Title: 'Htmlwidgets' in Responsive 'iframes'
Description: Provides two functions 'frameableWidget()', and 'frameWidget()'.
The 'frameableWidget()' is used to add extra code to a 'htmlwidget' which
allows is to be rendered correctly inside a responsive 'iframe'.
The 'frameWidget()' is a 'htmlwidget' which displays content of another 'htmlwidget'
inside a responsive 'iframe'.
These functions allow for easier embedding of 'htmlwidgets' in content management systems
such as 'wordpress', 'blogger' etc.
They also allow for separation of widget content from main HTML content where
CSS of the main HTML could interfere with the widget.
Author: Bhaskar Karambelkar [aut, cre],
Yihui Xie [ctb],
NPR Visual Team [ctb, cph] (pym.js JavaScript library),
Bjørn Klinggaard [ctb, cph] (bLazy.js JavaScript library)
Maintainer: Bhaskar Karambelkar <bhaskarvk@gmail.com>
Diff between widgetframe versions 0.3.0 dated 2017-08-07 and 0.3.1 dated 2017-12-19
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ R/knitr_support.R | 5 +++-- R/widgetframe.R | 24 ++++++++++++++++++++---- build/vignette.rds |binary inst/doc/Using_widgetframe.Rmd | 19 ++++++++++--------- inst/doc/Using_widgetframe.html | 23 ++++++++++++----------- inst/doc/widgetframe_and_knitr.Rmd | 11 +++++++---- inst/doc/widgetframe_and_knitr.html | 17 +++++++++-------- inst/htmlwidgets/widgetframe.yaml | 4 ---- man/frameOptions.Rd | 2 +- vignettes/Using_widgetframe.Rmd | 19 ++++++++++--------- vignettes/widgetframe_and_knitr.Rmd | 11 +++++++---- 14 files changed, 101 insertions(+), 72 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (0000-0003-0645-5666),
RStudio, Inc. [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.1 dated 2017-12-13 and 0.2 dated 2017-12-19
DESCRIPTION | 17 +++++++++-------- MD5 | 14 +++++++------- R/install.R | 48 ++++++++++++++++++++++++++++++++++++------------ R/latex.R | 38 +++++++++++++++++++++++++++++++++----- R/tlmgr.R | 4 +++- README.md | 5 +++-- man/install_tinytex.Rd | 3 ++- man/parse_packages.Rd | 5 ++++- 8 files changed, 97 insertions(+), 37 deletions(-)
Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GWmodel versions 2.0-4 dated 2017-05-21 and 2.0-5 dated 2017-12-19
DESCRIPTION | 10 MD5 | 24 + NAMESPACE | 5 R/BootstrapGWR.r |only R/GeneralizedGWR.r | 681 ++++++++++++++++++++++++++----------------------- R/bw.ggwr.r | 2 R/gwpca.r | 4 R/gwr.psdm.r |only R/zzz.r | 2 man/GWmodel-package.Rd | 4 man/ggwr.basic.Rd | 12 man/gwpca.rd | 3 man/gwr.bootstrap.rd |only man/gwr.psdm.rd |only src/init.c | 2 15 files changed, 406 insertions(+), 343 deletions(-)
Title: Backwards Variable Selection for Paths using M Plus
Description: Primarily for use with datasets containing only categorical variables, although continuous variables may be included as independent variables in paths. Using M Plus, backward variable selection is performed on all Total, Total Indirect, and then Direct effects until none of these effects have p-values greater than the specified target p-value. If there are missing values in the data, imputations are performed using the Mice package. Then selection is performed with the imputed data sets, and results are averaged.
Author: William Terry, Meredith Ray, Hongmei Zhang
Maintainer: William Terry <wterryj6a214@gmail.com>
Diff between PathSelectMP versions 1.0 dated 2016-05-19 and 1.1 dated 2017-12-19
PathSelectMP-1.0/PathSelectMP/R/PathSelectMP.R |only PathSelectMP-1.1/PathSelectMP/DESCRIPTION | 8 +-- PathSelectMP-1.1/PathSelectMP/MD5 | 36 ++++++++++++++- PathSelectMP-1.1/PathSelectMP/R/AddOnAllInd.R |only PathSelectMP-1.1/PathSelectMP/R/AddOnINDStatements.R |only PathSelectMP-1.1/PathSelectMP/R/AllBackwardSelect.R |only PathSelectMP-1.1/PathSelectMP/R/AllSummary.R |only PathSelectMP-1.1/PathSelectMP/R/AllSummary2.R |only PathSelectMP-1.1/PathSelectMP/R/AllTotalEffOutput.R |only PathSelectMP-1.1/PathSelectMP/R/AverageRRs.R |only PathSelectMP-1.1/PathSelectMP/R/CalculatRiskRatios.R |only PathSelectMP-1.1/PathSelectMP/R/CheckVarNames.R |only PathSelectMP-1.1/PathSelectMP/R/ConvertData2.R |only PathSelectMP-1.1/PathSelectMP/R/ConvertData3.R |only PathSelectMP-1.1/PathSelectMP/R/CountImputedEffect.R |only PathSelectMP-1.1/PathSelectMP/R/CreateInitializeMatrix.R |only PathSelectMP-1.1/PathSelectMP/R/CreateSummaryMats.R |only PathSelectMP-1.1/PathSelectMP/R/CreateSummaryMats2.R |only PathSelectMP-1.1/PathSelectMP/R/CreateTotalEffMat.R |only PathSelectMP-1.1/PathSelectMP/R/CreateTotalSummary.R |only PathSelectMP-1.1/PathSelectMP/R/DatImputations.R |only PathSelectMP-1.1/PathSelectMP/R/Initialize.R |only PathSelectMP-1.1/PathSelectMP/R/MPlusBackwardSelect.R |only PathSelectMP-1.1/PathSelectMP/R/NewBinseqWrap.R |only PathSelectMP-1.1/PathSelectMP/R/NewNamesThresh.R |only PathSelectMP-1.1/PathSelectMP/R/NumCat.R |only PathSelectMP-1.1/PathSelectMP/R/NumEndFile.R |only PathSelectMP-1.1/PathSelectMP/R/OnlyNumberElement.R |only PathSelectMP-1.1/PathSelectMP/R/ParseTotalEffects.R |only PathSelectMP-1.1/PathSelectMP/R/ParseTotalEffects2.R |only PathSelectMP-1.1/PathSelectMP/R/PathNames.R |only PathSelectMP-1.1/PathSelectMP/R/Simulate.R |only PathSelectMP-1.1/PathSelectMP/R/SpecialMatch.R |only PathSelectMP-1.1/PathSelectMP/R/TotalRiskRatios.R |only PathSelectMP-1.1/PathSelectMP/R/WriteInitialInpFile.R |only PathSelectMP-1.1/PathSelectMP/R/mod.R |only 36 files changed, 38 insertions(+), 6 deletions(-)
Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and temporarily
modified global state. Many of these functions were originally a part of the
'devtools' package, this provides a simple package with limited dependencies
to provide access to these functions.
