529-9045>),
Hisashi Noma [aut],
Toshi A. Furukawa [aut]
Maintainer: Kengo Nagashima <nshi1201@gmail.com>
Diff between pimeta versions 1.1.0 dated 2018-09-14 and 1.1.2 dated 2019-03-11
pimeta-1.1.0/pimeta/R/RcppExports.R |only pimeta-1.1.0/pimeta/man/pima_boot.Rd |only pimeta-1.1.0/pimeta/man/pima_hts.Rd |only pimeta-1.1.0/pimeta/man/pima_htsreml.Rd |only pimeta-1.1.2/pimeta/DESCRIPTION | 10 pimeta-1.1.2/pimeta/MD5 | 82 ++- pimeta-1.1.2/pimeta/NAMESPACE | 9 pimeta-1.1.2/pimeta/NEWS.md | 80 ++- pimeta-1.1.2/pimeta/R/RcppExports.r |only pimeta-1.1.2/pimeta/R/cima-.r |only pimeta-1.1.2/pimeta/R/cima-bc.r |only pimeta-1.1.2/pimeta/R/cima-pl.r |only pimeta-1.1.2/pimeta/R/convert-.r |only pimeta-1.1.2/pimeta/R/data.r | 55 ++ pimeta-1.1.2/pimeta/R/i2h-.r |only pimeta-1.1.2/pimeta/R/pima-.r | 640 ++++++++++++++++++---------- pimeta-1.1.2/pimeta/R/pima-boot.r | 164 +++---- pimeta-1.1.2/pimeta/R/pima-hts.r | 94 +--- pimeta-1.1.2/pimeta/R/pima-htsreml.r | 176 +++---- pimeta-1.1.2/pimeta/R/pwchisq-.r |only pimeta-1.1.2/pimeta/R/tau2h-.r |only pimeta-1.1.2/pimeta/R/tau2h-areml.r |only pimeta-1.1.2/pimeta/R/tau2h-bm.r |only pimeta-1.1.2/pimeta/R/tau2h-dl.r |only pimeta-1.1.2/pimeta/R/tau2h-eb.r |only pimeta-1.1.2/pimeta/R/tau2h-hm.r |only pimeta-1.1.2/pimeta/R/tau2h-hs.r |only pimeta-1.1.2/pimeta/R/tau2h-ml.r |only pimeta-1.1.2/pimeta/R/tau2h-pm.r |only pimeta-1.1.2/pimeta/R/tau2h-reml.r |only pimeta-1.1.2/pimeta/R/tau2h-sj.r |only pimeta-1.1.2/pimeta/R/tau2h-sj2.r |only pimeta-1.1.2/pimeta/R/tau2h-vc.r |only pimeta-1.1.2/pimeta/R/tau2h-wald-ml.r |only pimeta-1.1.2/pimeta/R/tau2h-wald-reml.r |only pimeta-1.1.2/pimeta/R/util-check.r |only pimeta-1.1.2/pimeta/build/vignette.rds |binary pimeta-1.1.2/pimeta/data/hyp.RData |only pimeta-1.1.2/pimeta/data/sbp.RData |binary pimeta-1.1.2/pimeta/inst/doc/pimeta.R |only pimeta-1.1.2/pimeta/inst/doc/pimeta.Rmd | 65 +- pimeta-1.1.2/pimeta/inst/doc/pimeta.html | 230 ++++++++-- pimeta-1.1.2/pimeta/man/cima.Rd |only pimeta-1.1.2/pimeta/man/convert_bin.Rd |only pimeta-1.1.2/pimeta/man/hyp.Rd |only pimeta-1.1.2/pimeta/man/i2h.Rd |only pimeta-1.1.2/pimeta/man/pain.Rd | 10 pimeta-1.1.2/pimeta/man/pima.Rd | 169 ++++--- pimeta-1.1.2/pimeta/man/plot.cima.Rd |only pimeta-1.1.2/pimeta/man/plot.pima.Rd |only pimeta-1.1.2/pimeta/man/print.cima.Rd |only pimeta-1.1.2/pimeta/man/print.pima_tau2h.Rd |only pimeta-1.1.2/pimeta/man/pwchisq.Rd |only pimeta-1.1.2/pimeta/man/sbp.Rd | 5 pimeta-1.1.2/pimeta/man/setshift.Rd | 5 pimeta-1.1.2/pimeta/man/tau2h.Rd |only pimeta-1.1.2/pimeta/src/Makevars |only pimeta-1.1.2/pimeta/src/RcppExports.cpp | 25 - pimeta-1.1.2/pimeta/src/init.c | 6 pimeta-1.1.2/pimeta/src/pi-boot.cpp | 265 +++++++++-- pimeta-1.1.2/pimeta/src/pimeta.h | 10 pimeta-1.1.2/pimeta/vignettes/pimeta.Rmd | 65 +- 62 files changed, 1440 insertions(+), 725 deletions(-)
