Title: Kernel for 'Jupyter'
Description: Provides a full implementation of the 'Jupyter' <http://jupyter.org/> messaging protocol in C++ by leveraging 'Rcpp' and 'Xeus' <https://github.com/QuantStack/xeus>.
'Jupyter' supplies an interactive computing environment and a messaging protocol defined over 'ZeroMQ' for multiple programming languages. This package implements
the 'Jupyter' kernel interface so that 'R' is exposed to this interactive computing environment. 'ZeroMQ' functionality is provided by the 'pbdZMQ' package.
'Xeus' is a C++ library that facilitates the implementation of kernels for 'Jupyter'. Additionally, 'Xeus' provides an interface to libraries that exist in the 'Jupyter' ecosystem for building widgets,
plotting, and more <https://blog.jupyter.org/interactive-workflows-for-c-with-jupyter-fe9b54227d92>. 'JuniperKernel' uses 'Xeus' as a library for the 'Jupyter' messaging protocol.
Author: Spencer Aiello [aut, cre, cph],
Wei-Chen Chen [ctb],
Stephan Brumme [cph],
Jake Luciani [cph],
Tony Plate [cph],
Matthieu Decorde [cph],
RStudio (Hadley Wickham) [cph],
Sylvain Corlay [cph],
Johan Mabille [cph],
Niels Lohmann [cph]
Maintainer: Spencer Aiello <spnrpa@gmail.com>
Diff between JuniperKernel versions 1.2.3.0 dated 2018-02-05 and 1.4.0.0 dated 2018-04-23
DESCRIPTION | 15 MD5 | 157 NAMESPACE | 50 NEWS.md | 109 R/RcppExports.R | 142 R/booter.R | 182 R/comm_close.R | 80 R/comm_info_request.R | 90 R/comm_msg.R | 80 R/comm_open.R | 80 R/complete_request.R | 122 R/execute_request.R | 197 R/graphics_device.R |only R/history_request.R | 76 R/inspect_request.R | 337 R/is_complete_request.R | 120 R/juniper.R | 109 R/kernel_info_request.R | 112 R/kernelspec.R | 392 R/request.R | 185 R/shutdown_request.R | 86 R/zzz.R | 52 cleanup.win | 28 configure | 5 inst/COPYRIGHTS | 54 inst/include/hmac.h | 166 inst/include/jclient/control.h | 60 inst/include/jclient/dealer.h | 94 inst/include/jclient/hb.h | 190 inst/include/jclient/iomsg.h | 102 inst/include/jclient/iopub.h | 134 inst/include/jclient/jclient.h | 180 inst/include/jclient/shell.h | 138 inst/include/jclient/stdin.h | 62 inst/include/juniper/background.h | 155 inst/include/juniper/conf.h | 160 inst/include/juniper/external.h | 62 inst/include/juniper/gdevice.h | 1330 - inst/include/juniper/jmessage.h | 360 inst/include/juniper/juniper.h | 270 inst/include/juniper/requests.h | 352 inst/include/juniper/sockets.h | 182 inst/include/juniper/utils.h | 341 inst/include/juniper/xbridge.h | 293 inst/include/sha256.h | 966 - inst/include/xeus/nl_json.hpp |29736 ++++++++++++++++++------------------- inst/include/zmq.h | 1286 - inst/include/zmq.hpp | 1982 +- inst/include/zmq_addon.hpp | 1182 - inst/include/zmq_utils.h | 96 inst/runits/runit.testCommInfo.R | 20 inst/runits/runit.testComplete.R | 56 inst/runits/runit.testExecute.R | 264 inst/runits/runit.testInspect.R | 96 inst/runits/runit.testIsComplete.R | 120 inst/runits/runit.testKernelInfo.R | 44 man/JuniperKernel.Rd | 20 man/bootKernel.Rd | 88 man/comm_close.Rd | 56 man/comm_info_request.Rd | 70 man/comm_msg.Rd | 56 man/comm_open.Rd | 56 man/complete_request.Rd | 70 man/defaultDisplayName.Rd | 40 man/defaultKernelName.Rd | 40 man/doRequest.Rd | 118 man/execute_request.Rd | 70 man/history_request.Rd | 56 man/inspect_request.Rd | 70 man/installJuniper.Rd | 112 man/is_complete_request.Rd | 80 man/jk_device_defaults.Rd |only man/jk_device_settings.Rd |only man/kernel_info_request.Rd | 68 man/listKernels.Rd | 40 man/shutdown_request.Rd | 70 man/the_xmock.Rd | 30 src/Makevars.win | 17 src/RcppExports.cpp | 35 src/install.libs.R | 56 src/juniper.cpp | 28 81 files changed, 22420 insertions(+), 22265 deletions(-)
Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Kent Russell [aut, cre] (R interface),
Gregor Aisch [aut, cph] (d3-jetpack creator,
https://github.com/gka/d3-jetpack),
Adam Pearce [aut] (core contributor to d3-jetpack),
Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between d3r versions 0.8.0 dated 2018-03-17 and 0.8.1 dated 2018-04-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/dependencies.R | 4 ++-- inst/www/d3/v5/API.md | 5 ++++- inst/www/d3/v5/CHANGES.md | 40 ++++++++++++++++++++++++++++++++++++++++ inst/www/d3/v5/dist/d3.min.js | 4 ++-- tests/testthat/test_deps.R | 4 ++-- 8 files changed, 65 insertions(+), 18 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables
for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A
Kenward-Roger method is also available via the pbkrtest package. Model selection
methods include step, drop1 and anova-like tables for random effects (ranova).
Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed
effects are also available.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths, cre],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between lmerTest versions 3.0-0 dated 2018-04-16 and 3.0-1 dated 2018-04-23
DESCRIPTION | 22 ++--- MD5 | 44 +++++------ NAMESPACE | 8 +- R/contest.R | 6 + R/drop1.R | 5 - R/lmer.R | 24 ++++++ R/lmer_anova.R | 6 + R/lmer_summary.R | 13 ++- man/anova.lmerModLmerTest.Rd | 6 + man/drop1.lmerModLmerTest.Rd | 5 - man/summary.lmerModLmerTest.Rd | 13 ++- tests/test_anova.R | 157 ++++++++++++++++++++++++----------------- tests/test_compare_sas.R | 32 +++----- tests/test_contest1D.R | 44 +++++++---- tests/test_contestMD.R | 56 +++++++++----- tests/test_drop1.R | 13 ++- tests/test_lmer.R | 5 - tests/test_lmerTest_paper.R | 31 +++++--- tests/test_ls_means.R | 24 +++--- tests/test_ranova_step.R | 21 ++--- tests/test_summary.R | 40 +++++++--- tests/test_zerovar.R | 2 tests/zlmerTest_zeroDenom.R | 4 - 23 files changed, 368 insertions(+), 213 deletions(-)
Title: 'ESRI' Bindings for the 'leaflet' Package
Description: An add-on package to the 'leaflet' package, which provides bindings for 'ESRI' services. This package allows a user to add 'ESRI' provided services such as 'MapService', 'ImageMapService', 'TiledMapService' etc. to a 'leaflet' map.
Author: Bhaskar Karambelkar [aut, cre],
Barret Schloerke [aut],
Patrick Arlt [ctb, cph] (esri-leaflet, esri-leaflet-cluster,
esri-leaflet-geocoder, and esri-leaflet-heatmap libraries),
Rachel Nehmer [ctb, cph] (esri-leaflet-renderers library),
Vladimir Agafonkin [ctb, cph] (leaflet.heat and simpleheat libraries),
Leaflet [ctb, cph] (leaflet.markercluster library)
Maintainer: Bhaskar Karambelkar <bhaskarvk@gmail.com>
Diff between leaflet.esri versions 0.2 dated 2017-06-25 and 1.0.0 dated 2018-04-23
leaflet.esri-0.2/leaflet.esri/inst/htmlwidgets/lib |only leaflet.esri-1.0.0/leaflet.esri/DESCRIPTION | 34 ++- leaflet.esri-1.0.0/leaflet.esri/LICENSE.note |only leaflet.esri-1.0.0/leaflet.esri/MD5 | 100 +++++----- leaflet.esri-1.0.0/leaflet.esri/NAMESPACE | 1 leaflet.esri-1.0.0/leaflet.esri/NEWS.md |only leaflet.esri-1.0.0/leaflet.esri/R/basemapLayers.R | 47 ++-- leaflet.esri-1.0.0/leaflet.esri/R/dynamicMapLayers.R | 77 ++++--- leaflet.esri-1.0.0/leaflet.esri/R/featureLayers.R | 91 +++++---- leaflet.esri-1.0.0/leaflet.esri/R/htmlDependencies.R | 79 +++++-- leaflet.esri-1.0.0/leaflet.esri/R/iconFunctions.R | 6 leaflet.esri-1.0.0/leaflet.esri/R/imageMapLayers.R | 81 ++++---- leaflet.esri-1.0.0/leaflet.esri/R/leaflet.esri-package.r | 1 leaflet.esri-1.0.0/leaflet.esri/R/tiledMapLayers.R | 23 +- leaflet.esri-1.0.0/leaflet.esri/inst/examples/basemaps.R | 8 leaflet.esri-1.0.0/leaflet.esri/inst/examples/buildExamples.R | 34 +-- leaflet.esri-1.0.0/leaflet.esri/inst/examples/dynamicMapLayers.R | 34 +-- leaflet.esri-1.0.0/leaflet.esri/inst/examples/featureLayers.R | 73 +++---- leaflet.esri-1.0.0/leaflet.esri/inst/examples/imageMapLayers.R | 35 +-- leaflet.esri-1.0.0/leaflet.esri/inst/examples/multipleFeatureLayers.R | 30 +-- leaflet.esri-1.0.0/leaflet.esri/inst/examples/tiledMapLayers.R | 8 leaflet.esri-1.0.0/leaflet.esri/inst/htmlwidgets/build |only leaflet.esri-1.0.0/leaflet.esri/man/addEsriBasemapLayer.Rd | 4 leaflet.esri-1.0.0/leaflet.esri/man/addEsriDynamicMapLayer.Rd | 20 ++ leaflet.esri-1.0.0/leaflet.esri/man/addEsriFeatureLayer.Rd | 26 ++ leaflet.esri-1.0.0/leaflet.esri/man/addEsriImageMapLayer.Rd | 14 + leaflet.esri-1.0.0/leaflet.esri/man/addEsriTiledMapLayer.Rd | 8 leaflet.esri-1.0.0/leaflet.esri/man/dynamicMapLayerOptions.Rd | 4 leaflet.esri-1.0.0/leaflet.esri/man/featureLayerOptions.Rd | 36 +-- leaflet.esri-1.0.0/leaflet.esri/man/imageMapLayerOptions.Rd | 4 30 files changed, 526 insertions(+), 352 deletions(-)
Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph],
Michael Hahsler [aut, cph]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>
Diff between arulesCBA versions 1.1.3 dated 2018-03-07 and 1.1.3-1 dated 2018-04-23
arulesCBA-1.1.3-1/arulesCBA/DESCRIPTION | 23 - arulesCBA-1.1.3-1/arulesCBA/MD5 | 42 +- arulesCBA-1.1.3-1/arulesCBA/NAMESPACE | 10 arulesCBA-1.1.3-1/arulesCBA/NEWS.md |only arulesCBA-1.1.3-1/arulesCBA/R/CBA.R | 201 ++++++++++++- arulesCBA-1.1.3-1/arulesCBA/R/CBA.object.R | 95 ++---- arulesCBA-1.1.3-1/arulesCBA/R/bCBA.R | 4 arulesCBA-1.1.3-1/arulesCBA/R/discretizeDF.supervised.R |only arulesCBA-1.1.3-1/arulesCBA/R/formula.R |only arulesCBA-1.1.3-1/arulesCBA/R/mineCARs.R |only arulesCBA-1.1.3-1/arulesCBA/R/wCBA.R | 4 arulesCBA-1.1.3-1/arulesCBA/README.md | 49 ++- arulesCBA-1.1.3-1/arulesCBA/inst/doc/arulesCBA.R | 34 +- arulesCBA-1.1.3-1/arulesCBA/inst/doc/arulesCBA.pdf |binary arulesCBA-1.1.3-1/arulesCBA/inst/doc/arulesCBA.rnw | 24 - arulesCBA-1.1.3-1/arulesCBA/man/CBA.Rd | 43 +- arulesCBA-1.1.3-1/arulesCBA/man/CBA.object.Rd | 48 +-- arulesCBA-1.1.3-1/arulesCBA/man/bCBA.Rd | 27 - arulesCBA-1.1.3-1/arulesCBA/man/discretizeDF.supervised.Rd |only arulesCBA-1.1.3-1/arulesCBA/man/mineCARs.Rd |only arulesCBA-1.1.3-1/arulesCBA/man/wCBA.Rd | 21 - arulesCBA-1.1.3-1/arulesCBA/src/cba.c | 6 arulesCBA-1.1.3-1/arulesCBA/tests/testthat/tests.R | 18 + arulesCBA-1.1.3-1/arulesCBA/vignettes/arulesCBA.rnw | 24 - arulesCBA-1.1.3/arulesCBA/R/CBAInternal.R |only arulesCBA-1.1.3/arulesCBA/R/disc.R |only 26 files changed, 467 insertions(+), 206 deletions(-)
Title: High-Dimensional Repeated Measures
Description: Methods for testing main and interaction effects in possibly
high-dimensional parametric or nonparametric repeated measures in factorial designs.
The observations of the subjects are assumed to be multivariate normal if using the parametric test.
The nonparametric version tests with regard to nonparametric relative effects (based on pseudo-ranks).
It is possible to use up to 2 whole- and 3 subplot factors.