Author: Jim Hester [aut, cre],
Kirill Müller [aut],
Kevin Ushey [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Richard Cotton [ctb],
RStudio [cph]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between withr versions 2.1.0 dated 2017-11-01 and 2.1.1 dated 2017-12-19
DESCRIPTION | 20 +++++----- MD5 | 26 +++++++++----- NAMESPACE | 2 + NEWS.md | 16 +++++--- R/file.R |only R/namespace.R | 12 +++--- R/utils.R | 10 +++++ README.md | 1 build |only inst |only man/with_file.Rd |only man/with_package.Rd | 9 ++-- tests/testthat/helper.R |only tests/testthat/test-file.R |only tests/testthat/test-sink.R | 83 --------------------------------------------- vignettes |only 16 files changed, 63 insertions(+), 116 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting
library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface),
Titouan Robert [aut, ctb]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between visNetwork versions 2.0.1 dated 2017-07-30 and 2.0.2 dated 2017-12-19
DESCRIPTION | 13 MD5 | 71 NAMESPACE | 12 NEWS | 15 R/visConfigure.R | 35 R/visEdges.R | 2 R/visExport.R | 2 R/visHclust.R |only R/visIgraph.R | 4 R/visIgraphLayout.R | 4 R/visLegend.R | 6 R/visNetwork.R | 22 R/visNetworkEditor.R |only R/visNetworkProxy.R | 3 R/visNodes.R | 2 R/visTree.R | 53 R/visTreeModule.R | 93 README.md | 22 build/vignette.rds |binary inst/doc/Introduction-to-visNetwork.html | 100 inst/doc/network/edges.html | 2032 +++++++++---------- inst/doc/network/index.html | 3311 +++++++++++++++---------------- inst/doc/network/nodes.html | 2213 ++++++++++---------- inst/htmlwidgets/lib/vis/vis.min.js | 92 inst/htmlwidgets/visNetwork.js | 245 +- inst/htmlwidgets/visNetwork.yaml | 2 man/visConfigure.Rd | 35 man/visEdges.Rd | 2 man/visExport.Rd | 2 man/visHclust.Rd |only man/visLegend.Rd | 4 man/visNetwork-shiny.Rd | 1 man/visNetwork-treeModule.Rd | 6 man/visNetwork.Rd | 11 man/visNetworkEditor-module.Rd |only man/visNetworkEditor.Rd |only man/visNodes.Rd | 2 man/visTree.Rd | 11 man/visTreeEditor.Rd | 9 39 files changed, 4282 insertions(+), 4155 deletions(-)
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
Author: Jeff Hallman <jeffhallman@gmail.com>
Maintainer: Brian Salzer <brian.m.salzer@frb.gov>
Diff between tis versions 1.32 dated 2017-01-26 and 1.34 dated 2017-12-19
DESCRIPTION | 7 ++++--- MD5 | 13 +++++++------ NAMESPACE | 3 --- NEWS | 11 +++++++++++ R/convert.R | 20 +++++++++++--------- R/ti.R | 16 ++++++++++------ R/tis.R | 2 +- src/tis_init.c |only 8 files changed, 44 insertions(+), 28 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package 'randomForest', written by Andy Liaw.
Author: Nicolai Meinshausen
Maintainer: Loris Michel <michel@stat.math.ethz.ch>
Diff between quantregForest versions 1.3-6 dated 2017-11-14 and 1.3-7 dated 2017-12-19
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/quantregForest.R | 18 ++++++++++-------- 3 files changed, 18 insertions(+), 16 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: Bayesian Inference for Multivariate Stochastic Differential
Equations
Description: Implements an MCMC sampler for the posterior distribution of arbitrary time-homogeneous multivariate stochastic differential equation (SDE) models with possibly latent components. The package provides a simple entry point to integrate user-defined models directly with the sampler's C++ code, and parallelizes large portions of the calculations when compiled with 'OpenMP'.
Author: Martin Lysy [aut, cre],
JunYong Tong [aut],
Nigel Delaney [ctb]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between msde versions 1.0.2 dated 2017-10-11 and 1.0.3 dated 2017-12-19
msde-1.0.2/msde/inst/tools |only msde-1.0.3/msde/DESCRIPTION | 8 +- msde-1.0.3/msde/MD5 | 34 ++++----- msde-1.0.3/msde/R/mou.loglik.R | 17 ++-- msde-1.0.3/msde/R/sde.loglik.R | 2 msde-1.0.3/msde/R/sde.post.R | 8 +- msde-1.0.3/msde/R/zzz.R | 8 +- msde-1.0.3/msde/build/vignette.rds |binary msde-1.0.3/msde/inst/doc/msde-exmodels.html | 4 - msde-1.0.3/msde/inst/doc/msde-quicktut.html | 36 ++++----- msde-1.0.3/msde/inst/include/MissGibbsUpdate.h | 24 +++--- msde-1.0.3/msde/inst/include/R |only msde-1.0.3/msde/inst/include/mvnUtils.h | 84 ++++++++++++++++++----- msde-1.0.3/msde/inst/include/sdeInterface.h | 3 msde-1.0.3/msde/inst/include/sdeLogLik.h | 2 msde-1.0.3/msde/inst/include/sdeSim.h | 2 msde-1.0.3/msde/inst/include/sdeUtils.h | 57 ++++++++++++--- msde-1.0.3/msde/man/mou.loglik.Rd | 4 - msde-1.0.3/msde/tests/testthat/msde-test_debug.R | 49 +++++++------ 19 files changed, 222 insertions(+), 120 deletions(-)
Title: The MBESS R Package
Description: Implements methods that useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but at this
point MBESS contains methods applicable and used in a wide variety of fields and is an
orphan acronym, in the sense that what was an acronym is now literally its name. MBESS has
greatly benefited from others, see <http://nd.edu/~kkelley/site/MBESS.html> for a detailed
list of those that have contributed and other details.
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.4.1 dated 2017-11-01 and 4.4.2 dated 2017-12-19
DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/upsilon.R | 81 ++++++++++++++++++++++++++++++++++++++------------------- man/upsilon.Rd | 20 ++++++++------ 4 files changed, 73 insertions(+), 42 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from
'SPSS' or 'Stata' with 'haven' or 'foreign'.