Title: Testing the Equality of a High Dimensional Set of Densities
Description: The equality of a large number k of densities is tested by measuring the L2 distance between the corresponding kernel density estimators and the one based on the pooled sample. The test even works for sample sizes as small as 2.
Author: Marta Cousido Rocha [aut, cre],
José Carlos Soage González [ctr],
Jacobo de Uña Álvarez [aut, ths],
Jeffrey D. Hart [aut],
Ivan Kojadinovic [cph],
A. Patton [cph],
C. Parmeter [cph],
J. Racine [cph]
Maintainer: Marta Cousido Rocha <martacousido@uvigo.es>
Diff between Equalden.HD versions 1.1 dated 2018-10-24 and 1.2 dated 2019-03-11
DESCRIPTION | 8 +- MD5 | 19 +++--- NAMESPACE | 2 R/Equalden.HDpackage.R | 7 +- R/Equalden.test.HD.R | 133 +++++++++++++++++++++++++++++++-------------- R/Rat.R | 2 R/utilities.R |only man/Equalden.HD-package.Rd | 9 +-- man/Equalden.test.HD.Rd | 6 +- man/Rat.Rd | 2 src/utilities.c | 2 11 files changed, 122 insertions(+), 68 deletions(-)
Title: Robust Tests for Equal Correlation
Description: There are 6 novel robust tests for equal correlation. They are all based on logistic regressions. U are proportion to different types of correlation in 6 methods. The ST1() is based on Pearson correlation. ST2() improved ST1() by using median absolute deviation. ST3() utilized type M correlation and ST4() used Spearman correlation. ST5() and ST6() used two different ways to combine ST3() and ST4(). We highly recommend ST5() according to the passage New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs published in Scientific Reports.
Author: Danyang Yu, Weiliang Qiu, Zeyu Zhang, Kimberly Glass, Jessica Su, Dawn L. DeMeo, Kelan Tantisira, Scott T. Weiss
Maintainer: Danyang Yu <danyangyu@hnu.edu.cn>
Diff between corTest versions 0.9.7 dated 2019-02-11 and 0.9.8 dated 2019-03-11
corTest |only 1 file changed
Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various operations including basic arithmetic, trigonometry operations, and linear algebra operations. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
Diff between cgraph versions 4.0.0 dated 2019-03-08 and 4.0.1 dated 2019-03-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 19 +++++++++++++++---- R/session.R | 2 +- src/internal.c | 8 ++++---- src/math.c | 20 +++++++++++++++++++- src/session.c | 4 ++-- 7 files changed, 51 insertions(+), 22 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-24 0.1.13-4
2018-09-16 0.1.13-3
2018-09-15 0.1.13-2
2018-02-08 0.1.12-5
2017-08-21 0.1.11-8
2017-06-16 0.1.11-2
2017-05-21 0.1.10-10
2017-02-24 0.1.9-20
2017-01-09 0.1.8-17
2016-06-13 0.1.7
Title: Classification with Mixture Modelling
Description: Interface of 'MIXMOD' software for supervised, unsupervised and
semi-supervised classification with mixture modelling.
Author: Florent Langrognet [aut],
Remi Lebret [aut],
Christian Poli [aut],
Serge Iovleff [aut],
Benjamin Auder [aut, cre],
Parmeet Bhatia [ctb],
Anwuli Echenim [ctb],
Serge Iovleff [aut],
Christophe Biernacki [ctb],
Gilles Celeux [ctb],
G<c3><a9>rard Govaert [ctb]
Maintainer: ORPHANED
Diff between Rmixmod versions 2.1.2.1 dated 2019-03-02 and 2.1.2.2 dated 2019-03-11
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- configure | 44 ++++++++++++++++++++++++++++---------------- configure.ac |only data/birds.rda |binary data/car.rda |binary data/finance.rda |binary data/geyser.rda |binary data/heterodata.rda |binary data/heterodatatest.rda |binary data/heterodatatrain.rda |binary data/titanic.rda |binary 12 files changed, 44 insertions(+), 31 deletions(-)
Title: Probabilistic Sex Estimate using Logistic Regression, Based on
VISual Traits of the Human Os Coxae
Description: An R-Shiny application implementing two methods for sexing the human os coxae based on eleven trichotomic traits, following Bruzek (2002) <doi:10.1002/ajpa.10012>.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>)
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>
Diff between PELVIS versions 1.0.5 dated 2018-12-18 and 1.1.0 dated 2019-03-11
PELVIS-1.0.5/PELVIS/data/refData.RData |only PELVIS-1.1.0/PELVIS/DESCRIPTION | 11 ++++++----- PELVIS-1.1.0/PELVIS/LICENSE |only PELVIS-1.1.0/PELVIS/MD5 | 23 +++++++++++++---------- PELVIS-1.1.0/PELVIS/NEWS.md |only PELVIS-1.1.0/PELVIS/README.md |only PELVIS-1.1.0/PELVIS/data/refData.rda |only PELVIS-1.1.0/PELVIS/inst/CITATION | 6 +++--- PELVIS-1.1.0/PELVIS/inst/PELVISShinyApp/server.R | 20 ++++++++++---------- PELVIS-1.1.0/PELVIS/man/PELVIS-package.Rd | 6 +++--- PELVIS-1.1.0/PELVIS/man/StartPELVIS.Rd | 2 +- PELVIS-1.1.0/PELVIS/man/indivSexing.Rd | 2 +- PELVIS-1.1.0/PELVIS/man/refData.Rd | 7 +++---- PELVIS-1.1.0/PELVIS/man/sexingFromFile.Rd | 2 +- PELVIS-1.1.0/PELVIS/man/tenFoldCV.glm.Rd | 2 +- 15 files changed, 42 insertions(+), 39 deletions(-)
Title: Gender Prediction Based on First Names
Description: Utilizes the 'genderize.io' Application Programming Interface
to predict gender from first names extracted from a text vector.
The accuracy of prediction could be controlled by two parameters:
counts of a first name in the database and probability of prediction.