Author: Joseph Larmarange [aut, cre],
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Bojanowski Michał [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 1.0.0 dated 2016-11-20 and 1.0.1 dated 2017-12-19
DESCRIPTION | 18 MD5 | 60 +- NEWS.md | 6 R/as.data.frame.R | 4 R/remove_labels.R | 2 R/to_factor.R | 9 R/to_labelled.R | 63 +- R/var_label.R | 6 README.md | 4 build/vignette.rds |binary inst/doc/intro_labelled.R | 8 inst/doc/intro_labelled.Rmd | 29 inst/doc/intro_labelled.html | 1144 +++++++++++++-------------------------- man/as.data.frame.labelled.Rd | 1 man/copy_labels.Rd | 1 man/labelled.Rd | 3 man/labelled_spss.Rd | 1 man/mean.labelled.Rd | 1 man/na_values.Rd | 7 man/nolabel_to_na.Rd | 1 man/remove_labels.Rd | 5 man/sort_val_labels.Rd | 3 man/to_character.Rd | 1 man/to_factor.Rd | 6 man/to_labelled.Rd | 53 + man/val_labels.Rd | 29 man/val_labels_to_na.Rd | 1 man/var_label.Rd | 5 tests/testthat/test-dataframes.R |only tests/testthat/test-labelled.r | 33 + vignettes/intro_labelled.Rmd | 29 vignettes/intro_labelled.md |only 32 files changed, 651 insertions(+), 882 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between Hmisc versions 4.0-3 dated 2017-05-02 and 4.1-0 dated 2017-12-19
Hmisc-4.0-3/Hmisc/INDEX |only Hmisc-4.0-3/Hmisc/R/inc-dec.s |only Hmisc-4.0-3/Hmisc/man/inc-dec.Rd |only Hmisc-4.1-0/Hmisc/DESCRIPTION | 12 - Hmisc-4.1-0/Hmisc/MD5 | 82 ++++++----- Hmisc-4.1-0/Hmisc/NAMESPACE | 27 +++ Hmisc-4.1-0/Hmisc/NEWS | 34 ++++ Hmisc-4.1-0/Hmisc/R/Misc.s | 25 ++- Hmisc-4.1-0/Hmisc/R/consolidate.s | 4 Hmisc-4.1-0/Hmisc/R/dates.s | 8 - Hmisc-4.1-0/Hmisc/R/describe.s | 64 +++++---- Hmisc-4.1-0/Hmisc/R/dotchartpl.s | 200 ++++++++++++++++++++++++----- Hmisc-4.1-0/Hmisc/R/errbar.s | 2 Hmisc-4.1-0/Hmisc/R/fit.mult.impute.s | 1 Hmisc-4.1-0/Hmisc/R/html.s | 113 ++++++++++++---- Hmisc-4.1-0/Hmisc/R/latex.s | 11 + Hmisc-4.1-0/Hmisc/R/latexCheckOptions.r |only Hmisc-4.1-0/Hmisc/R/popower.s | 123 ++++++++++++++--- Hmisc-4.1-0/Hmisc/R/scat1d.s | 5 Hmisc-4.1-0/Hmisc/R/summary.formula.s | 57 +++----- Hmisc-4.1-0/Hmisc/R/summaryM.s | 7 - Hmisc-4.1-0/Hmisc/R/summaryP.s | 8 - Hmisc-4.1-0/Hmisc/R/transcan.s | 12 + Hmisc-4.1-0/Hmisc/R/wtd.stats.s | 28 +++- Hmisc-4.1-0/Hmisc/R/xtfrm.labelled.s | 2 Hmisc-4.1-0/Hmisc/inst/tests/describe.Rmd |only Hmisc-4.1-0/Hmisc/inst/tests/dotchartpl.r | 64 ++++++++- Hmisc-4.1-0/Hmisc/inst/tests/examples.Rmd | 28 ++++ Hmisc-4.1-0/Hmisc/inst/tests/hoeff.r | 4 Hmisc-4.1-0/Hmisc/inst/tests/simRegOrd.r |only Hmisc-4.1-0/Hmisc/man/Misc.Rd | 12 + Hmisc-4.1-0/Hmisc/man/describe.Rd | 5 Hmisc-4.1-0/Hmisc/man/dotchartpl.Rd | 49 ++++++- Hmisc-4.1-0/Hmisc/man/errbar.Rd | 4 Hmisc-4.1-0/Hmisc/man/histboxp.Rd | 3 Hmisc-4.1-0/Hmisc/man/knitrSet.Rd | 8 - Hmisc-4.1-0/Hmisc/man/latex.Rd | 6 Hmisc-4.1-0/Hmisc/man/latexCheckOptions.Rd |only Hmisc-4.1-0/Hmisc/man/popower.Rd | 52 ++++++- Hmisc-4.1-0/Hmisc/man/simRegOrd.Rd |only Hmisc-4.1-0/Hmisc/man/summarize.Rd | 9 - Hmisc-4.1-0/Hmisc/man/summaryP.Rd | 16 +- Hmisc-4.1-0/Hmisc/man/trunc.POSIXt.Rd | 35 ++--- Hmisc-4.1-0/Hmisc/man/upFirst.Rd | 2 Hmisc-4.1-0/Hmisc/man/wtd.stats.Rd | 4 Hmisc-4.1-0/Hmisc/man/yearDays.Rd | 10 - 46 files changed, 844 insertions(+), 292 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Mike Bostock [cph] (d3.js),
Speros Kokenes [cph] (d3-lasso)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.4.1 dated 2017-09-05 and 0.4.2 dated 2017-12-19
ggiraph-0.4.1/ggiraph/inst/doc/an_introduction.R |only ggiraph-0.4.1/ggiraph/inst/doc/an_introduction.Rmd |only ggiraph-0.4.1/ggiraph/inst/doc/an_introduction.html |only ggiraph-0.4.1/ggiraph/inst/doc/custom_animation_effects.R |only ggiraph-0.4.1/ggiraph/inst/doc/custom_animation_effects.Rmd |only ggiraph-0.4.1/ggiraph/inst/doc/custom_animation_effects.html |only ggiraph-0.4.1/ggiraph/inst/doc/shiny_usage.R |only ggiraph-0.4.1/ggiraph/inst/doc/shiny_usage.Rmd |only ggiraph-0.4.1/ggiraph/inst/doc/shiny_usage.html |only ggiraph-0.4.1/ggiraph/inst/htmlwidgets/lib/ggiraph-0.2.0 |only ggiraph-0.4.1/ggiraph/vignettes/an_introduction.Rmd |only ggiraph-0.4.1/ggiraph/vignettes/custom_animation_effects.Rmd |only ggiraph-0.4.1/ggiraph/vignettes/shiny_usage.Rmd |only ggiraph-0.4.2/ggiraph/DESCRIPTION | 11 ggiraph-0.4.2/ggiraph/MD5 | 80 +-- ggiraph-0.4.2/ggiraph/NAMESPACE | 17 ggiraph-0.4.2/ggiraph/NEWS | 9 ggiraph-0.4.2/ggiraph/R/geom_histogram_interactive.R |only ggiraph-0.4.2/ggiraph/R/geom_path_interactive.R | 19 ggiraph-0.4.2/ggiraph/R/geom_rect_interactive.R | 15 ggiraph-0.4.2/ggiraph/R/geom_segment_interactive.R | 8 ggiraph-0.4.2/ggiraph/R/ggiraph.R | 225 ++++---- ggiraph-0.4.2/ggiraph/R/utils.R | 41 + ggiraph-0.4.2/ggiraph/R/zz_geom_bar_interactive.r | 1 ggiraph-0.4.2/ggiraph/README.md | 47 + ggiraph-0.4.2/ggiraph/build/vignette.rds |binary ggiraph-0.4.2/ggiraph/inst/doc/overview.Rmd |only ggiraph-0.4.2/ggiraph/inst/doc/overview.html |only ggiraph-0.4.2/ggiraph/inst/htmlwidgets/ggiraph.js | 259 +--------- ggiraph-0.4.2/ggiraph/inst/htmlwidgets/ggiraph.yaml | 10 ggiraph-0.4.2/ggiraph/inst/htmlwidgets/lib/ggiraph-0.3.0 |only ggiraph-0.4.2/ggiraph/inst/medias |only ggiraph-0.4.2/ggiraph/inst/rmd/flexdashboard/flexdashboard.Rmd | 3 ggiraph-0.4.2/ggiraph/inst/shiny/crimes/server.R | 3 ggiraph-0.4.2/ggiraph/inst/shiny/crimes/ui.R | 4 ggiraph-0.4.2/ggiraph/inst/shiny/iris/server.R | 2 ggiraph-0.4.2/ggiraph/man/geom_bar_interactive.Rd | 1 ggiraph-0.4.2/ggiraph/man/geom_boxplot_interactive.Rd | 2 ggiraph-0.4.2/ggiraph/man/geom_histogram_interactive.Rd |only ggiraph-0.4.2/ggiraph/man/geom_map_interactive.Rd | 2 ggiraph-0.4.2/ggiraph/man/geom_path_interactive.Rd | 1 ggiraph-0.4.2/ggiraph/man/geom_point_interactive.Rd | 17 ggiraph-0.4.2/ggiraph/man/geom_polygon_interactive.Rd | 2 ggiraph-0.4.2/ggiraph/man/geom_rect_interactive.Rd | 3 ggiraph-0.4.2/ggiraph/man/geom_segment_interactive.Rd | 2 ggiraph-0.4.2/ggiraph/man/geom_text_interactive.Rd | 2 ggiraph-0.4.2/ggiraph/man/ggiraph.Rd | 67 +- ggiraph-0.4.2/ggiraph/vignettes/overview.Rmd |only 48 files changed, 400 insertions(+), 453 deletions(-)
Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed
by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is
estimated such that it maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore, avoids an iteration
between model fitting and balance checking. The package also implements several
extensions of the CBPS beyond the cross-sectional, binary treatment setting.