Author: Kamil Wais [aut, cre] (<https://orcid.org/0000-0002-4062-055X>),
Nathan VanHoudnos [ctb],
John Ramey [ctb],
Thomas Klebel [ctb]
Maintainer: Kamil Wais <kamil.wais@gmail.com>
Diff between genderizeR versions 2.0.0 dated 2016-05-11 and 2.1.0 dated 2019-03-11
genderizeR-2.0.0/genderizeR/R/classificatonErrors.R |only genderizeR-2.0.0/genderizeR/man/classificatonErrors.Rd |only genderizeR-2.0.0/genderizeR/tests/testthat/test.R |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-11_b156c60a593a86752d78cab73ba48065.RData |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-11_b156c60a593a86752d78cab73ba48065.rdb |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-11_b156c60a593a86752d78cab73ba48065.rdx |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-12_6eef7bddfd5e752e153c296a47a3d179.RData |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-12_6eef7bddfd5e752e153c296a47a3d179.rdb |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-12_6eef7bddfd5e752e153c296a47a3d179.rdx |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-13_aa9664be6a2c8926769dc1d121de382a.RData |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-13_aa9664be6a2c8926769dc1d121de382a.rdb |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-13_aa9664be6a2c8926769dc1d121de382a.rdx |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-6_6c7967f9a0e9eff284b5fbb7256af045.RData |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-6_6c7967f9a0e9eff284b5fbb7256af045.rdb |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-6_6c7967f9a0e9eff284b5fbb7256af045.rdx |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-7_2b80133cd703367683df4235d858df95.RData |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-7_2b80133cd703367683df4235d858df95.rdb |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-7_2b80133cd703367683df4235d858df95.rdx |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-8_1f302df1360e54e24b088d2fe40beeb6.RData |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-8_1f302df1360e54e24b088d2fe40beeb6.rdb |only genderizeR-2.0.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-8_1f302df1360e54e24b088d2fe40beeb6.rdx |only genderizeR-2.1.0/genderizeR/DESCRIPTION | 32 - genderizeR-2.1.0/genderizeR/MD5 | 124 ++--- genderizeR-2.1.0/genderizeR/NAMESPACE | 1 genderizeR-2.1.0/genderizeR/NEWS | 56 +- genderizeR-2.1.0/genderizeR/R/authorships.R | 16 genderizeR-2.1.0/genderizeR/R/classificationErrors.R | 65 ++ genderizeR-2.1.0/genderizeR/R/findGivenNames.R | 48 +- genderizeR-2.1.0/genderizeR/R/genderize.R | 27 - genderizeR-2.1.0/genderizeR/R/genderizeAPI.R | 43 + genderizeR-2.1.0/genderizeR/R/genderizeBootstrapError.R | 15 genderizeR-2.1.0/genderizeR/R/genderizePredict.R | 13 genderizeR-2.1.0/genderizeR/R/genderizeR.R | 10 genderizeR-2.1.0/genderizeR/R/genderizeTrain.R | 26 - genderizeR-2.1.0/genderizeR/R/givenNamesDB_authorships.R | 15 genderizeR-2.1.0/genderizeR/R/givenNamesDB_titles.R | 16 genderizeR-2.1.0/genderizeR/R/numberOfNames.R | 2 genderizeR-2.1.0/genderizeR/R/textPrepare.R | 13 genderizeR-2.1.0/genderizeR/R/titles.R | 13 genderizeR-2.1.0/genderizeR/README.md | 38 + genderizeR-2.1.0/genderizeR/build/vignette.rds |binary genderizeR-2.1.0/genderizeR/inst/CITATION |only genderizeR-2.1.0/genderizeR/inst/doc/tutorial.R | 4 genderizeR-2.1.0/genderizeR/inst/doc/tutorial.Rmd | 82 ++- genderizeR-2.1.0/genderizeR/inst/doc/tutorial.html | 219 ++++++---- genderizeR-2.1.0/genderizeR/man/authorships.Rd | 17 genderizeR-2.1.0/genderizeR/man/classificationErrors.Rd | 65 ++ genderizeR-2.1.0/genderizeR/man/findGivenNames.Rd | 42 + genderizeR-2.1.0/genderizeR/man/genderize.Rd | 28 - genderizeR-2.1.0/genderizeR/man/genderizeAPI.Rd | 32 + genderizeR-2.1.0/genderizeR/man/genderizeBootstrapError.Rd | 6 genderizeR-2.1.0/genderizeR/man/genderizePredict.Rd | 14 genderizeR-2.1.0/genderizeR/man/genderizeR.Rd | 11 genderizeR-2.1.0/genderizeR/man/genderizeTrain.Rd | 27 - genderizeR-2.1.0/genderizeR/man/givenNamesDB_authorships.Rd | 16 genderizeR-2.1.0/genderizeR/man/givenNamesDB_titles.Rd | 16 genderizeR-2.1.0/genderizeR/man/numberOfNames.Rd | 3 genderizeR-2.1.0/genderizeR/man/textPrepare.Rd | 14 genderizeR-2.1.0/genderizeR/man/titles.Rd | 13 genderizeR-2.1.0/genderizeR/tests/testthat/test-api_functions.R |only genderizeR-2.1.0/genderizeR/tests/testthat/test-nonapi_functions.R |only genderizeR-2.1.0/genderizeR/vignettes/tutorial.Rmd | 82 ++- genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-10_13ae8bc5c10cd0365dd4f04e0d81f4e6.RData |binary genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-10_13ae8bc5c10cd0365dd4f04e0d81f4e6.rdx |binary genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-11_fa2475170c33b88e10d0fc7683d0c7cf.RData |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-11_fa2475170c33b88e10d0fc7683d0c7cf.rdb |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-11_fa2475170c33b88e10d0fc7683d0c7cf.rdx |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-12_625cfb3364a8e5d0f3701264e29d7d32.RData |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-12_625cfb3364a8e5d0f3701264e29d7d32.rdb |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-12_625cfb3364a8e5d0f3701264e29d7d32.rdx |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-13_fdabe790fce8f9761e53df9b8c4bf401.RData |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-13_fdabe790fce8f9761e53df9b8c4bf401.rdb |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-13_fdabe790fce8f9761e53df9b8c4bf401.rdx |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-6_310b31a566aa8ace3389198a2d9fa0a0.RData |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-6_310b31a566aa8ace3389198a2d9fa0a0.rdb |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-6_310b31a566aa8ace3389198a2d9fa0a0.rdx |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-7_1f8a055698d063628a1693dc5b8ef1d7.RData |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-7_1f8a055698d063628a1693dc5b8ef1d7.rdb |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-7_1f8a055698d063628a1693dc5b8ef1d7.rdx |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-8_327fad3093788b371157cfa8d935b6c4.RData |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-8_327fad3093788b371157cfa8d935b6c4.rdb |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-8_327fad3093788b371157cfa8d935b6c4.rdx |only genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-9_5d752865fd9e7ee53c1c95f91e60471a.RData |binary genderizeR-2.1.0/genderizeR/vignettes/tutorial_cache/html/unnamed-chunk-9_5d752865fd9e7ee53c1c95f91e60471a.rdx |binary 84 files changed, 778 insertions(+), 486 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-30 0.99.4