The current version implements the CBPS for longitudinal settings so that it can
be used in conjunction with marginal structural models from Imai and Ratkovic
(2015) <DOI:10.1080/01621459.2014.956872>, treatments with three- and four-
valued treatment variables, continuous-valued treatments from Fong, Hazlett,
and Imai (2015) <http://imai.princeton.edu/research/files/CBGPS.pdf>, and the
situation with multiple distinct binary treatments administered simultaneously.
In the future it will be extended to other settings including the generalization
of experimental and instrumental variable estimates. Recently we have added the
optimal CBPS which chooses the optimal balancing function and results in doubly
robust and efficient estimator for the treatment effect as well as high dimensional
CBPS when a large number of covariates exist.
Author: Christian Fong [aut, cre],
Marc Ratkovic [aut],
Kosuke Imai [aut],
Chad Hazlett [ctb],
Xiaolin Yang [ctb],
Sida Peng [ctb]
Maintainer: Christian Fong <christianfong@stanford.edu>
Diff between CBPS versions 0.15 dated 2017-11-26 and 0.16 dated 2017-12-19
ChangeLog | 3 ++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/CBPSBinary.R | 7 ++++++- man/CBPS.Rd | 1 + man/balance.Rd | 3 ++- man/plot.CBPS.Rd | 5 +++-- tests/testthat/test-all.R | 12 ++++++++++++ 8 files changed, 37 insertions(+), 16 deletions(-)
Title: Bayesian Variable Selection in High Dimensional Settings using
Non-Local Prior
Description: Variable/Feature selection in high or ultra-high dimensional
settings has gained a lot of attention recently specially in cancer genomic
studies. This package provides a Bayesian approach to tackle this problem,
where it exploits mixture of point masses at zero and nonlocal priors to
improve the performance of variable selection and coefficient estimation.
It performs variable selection for binary response and survival time
response datasets which are widely used in biostatistic and bioinformatics
community. Benefiting from parallel computing ability, it reports necessary
outcomes of Bayesian variable selection such as Highest Posterior
Probability Model (HPPM), Median Probability Model (MPM) and posterior
inclusion probability for each of the covariates in the model. The option
to use Bayesian Model Averaging (BMA) is also part of this package that can
be exploited for predictive power measurements in real datasets.
Author: Amir Nikooienejad [aut, cre]
Maintainer: Amir Nikooienejad <amir@stat.tamu.edu>
Diff between BVSNLP versions 0.9.5 dated 2017-12-18 and 0.9.6 dated 2017-12-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/zzz.R | 2 +- src/Functions.cpp | 8 +++++--- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Bridge Sampling for Marginal Likelihoods and Bayes Factors
Description: Provides functions for estimating marginal likelihoods, Bayes
factors, posterior model probabilities, and normalizing constants in general,
via different versions of bridge sampling (Meng & Wong, 1996,
<http://www3.stat.sinica.edu.tw/statistica/j6n4/j6n43/j6n43.htm>).
Author: Quentin F. Gronau [aut, cre] (<https://orcid.org/0000-0001-5510-6943>),
Henrik Singmann [aut] (<https://orcid.org/0000-0002-4842-3657>),
Jonathan J. Forster [ctb],
Eric-Jan Wagenmakers [ths],
The JASP Team [ctb],
Jiqiang Guo [ctb],
Jonah Gabry [ctb],
Ben Goodrich [ctb]
Maintainer: Quentin F. Gronau <Quentin.F.Gronau@gmail.com>
Diff between bridgesampling versions 0.3-0 dated 2017-10-22 and 0.4-0 dated 2017-12-19
bridgesampling-0.3-0/bridgesampling/tests/testthat/test-bf_print_method.R |only bridgesampling-0.4-0/bridgesampling/DESCRIPTION | 10 bridgesampling-0.4-0/bridgesampling/MD5 | 41 +- bridgesampling-0.4-0/bridgesampling/NAMESPACE | 6 bridgesampling-0.4-0/bridgesampling/NEWS | 156 +++++++--- bridgesampling-0.4-0/bridgesampling/R/bf.R | 16 - bridgesampling-0.4-0/bridgesampling/R/bridge_methods.R |only bridgesampling-0.4-0/bridgesampling/R/bridge_sampler.R | 34 -- bridgesampling-0.4-0/bridgesampling/R/error_measures.R | 52 ++- bridgesampling-0.4-0/bridgesampling/R/post_prob.R | 13 bridgesampling-0.4-0/bridgesampling/inst/doc/bridgesampling_example_jags.html | 4 bridgesampling-0.4-0/bridgesampling/inst/doc/bridgesampling_example_stan.html | 4 bridgesampling-0.4-0/bridgesampling/inst/doc/bridgesampling_paper.pdf |binary bridgesampling-0.4-0/bridgesampling/inst/doc/bridgesampling_stan_ttest.Rmd | 2 bridgesampling-0.4-0/bridgesampling/inst/doc/bridgesampling_stan_ttest.html | 6 bridgesampling-0.4-0/bridgesampling/inst/doc/bridgesampling_tutorial.pdf |binary bridgesampling-0.4-0/bridgesampling/man/bridge-methods.Rd |only bridgesampling-0.4-0/bridgesampling/man/bridge_sampler.Rd | 3 bridgesampling-0.4-0/bridgesampling/man/error_measures.Rd | 33 +- bridgesampling-0.4-0/bridgesampling/tests/testthat/test-bf.R |only bridgesampling-0.4-0/bridgesampling/tests/testthat/test-bridge_sampler_mcmc.list.R | 22 + bridgesampling-0.4-0/bridgesampling/tests/testthat/test-bridge_sampler_summary_method.R |only bridgesampling-0.4-0/bridgesampling/tests/testthat/test-post_prob.R | 4 bridgesampling-0.4-0/bridgesampling/vignettes/bridgesampling_stan_ttest.Rmd | 2 24 files changed, 281 insertions(+), 127 deletions(-)
More information about bridgesampling at CRAN
Permanent link
Title: Recurrent Event Data Analysis
Description: Functions for (1) simulating survival and recurrent event data from
stochastic process point of view, (2) exploring and modeling recurrent event
data through the mean cumulative function (MCF) or also called the
Nelson-Aalen estimator of the cumulative hazard rate function, and gamma
frailty model with spline rate function, and (3) comparing two-sample
recurrent event responses with the pseudo-score tests.
Author: Wenjie Wang [aut, cre],
Haoda Fu [aut],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between reda versions 0.4.0 dated 2017-12-18 and 0.4.1 dated 2017-12-19
DESCRIPTION | 20 ++++++++++---------- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ inst/CITATION | 4 ++-- inst/doc/reda-intro.html | 4 ++-- inst/doc/reda-simulate.html | 6 +++--- src/relativeRisk.cpp | 12 ++++++------ 7 files changed, 36 insertions(+), 29 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging and a distance based on global alignment kernels
are also provided. All included distance functions have custom loops
optimized for the calculation of cross-distance matrices, including
parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.0.0 dated 2017-12-09 and 5.1.0 dated 2017-12-19
DESCRIPTION | 15 MD5 | 105 - NAMESPACE | 3 R/SparseDistmat.R | 228 +- R/TSClusters-methods.R | 2184 +++++++++++++-------------- R/all-cent2.R | 491 +++--- R/compare-clusterings.R | 52 R/dtw-basic.R | 528 +++--- R/globals-internal.R | 12 R/partitional-fuzzy.R | 284 +-- R/pkg.R | 344 ++-- R/sdtw-cent.R |only R/sdtw.R |only R/tsclust.R | 1675 ++++++++++---------- R/utils.R | 644 ++++--- inst/NEWS.Rd | 19 inst/doc/dtwclust.pdf |binary inst/include/dtwclust.hpp | 17 man/dtw_basic.Rd | 22 man/sdtw.Rd |only man/sdtw_cent.Rd |only man/tsclust.Rd | 16 src/dtwclust++.h | 10 src/init.cpp | 5 src/sdtw-cent.cpp |only src/sdtw-loop.cpp |only src/soft-dtw.cpp |only tests/testthat.R | 4 tests/testthat/acceptance/dtwb.R | 2 tests/testthat/acceptance/gak.R | 76 tests/testthat/acceptance/lbs.R | 210 +- tests/testthat/acceptance/symmetric-proxy.R | 2 tests/testthat/integration/custom-dist.R | 130 - tests/testthat/integration/families.R | 70 tests/testthat/integration/proxy.R | 233 +- tests/testthat/regression/clusterings.R | 168 +- tests/testthat/regression/comparisons.R | 55 tests/testthat/regression/custom-dist.R | 8 tests/testthat/regression/cvis.R | 62 tests/testthat/regression/dtwb.R | 6 tests/testthat/regression/family-centroids.R | 26 tests/testthat/regression/family-distmat.R | 65 tests/testthat/regression/proxy.R | 98 - tests/testthat/system/comparisons.R | 598 +++---- tests/testthat/system/data-formats.R | 90 - tests/testthat/system/fuzzy.R | 8 tests/testthat/system/hierarchical.R | 212 +- tests/testthat/system/invalid-inputs.R | 364 ++-- tests/testthat/system/partitional.R | 24 tests/testthat/system/preproc.R | 106 - tests/testthat/test-06-parallel.R | 24 tests/testthat/unit/centroids.R | 92 + tests/testthat/unit/configs.R | 290 +-- tests/testthat/unit/cvis.R | 2 tests/testthat/unit/distances.R | 550 +++--- tests/testthat/unit/methods.R | 2 tests/testthat/unit/misc.R | 2 57 files changed, 5316 insertions(+), 4917 deletions(-)
Title: Interface to the 'g:Profiler' Toolkit
Description: Functional enrichment analysis, gene identifier conversion and
mapping homologous genes across related organisms via the 'g:Profiler' toolkit
(<https://biit.cs.ut.ee/gprofiler/>).
Author: Juri Reimand <juri.reimand@ut.ee>, Raivo Kolde
<rkolde@gmail.com>, Tambet Arak <tambet.arak@gmail.com>
Maintainer: Ivan Kuzmin <ivan.kuzmin@ut.ee>
Diff between gProfileR versions 0.6.1 dated 2016-04-27 and 0.6.2 dated 2017-12-19
ChangeLog | 5 +++++ DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 11 +++++------ R/gProfileR.R | 26 +++++++++++++++++--------- man/gconvert.Rd | 11 ++++++----- man/get_base_url.Rd | 1 - man/get_user_agent.Rd | 1 - man/gorth.Rd | 11 ++++++----- man/gprofiler.Rd | 13 ++++++++----- man/set_base_url.Rd | 3 +-- man/set_user_agent.Rd | 1 - 12 files changed, 65 insertions(+), 52 deletions(-)
Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning,
including origin-destination analysis, route allocation and modelling travel
patterns.
Author: Robin Lovelace [aut, cre] (0000-0001-5679-6536),
Richard Ellison [aut],
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Malcolm Morgan [ctb] (Co-author of angle_diff),
Nikolai Berkoff [ctb] (Co-author of line2route),
Scott Chamberlin [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.2.1 dated 2017-11-23 and 0.2.2 dated 2017-12-19
DESCRIPTION | 10 +-- MD5 | 97 +++++++++++++++++++------------------- NAMESPACE | 11 +++- NEWS.md | 11 ++++ R/SpatialLinesNetwork.R | 4 - R/aggregate_funs.R | 76 +++++++++++++---------------- R/catchmentArea.R | 2 R/crs-funs.R | 22 +++----- R/cyclestreets.R | 2 R/data.r | 10 +-- R/geo-functions.R | 3 - R/geo_projected.R | 26 ++++------ R/google-functions.R | 2 R/line_match.R | 2 R/line_sample.R | 6 +- R/linefuns.R | 21 +++----- R/od-funs.R | 3 - R/od_coords.R | 5 + R/oneway.R | 2 R/osrmfunctions.R | 4 - R/overline.R | 8 +-- R/route-transport-api.R | 2 R/routes.R | 4 - R/stplanr-package.R | 2 R/toptail.R | 21 ++++---- build/vignette.rds |binary demo/route-analysis.R | 4 - inst/doc/introducing-stplanr.html | 24 ++++----- inst/doc/stplanr-paper.R | 2 inst/doc/stplanr-paper.Rmd | 2 man/buff_geo.Rd | 11 ++-- man/ca_local.Rd | 2 man/cents.Rd | 4 - man/crs_select_aeq.Rd | 5 - man/destination_zones.Rd | 4 - man/gclip.Rd | 1 man/geo_bb.Rd | 2 man/geo_buffer.Rd | 1 man/geo_projected.Rd | 5 - man/geo_select_aeq.Rd | 10 +-- man/line_segment.Rd | 9 --- man/od2line.Rd | 2 man/od_aggregate.Rd | 17 +----- man/od_coords.Rd | 3 - man/points2line.Rd | 1 man/reproject.Rd | 9 --- man/sp_aggregate.Rd | 7 +- man/toptailgs.Rd | 4 - src/Makevars |only vignettes/stplanr-paper.Rmd | 2 50 files changed, 232 insertions(+), 255 deletions(-)
Title: Regression Modelling using I-Priors
Description: Provides methods to perform and analyse I-prior regression models.