2018-06-04 0.99.3
2018-04-12 0.99.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-15 0.0.2
2017-07-13 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-05 0.1.3
Title: Extensible, Parallelizable Implementation of the Random Forest
Algorithm
Description: Scalable decision tree training and prediction.
Author: Mark Seligman
Maintainer: Mark Seligman <mseligman@suiji.org>
Diff between Rborist versions 0.1-8 dated 2017-08-01 and 0.1-13 dated 2019-03-11
Rborist-0.1-13/Rborist/DESCRIPTION | 16 Rborist-0.1-13/Rborist/MD5 | 181 +-- Rborist-0.1-13/Rborist/NAMESPACE | 1 Rborist-0.1-13/Rborist/R/ForestFloorExport.Rborist.R | 4 Rborist-0.1-13/Rborist/R/PreFormat.R | 7 Rborist-0.1-13/Rborist/R/PreFormat.default.R | 90 + Rborist-0.1-13/Rborist/R/PreTrain.R | 2 Rborist-0.1-13/Rborist/R/PreTrain.default.R | 18 Rborist-0.1-13/Rborist/R/Rborist.R | 2 Rborist-0.1-13/Rborist/R/Rborist.default.R | 380 +++--- Rborist-0.1-13/Rborist/R/Streamline.R | 2 Rborist-0.1-13/Rborist/R/Streamline.default.R | 9 Rborist-0.1-13/Rborist/R/Validate.R | 4 Rborist-0.1-13/Rborist/R/Validate.default.R | 37 Rborist-0.1-13/Rborist/R/predict.Rborist.R | 43 Rborist-0.1-13/Rborist/build/vignette.rds |binary Rborist-0.1-13/Rborist/inst/NEWS | 20 Rborist-0.1-13/Rborist/inst/doc/rborist.R | 3 Rborist-0.1-13/Rborist/inst/doc/rborist.Rmd | 8 Rborist-0.1-13/Rborist/inst/doc/rborist.html | 9 Rborist-0.1-13/Rborist/man/PreFormat.default.Rd | 43 Rborist-0.1-13/Rborist/man/Rborist.Rd | 129 +- Rborist-0.1-13/Rborist/man/Validate.Rd | 32 Rborist-0.1-13/Rborist/man/predict.Rborist.Rd | 7 Rborist-0.1-13/Rborist/src/Makevars | 4 Rborist-0.1-13/Rborist/src/Makevars.win |only Rborist-0.1-13/Rborist/src/bagBridge.cc |only Rborist-0.1-13/Rborist/src/bagBridge.h |only Rborist-0.1-13/Rborist/src/block.cc |only Rborist-0.1-13/Rborist/src/block.h |only Rborist-0.1-13/Rborist/src/blockBridge.cc |only Rborist-0.1-13/Rborist/src/blockBridge.h |only Rborist-0.1-13/Rborist/src/bottom.cc | 422 ++----- Rborist-0.1-13/Rborist/src/bottom.h | 388 +++++- Rborist-0.1-13/Rborist/src/bv.cc | 97 - Rborist-0.1-13/Rborist/src/bv.h | 146 +- Rborist-0.1-13/Rborist/src/callback.cc | 54 Rborist-0.1-13/Rborist/src/callback.h | 31 Rborist-0.1-13/Rborist/src/coproc.cc | 6 Rborist-0.1-13/Rborist/src/coproc.h | 4 Rborist-0.1-13/Rborist/src/coprocrowrank.cc |only Rborist-0.1-13/Rborist/src/decnode.h |only Rborist-0.1-13/Rborist/src/exportBridge.cc |only Rborist-0.1-13/Rborist/src/exportBridge.h |only Rborist-0.1-13/Rborist/src/forest.cc | 357 +---- Rborist-0.1-13/Rborist/src/forest.h | 546 +++++++-- Rborist-0.1-13/Rborist/src/forestBridge.cc |only Rborist-0.1-13/Rborist/src/forestBridge.h |only Rborist-0.1-13/Rborist/src/framemap.cc |only Rborist-0.1-13/Rborist/src/framemap.h |only Rborist-0.1-13/Rborist/src/framemapBridge.cc |only Rborist-0.1-13/Rborist/src/framemapBridge.h |only Rborist-0.1-13/Rborist/src/index.cc | 672 ++++------- Rborist-0.1-13/Rborist/src/index.h | 591 +++++++-- Rborist-0.1-13/Rborist/src/jagged.h |only Rborist-0.1-13/Rborist/src/leaf.cc | 761 +++++++----- Rborist-0.1-13/Rborist/src/leaf.h | 1145 +++++++++++++++---- Rborist-0.1-13/Rborist/src/leafBridge.cc |only Rborist-0.1-13/Rborist/src/leafBridge.h |only Rborist-0.1-13/Rborist/src/level.cc | 555 +++------ Rborist-0.1-13/Rborist/src/level.h | 551 ++++++--- Rborist-0.1-13/Rborist/src/ompthread.cc |only Rborist-0.1-13/Rborist/src/ompthread.h |only Rborist-0.1-13/Rborist/src/path.cc | 11 Rborist-0.1-13/Rborist/src/path.h | 300 ++-- Rborist-0.1-13/Rborist/src/predict.cc | 435 +------ Rborist-0.1-13/Rborist/src/predict.h | 245 ++-- Rborist-0.1-13/Rborist/src/predictBridge.cc |only Rborist-0.1-13/Rborist/src/predictBridge.h |only Rborist-0.1-13/Rborist/src/pretree.cc | 213 +-- Rborist-0.1-13/Rborist/src/pretree.h | 176 +- Rborist-0.1-13/Rborist/src/quant.cc | 206 +-- Rborist-0.1-13/Rborist/src/quant.h | 172 ++ Rborist-0.1-13/Rborist/src/rankedsetBridge.cc |only Rborist-0.1-13/Rborist/src/rankedsetBridge.h |only Rborist-0.1-13/Rborist/src/rcppInit.cc | 8 Rborist-0.1-13/Rborist/src/rcppInit.h |only Rborist-0.1-13/Rborist/src/rowSample.cc |only Rborist-0.1-13/Rborist/src/rowSample.h |only Rborist-0.1-13/Rborist/src/rowrank.cc | 508 +++----- Rborist-0.1-13/Rborist/src/rowrank.h | 416 +++++- Rborist-0.1-13/Rborist/src/runset.cc | 438 ++----- Rborist-0.1-13/Rborist/src/runset.h | 479 ++++++- Rborist-0.1-13/Rborist/src/sample.cc | 316 +---- Rborist-0.1-13/Rborist/src/sample.h | 403 ++++-- Rborist-0.1-13/Rborist/src/samplenux.cc |only Rborist-0.1-13/Rborist/src/samplenux.h |only Rborist-0.1-13/Rborist/src/samplepred.cc | 306 +++-- Rborist-0.1-13/Rborist/src/samplepred.h | 379 +++--- Rborist-0.1-13/Rborist/src/splitcand.cc |only Rborist-0.1-13/Rborist/src/splitcand.h |only Rborist-0.1-13/Rborist/src/splitnode.cc |only Rborist-0.1-13/Rborist/src/splitnode.h |only Rborist-0.1-13/Rborist/src/train.cc | 296 ++-- Rborist-0.1-13/Rborist/src/train.h | 225 +++ Rborist-0.1-13/Rborist/src/trainBridge.cc |only Rborist-0.1-13/Rborist/src/trainBridge.h |only Rborist-0.1-13/Rborist/src/typeparam.h |only Rborist-0.1-13/Rborist/vignettes/rborist.Rmd | 8 Rborist-0.1-8/Rborist/src/coprocsample.cc |only Rborist-0.1-8/Rborist/src/param.h |only Rborist-0.1-8/Rborist/src/predblock.cc |only Rborist-0.1-8/Rborist/src/predblock.h |only Rborist-0.1-8/Rborist/src/rcppArmadilloSample.cc |only Rborist-0.1-8/Rborist/src/rcppExport.cc |only Rborist-0.1-8/Rborist/src/rcppForest.cc |only Rborist-0.1-8/Rborist/src/rcppForest.h |only Rborist-0.1-8/Rborist/src/rcppLeaf.cc |only Rborist-0.1-8/Rborist/src/rcppLeaf.h |only Rborist-0.1-8/Rborist/src/rcppPredblock.cc |only Rborist-0.1-8/Rborist/src/rcppPredblock.h |only Rborist-0.1-8/Rborist/src/rcppPredict.cc |only Rborist-0.1-8/Rborist/src/rcppRowrank.cc |only Rborist-0.1-8/Rborist/src/rcppRowrank.h |only Rborist-0.1-8/Rborist/src/rcppSample.h |only Rborist-0.1-8/Rborist/src/rcppTrain.cc |only Rborist-0.1-8/Rborist/src/response.cc |only Rborist-0.1-8/Rborist/src/response.h |only Rborist-0.1-8/Rborist/src/splitpred.cc |only Rborist-0.1-8/Rborist/src/splitpred.h |only Rborist-0.1-8/Rborist/src/splitsig.cc |only Rborist-0.1-8/Rborist/src/splitsig.h |only 122 files changed, 7703 insertions(+), 5214 deletions(-)