Estimation is done either via direct optimisation of the log-likelihood or
an EM algorithm.
Author: Haziq Jamil [aut, cre]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between iprior versions 0.7.0 dated 2017-11-03 and 0.7.1 dated 2017-12-19
iprior-0.7.0/iprior/man/kernL_old.Rd |only iprior-0.7.0/iprior/tests/testthat/test-05-fitted_and_predict.R |only iprior-0.7.0/iprior/tests/testthat/test-06-plots.R |only iprior-0.7.0/iprior/tests/testthat/test-07-ipriorMod_methods.R |only iprior-0.7.0/iprior/tests/testthat/test-08-iprior_helpers.R |only iprior-0.7.0/iprior/tests/testthat/test-09-utilities.R |only iprior-0.7.0/iprior/vignettes/iprior2_test.Rmd |only iprior-0.7.1/iprior/DESCRIPTION | 8 iprior-0.7.1/iprior/MD5 | 97 - iprior-0.7.1/iprior/NAMESPACE | 46 iprior-0.7.1/iprior/NEWS.md | 11 iprior-0.7.1/iprior/R/Accessor_functions.R | 35 iprior-0.7.1/iprior/R/Data.R | 76 iprior-0.7.1/iprior/R/Kernel_functions.R | 19 iprior-0.7.1/iprior/R/Kernel_loader.R | 124 - iprior-0.7.1/iprior/R/Kernel_loader_helper.R | 63 iprior-0.7.1/iprior/R/LEGACY-Kernel_functions.R | 376 +-- iprior-0.7.1/iprior/R/LEGACY-Kernel_loader.R | 942 +++++----- iprior-0.7.1/iprior/R/LEGACY-Utilities.R | 485 ++--- iprior-0.7.1/iprior/R/Namespace.R | 13 iprior-0.7.1/iprior/R/Plots.R | 9 iprior-0.7.1/iprior/R/Utilities.R | 150 + iprior-0.7.1/iprior/R/fitted_and_predict.R | 54 iprior-0.7.1/iprior/R/iprior.R | 44 iprior-0.7.1/iprior/R/ipriorMod_methods.R | 77 iprior-0.7.1/iprior/R/iprior_cv.R |only iprior-0.7.1/iprior/R/iprior_est_em_closed.R | 4 iprior-0.7.1/iprior/R/iprior_est_parallel.R | 10 iprior-0.7.1/iprior/R/iprior_helper.R | 22 iprior-0.7.1/iprior/README.md | 9 iprior-0.7.1/iprior/build/vignette.rds |binary iprior-0.7.1/iprior/data/tecator.cv.rda |only iprior-0.7.1/iprior/inst/doc/iprior_paper.pdf |binary iprior-0.7.1/iprior/inst/doc/kernel_matrix.R | 4 iprior-0.7.1/iprior/inst/doc/kernel_matrix.Rmd | 5 iprior-0.7.1/iprior/inst/doc/kernel_matrix.html | 83 iprior-0.7.1/iprior/inst/doc/tecator.R |only iprior-0.7.1/iprior/inst/doc/tecator.Rmd |only iprior-0.7.1/iprior/inst/doc/tecator.html |only iprior-0.7.1/iprior/man/Accessors.Rd | 16 iprior-0.7.1/iprior/man/iprior.Rd | 11 iprior-0.7.1/iprior/man/iprior_cv.Rd |only iprior-0.7.1/iprior/man/is.iprior_x.Rd | 3 iprior-0.7.1/iprior/man/kernL.Rd | 15 iprior-0.7.1/iprior/man/plot.ipriorMod.Rd | 4 iprior-0.7.1/iprior/man/pollution.Rd | 3 iprior-0.7.1/iprior/man/tecator.cv.Rd |only iprior-0.7.1/iprior/tests/testthat/test-01-kernels.R | 14 iprior-0.7.1/iprior/tests/testthat/test-02-kernel_loader.R | 49 iprior-0.7.1/iprior/tests/testthat/test-03-kernel_loader_helpers.R | 152 - iprior-0.7.1/iprior/tests/testthat/test-04-iprior.R | 6 iprior-0.7.1/iprior/tests/testthat/test-05-iprior_cv.R |only iprior-0.7.1/iprior/tests/testthat/test-06-fitted_and_predict.R |only iprior-0.7.1/iprior/tests/testthat/test-07-plots.R |only iprior-0.7.1/iprior/tests/testthat/test-08-ipriorMod_methods.R |only iprior-0.7.1/iprior/tests/testthat/test-09-iprior_helpers.R |only iprior-0.7.1/iprior/tests/testthat/test-10-utilities.R |only iprior-0.7.1/iprior/tests/testthat/test-LEGACY-kernel_loader.R | 134 - iprior-0.7.1/iprior/vignettes/kernel_matrix.Rmd | 5 iprior-0.7.1/iprior/vignettes/tecator.Rmd |only 60 files changed, 1775 insertions(+), 1403 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-09 1.0-10-1
2015-05-15 1.0-8
2015-05-13 1.0-7
2015-02-03 1.0-6
2015-01-05 1.0-5
2014-04-14 1.0-4
2014-02-12 1.0-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-09 1.1-0
2013-08-31 1.0-319
2012-08-01 1.0-249
2012-02-24 1.0-208
2011-10-17 1.0-191
2010-09-19 1.0-130
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-08 0.1-3-1
2017-07-08 0.1-3-2
2016-03-01 0.1-2
2016-02-29 0.1-1
2015-06-26 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-09 0.2-0
2015-02-06 0.1-360
2013-08-31 0.1-317
2013-06-22 0.1-315
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-09 1.4-1
2015-07-06 1.4-0
2012-09-06 1.3-250
2012-01-17 1.3-200
2011-10-17 1.3-190
2011-06-01 1.3-182
2010-10-09 1.2-139
2010-09-20 1.2-131
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.15-244 dated 2015-09-01 and 0.17-353 dated 2017-12-19
ChangeLog | 99 +++++++++------- DESCRIPTION | 8 - MD5 | 40 +++--- R/Rhpc.R | 54 ++++---- R/RhpcExt.R | 6 cleanup | 1 configure | 34 +++-- configure.ac | 4 src/Makevars.in | 2 src/Makevars.win | 7 - src/RhpcMPI.c | 224 ++++++++++++++++++++++++++++++++++++- src/common/Rhpc.h | 11 + src/common/Rhpc_ms.h | 6 src/common/fakemaster.h |only src/registerDynamicSymbol.c |only src/worker/Makefile.in | 2 src/worker/Makefile.win | 23 ++- src/worker/RhpcSpawnWin.cmd.in |only src/worker/RhpcWorker.c | 27 ++-- src/worker/RhpcWorker_LapplyLB.h | 8 - src/worker/RhpcWorker_Lapplyseq.h | 11 - src/worker/RhpcWorker_WorkerCall.h | 14 +- src/worker/fakemaster.c |only 23 files changed, 429 insertions(+), 152 deletions(-)
Title: Implements Measures for the Comparison of Two Partitions
Description: Provides several measures ((dis)similarity, distance/metric,
correlation, entropy) for comparing two partitions of the same set of
objects. The different measures can be assigned to three different
classes: Pair comparison (containing the famous Jaccard and Rand
indices), set based, and information theory based.
Many of the implemented measures can be found in
Albatineh AN, Niewiadomska-Bugaj M and Mihalko D (2006)
<doi:10.1007/s00357-006-0017-z> and
Meila M (2007) <doi:10.1016/j.jmva.2006.11.013>.
Partitions are represented by vectors of class labels which allow a
straightforward integration with existing clustering algorithms
(e.g. kmeans()). The package is mostly based on the S4 object system.
Author: Fabian Ball [aut, cre, cph, ctb],
Andreas Geyer-Schulz [cph]
Maintainer: Fabian Ball <fabian.ball@kit.edu>
Diff between partitionComparison versions 0.2.2 dated 2017-08-25 and 0.2.3 dated 2017-12-19
DESCRIPTION | 10 +-- MD5 | 88 +++++++++++++-------------- R/aab-helper.R | 12 +-- R/informationtheory_based.R | 22 ++++-- R/pair_counting.R | 119 ++++++++++++++++++------------------- R/set_based.R | 12 +-- build/partial.rdb |binary man/adjustedRandIndex.Rd | 4 - man/baulieu1.Rd | 4 - man/baulieu2.Rd | 4 - man/classificationErrorDistance.Rd | 4 - man/computePairCoefficients.Rd | 8 +- man/czekanowski.Rd | 4 - man/dongensMetric.Rd | 4 - man/entropy.Rd | 8 +- man/fagerMcGowan.Rd | 4 - man/folwkesMallowsIndex.Rd | 4 - man/gammaStatistics.Rd | 4 - man/goodmanKruskal.Rd | 4 - man/gowerLegendre.Rd | 4 - man/hamann.Rd | 3 man/jaccardCoefficient.Rd | 4 - man/kulczynski.Rd | 4 - man/larsenAone.Rd | 4 - man/lermanIndex.Rd | 4 - man/mcconnaughey.Rd | 4 - man/minkowskiMeasure.Rd | 4 - man/mirkinMetric.Rd | 4 - man/mutualInformation.Rd | 4 - man/normalizedLermanIndex.Rd | 4 - man/normalizedMutualInformation.Rd | 11 ++- man/pearson.Rd | 4 - man/peirce.Rd | 3 man/projectionNumber.Rd | 2 man/randIndex.Rd | 4 - man/rogersTanimoto.Rd | 4 - man/russelRao.Rd | 4 - man/rvCoefficient.Rd | 4 - man/sokalSneath1.Rd | 4 - man/sokalSneath2.Rd | 4 - man/sokalSneath3.Rd | 4 - man/variationOfInformation.Rd | 5 - man/wallaceI.Rd | 3 man/wallaceII.Rd | 4 - tests/testthat/test-helper.R | 6 - 45 files changed, 222 insertions(+), 206 deletions(-)
More information about partitionComparison at CRAN
Permanent link
Title: Bayesian Nonparametric Modeling in R
Description: Functions to perform inference via
simulation from the posterior distributions for Bayesian
nonparametric and semiparametric models. Although the name of
the package was motivated by the Dirichlet Process prior, the
package considers and will consider other priors on functional
spaces. So far, DPpackage includes models considering Dirichlet
Processes, Dependent Dirichlet Processes, Dependent Poisson-
Dirichlet Processes, Hierarchical Dirichlet Processes, Polya
Trees, Linear Dependent Tailfree Processes, Mixtures of
Triangular distributions, Random Bernstein polynomials priors
and Dependent Bernstein Polynomials. The package also includes
models considering Penalized B-Splines.
Includes semiparametric models for marginal and conditional
density estimation, ROC curve analysis, interval censored data,
binary regression models, generalized linear mixed models, IRT
type models, and generalized additive models. Also
contains functions to compute Pseudo-Bayes factors for model
comparison, and to elicitate the precision parameter of the
Dirichlet Process. To maximize computational efficiency, the
actual sampling for each model is done in compiled FORTRAN. The
functions return objects which can be subsequently analyzed
with functions provided in the 'coda' package.
Author: Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando
Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Maintainer: ORPHANED
Diff between DPpackage versions 1.1-7.1 dated 2017-12-05 and 1.1-7.2 dated 2017-12-19
DESCRIPTION | 6 ++--- MD5 | 56 ++++++++++++++++++++++++------------------------ src/DPMdencens.f | 5 +--- src/DPMrasch.f | 4 +-- src/DPMraschpoisson.f | 11 ++++----- src/DPMraschpoissonh.f | 9 +++---- src/DPrasch.f | 7 ++---- src/DPraschpoisson.f | 5 +--- src/HDPMdensity.f | 2 - src/LDBDPdensity.f | 2 - src/LDDPdensity.f | 4 +-- src/LDDPrasch.f | 3 -- src/LDDPraschpoisson.f | 3 -- src/LDDPtwopl.f | 14 +++++------- src/LDPDdoublyintsba.f | 10 +++----- src/LDTFPdensity.f | 26 +++------------------- src/LDTFPglmmpois.f | 19 +++------------- src/LDTFPsurvival.f | 24 +++----------------- src/PSgamprob.f | 1 src/PTmdensity.f | 4 +-- src/PTmdensityf.f | 5 +--- src/PTmdensityp.f | 4 +-- src/PTrasch.f | 17 ++++---------- src/PTraschpoisson.f | 19 +++++----------- src/ToolsLDTFP.f | 27 +++++++++++------------ src/ToolsPTsampler.f | 14 +++--------- src/ToolsRSBA.f | 12 +++++----- src/ToolsSB.f | 1 src/ToolsSparseMatrix.f | 20 ++++++++--------- 29 files changed, 127 insertions(+), 207 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-04 0.1.2
2015-11-28 0.1.1
2015-11-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-29 2.1
2015-12-26 0.99.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-14 0.2.0
2015-10-31 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-07 2.16.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-12 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-25 0.3
2016-05-26 0.2
2015-03-11 0.1
Title: Geometrically Designed Spline Regression
Description: Geometrically Designed Spline ('GeDS') Regression is a non-parametric geometrically
motivated method for fitting variable knots spline predictor models in one or two independent
variables, in the context of generalized (non-)linear models. 'GeDS' estimates the number and
position of the knots and the order of the spline, assuming the response variable has a
distribution from the exponential family. A description of the method can be found in
Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2017) <https://openaccess.city.ac.uk/18460>.
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Vladimir K. Kaishev <V.Kaishev@city.ac.uk>,
Andrea Lattuada <Andrea.Lattuada@unicatt.it> and
Richard J. Verrall <R.J.Verrall@city.ac.uk>
Maintainer: Andrea Lattuada <Andrea.Lattuada@unicatt.it>
Diff between GeDS versions 0.1.2 dated 2017-11-08 and 0.1.3 dated 2017-12-19
DESCRIPTION | 10 ++++++---- MD5 | 8 ++++---- R/GeDS-package.R | 4 ++-- R/dynlib.R | 2 +- man/GeDS-package.Rd | 4 ++-- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Detection of Isotope Pattern of a Mass Spectrometric Measurement
Description: Provides a low-level interface for a deisotoper container
implemented in the 'Java' programming language and means of S3 helper
functions for plotting and debugging isotopes of mass spectrometric data.
The deisotoper algorithm detects and aggregates peaks which belong to the
same isotopic cluster of a given mass spectrum.
Author: Christian Panse [cre, aut] (0000-0003-1975-3064),
Lucas Schmidt [ctb, aut] (0000-0003-4496-0487),
Witold E. Wolski [ctb, aut] (0000-0002-6468-120X)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
Diff between deisotoper versions 0.0.2 dated 2017-12-08 and 0.0.3 dated 2017-12-19
deisotoper-0.0.2/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/R |only deisotoper-0.0.2/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicClusterGraph.java |only deisotoper-0.0.2/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/R |only deisotoper-0.0.2/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/mspy |only deisotoper-0.0.3/deisotoper/DESCRIPTION | 10 deisotoper-0.0.3/deisotoper/MD5 | 100 ++-- deisotoper-0.0.3/deisotoper/R/deisotoper.R | 14 deisotoper-0.0.3/deisotoper/README.md | 63 -- deisotoper-0.0.3/deisotoper/build/vignette.rds |binary deisotoper-0.0.3/deisotoper/inst/doc/deisotoper.pdf |binary deisotoper-0.0.3/deisotoper/inst/java/deisotoper-1.0-SNAPSHOT.jar |binary deisotoper-0.0.3/deisotoper/java/Makefile | 3 deisotoper-0.0.3/deisotoper/java/deisotoper/deisotoper.iml | 8 deisotoper-0.0.3/deisotoper/java/deisotoper/pom.xml | 12 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/Version.java | 52 -- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/dto/MassSpecMeasure.java | 18 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/dto/MassSpecMeasureSerializer.java | 46 + deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/dto/MassSpecMeasureSummary.java | 233 ++++++--- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/dto/MassSpectrum.java | 53 -- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/Configuration.java | 200 ++++---- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/Connection.java | 10 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/Deisotoper.java | 119 +--- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/DeisotoperMassSpectrumAdapter.java | 10 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicCluster.java | 79 +-- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicSet.java | 188 ++++--- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicSetGraph.java |only deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicSetGraphToDotGraph.java |only deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/Peak.java | 10 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/PeakList.java | 93 +-- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/Score.java | 242 +++++----- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/ScoreFive.java | 62 +- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/ScoringConfiguration.java | 28 - deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mgf/ReadMGF.java | 67 +- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mgf/ReadStdIn.java | 38 - deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mgf/WriteMGF.java | 80 +-- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mgf/WriteStdOut.java | 20 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mspy/Convert.java | 109 +++- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mspy/Deisotoper.java | 20 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mspy/Mspy.java | 196 ++++---- deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mspy/Peak.java | 4 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/mspy/Peaklist.java | 17 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/r |only deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/utilities/FindNearestNeighbor.java | 5 deisotoper-0.0.3/deisotoper/java/deisotoper/src/main/java/ch/fgcz/proteomics/utilities/MathUtils.java | 4 deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/dto/MassSpecMeasureTest.java | 16 deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/fbdm/ConfigurationTest.java | 32 - deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/fbdm/DeisotoperTest.java | 89 +-- deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/fbdm/IsotopicClusterTest.java | 93 +++ deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/fbdm/IsotopicSetGraphTest.java |only deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/fbdm/IsotopicSetTest.java | 88 +++ deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/fbdm/ScoreTest.java | 112 ++-- deisotoper-0.0.3/deisotoper/java/deisotoper/src/test/java/ch/fgcz/proteomics/r |only deisotoper-0.0.3/deisotoper/java/runSonarcube.cmd |only deisotoper-0.0.3/deisotoper/tests/testthat/test-findNN.R | 12 54 files changed, 1441 insertions(+), 1214 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-06 1.2.2
2016-01-18 1.1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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2016-06-13 0.1.0
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2016-10-26 1.1
2015-11-11 1.0
2013-05-09 0.28
2013-04-04 0.27
2011-11-03 0.26
2011-10-04 0.25
2011-03-16 0.24
2011-01-19 0.23
2010-05-25 0.21
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2009-09-03 0.1-3
2009-06-25 0.1-1
2009-04-19 0.1-0
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2012-03-03 1.5.5
2012-01-18 1.5.4
2012-01-12 1.5.2
2010-05-01 1.5.0
2010-03-12 1.4.3
2010-03-10 1.4.1
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2007-01-13 0.1-2
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/svn-trunk/liblwgeom>, the geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (0000-0001-8049-7069),
Colin Rundel [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.1-1 dated 2017-12-17 and 0.1-2 dated 2017-12-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- configure | 8 +++++--- configure.ac | 6 +++--- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Complete Environment for Bayesian Inference
Description: Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.
Author: Byron Hall [aut],
Martina Hall [aut],
Statisticat, LLC [aut],
Eric Brown [ctb],
Richard Hermanson [ctb],
Emmanuel Charpentier [ctb],
Daniel Heck [ctb],
Stephane Laurent [ctb],
Quentin F. Gronau [ctb],
Henrik Singmann [cre]
Maintainer: Henrik Singmann <singmann+LaplacesDemon@gmail.com>
Diff between LaplacesDemon versions 16.0.1 dated 2016-07-16 and 16.1.0 dated 2017-12-19
CHANGELOG | 1317 +++++++++++---------- DESCRIPTION | 15 MD5 | 26 NAMESPACE | 2 R/distributions.R | 144 +- R/plot.demonoid.R | 322 ++--- R/plot.demonoid.hpc.R | 404 +++--- build/vignette.rds |binary inst/doc/BayesianInference.pdf |binary inst/doc/Examples.pdf |binary inst/doc/LaplacesDemonTutorial.pdf |binary man/LaplacesDemon.Rd | 2232 ++++++++++++++++++------------------- man/dist.Log.Normal.Precision.Rd | 195 +-- man/plot.demonoid.Rd | 191 +-- 14 files changed, 2458 insertions(+), 2390 deletions(-)
Title: Fit Univariate Distributions
Description: Wrapper for computing parameters for univariate distributions using MLE. It creates an object that stores d, p, q, r functions as well as parameters and statistics for diagnostics. Currently supports automated fitting from base and actuar packages. A manually fitting distribution fitting function is included to support directly specifying parameters for any distribution from ancillary packages.
Author: Thomas Roh [aut, cre]
Maintainer: Thomas Roh <thomas@roh.engineering>
Diff between fitur versions 0.5.0 dated 2017-10-09 and 0.5.20 dated 2017-12-19
DESCRIPTION | 11 -- MD5 | 37 ++++--- NAMESPACE | 5 NEWS.md | 14 ++ R/fit_empirical.R | 60 ++++++++--- R/fit_univariate.R | 61 ++++++++--- R/globals.R |only R/tests.R | 2 R/utils.R | 89 +++++++++++++++++ README.md | 2 build/vignette.rds |binary inst/doc/diagnostic_plots.R |only inst/doc/diagnostic_plots.Rmd |only inst/doc/diagnostic_plots.html |only inst/doc/introduction.R | 120 ++++++++++++++++------- inst/doc/introduction.Rmd | 128 ++++++++++++++++++------ inst/doc/introduction.html | 210 +++++++++++++++++++++++------------------ man/fit_empirical.Rd | 50 ++++++++- man/fit_univariate.Rd | 51 +++++++-- man/plot_pp.Rd |only man/plot_qq.Rd |only vignettes/diagnostic_plots.Rmd |only vignettes/introduction.Rmd | 128 ++++++++++++++++++------ 23 files changed, 697 insertions(+), 271 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-04 0.2.13
2017-11-30 0.2.12
2017-10-29 0.2.11
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