Author: Martin Happ [aut, cre],
Harrar W. Solomon [aut],
Arne C. Bathke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between HRM versions 0.8.0 dated 2018-02-14 and 0.9.1 dated 2018-04-23
DESCRIPTION | 15 +- MD5 | 81 +++++++------ NAMESPACE | 2 R/Repeated.R | 194 ++++++++++++++++++++++++++------- R/S3methods.R | 12 +- R/f1.R | 229 ++++++++++++++++++++++++++++++++++++--- R/f1_sub0.R | 81 +++++++++++-- R/f2.R | 89 +++++++++++---- R/f2_old.R | 97 ++++++++++++---- R/f3_sub1.R | 70 ++++++++++- R/f3_sub2.R | 71 +++++++++--- R/f3_sub3.R |only R/f4_sub2.R | 73 ++++++++++-- R/f4_sub3.R | 97 +++++++++++++--- R/f4_sub4.R |only R/f5_sub5.R |only R/utility.R | 101 ++++++++++++++++- man/HRM.Rd | 4 man/hrm.0w.2s.Rd |only man/hrm.0w.3s.Rd |only man/hrm.0w.4s.Rd |only man/hrm.0w.5s.Rd |only man/hrm.1f.Rd | 2 man/hrm.1w.0f.Rd | 2 man/hrm.1w.1f.Rd | 3 man/hrm.1w.2f.Rd | 3 man/hrm.1w.3f.Rd | 2 man/hrm.2w.1f.Rd | 3 man/hrm.2w.2f.Rd | 2 man/hrm.A.unweighted.Rd | 2 man/hrm.A.weighted.Rd | 2 man/hrm.AB.Rd | 2 man/hrm.A_B.Rd | 2 man/hrm.B.Rd | 2 man/hrm.test.1.none.Rd | 2 man/hrm.test.1.one.Rd | 6 - man/hrm.test.2.between.Rd | 2 man/hrm.test.2.between.within.Rd | 2 man/hrm.test.2.one.Rd | 2 man/hrm.test.2.two.Rd |only man/hrm.test.2.within.Rd | 2 man/hrm.test.3.between.Rd | 2 man/hrm.test.3.three.Rd |only man/hrm.test.4.four.Rd |only man/hrm.test.5.five.Rd |only man/hrm_test.Rd | 5 man/hrm_test_internal.Rd | 2 47 files changed, 1033 insertions(+), 235 deletions(-)
Title: R Markdown Templates for the 'KOMA-Script' Classes
Description: R Markdown templates based on the 'KOMA-Script' classes for
LaTeX, additionally offering cross-referencing via the 'bookdown' package.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>)
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between komadown versions 0.1.0 dated 2017-08-20 and 0.2.0 dated 2018-04-23
komadown-0.1.0/komadown/inst/rmarkdown/templates/scrartcl/resources/template.tex |only komadown-0.2.0/komadown/DESCRIPTION | 17 komadown-0.2.0/komadown/MD5 | 43 komadown-0.2.0/komadown/NAMESPACE | 6 komadown-0.2.0/komadown/NEWS.md | 26 komadown-0.2.0/komadown/R/komadown.R | 4 komadown-0.2.0/komadown/R/scrartcl.R | 64 komadown-0.2.0/komadown/R/utils.R | 72 komadown-0.2.0/komadown/README.md | 67 komadown-0.2.0/komadown/build/vignette.rds |binary komadown-0.2.0/komadown/inst/CITATION |only komadown-0.2.0/komadown/inst/doc/scrartcl.R | 40 komadown-0.2.0/komadown/inst/doc/scrartcl.Rmd | 744 +++++----- komadown-0.2.0/komadown/inst/doc/scrartcl.pdf |binary komadown-0.2.0/komadown/inst/rmarkdown/templates/scrartcl/resources/scrartcl.tex |only komadown-0.2.0/komadown/inst/rmarkdown/templates/scrartcl/resources/vancouver-brackets.csl | 702 ++++----- komadown-0.2.0/komadown/inst/rmarkdown/templates/scrartcl/skeleton/skeleton.Rmd | 90 - komadown-0.2.0/komadown/inst/rmarkdown/templates/scrartcl/template.yaml | 6 komadown-0.2.0/komadown/man/komadown-package.Rd | 48 komadown-0.2.0/komadown/man/scrartcl.Rd | 85 - komadown-0.2.0/komadown/tests/testthat.R | 8 komadown-0.2.0/komadown/tests/testthat/test-scrartcl.R | 82 - komadown-0.2.0/komadown/vignettes/komadown.bib | 18 komadown-0.2.0/komadown/vignettes/scrartcl.Rmd | 744 +++++----- 24 files changed, 1460 insertions(+), 1406 deletions(-)
Title: Render Graphs Using 'Sigma.js'
Description: Create interactive graph visualizations using 'Sigma.js' <http://sigmajs.org/>. This package is meant to be used in conjunction
with 'igraph', replacing the (somewhat underwhelming) plotting features of the package. The idea is to quickly render
graphs, regardless of their size, in a way that allows for easy, iterative modification of aesthetics. Because
'Sigma.js' is a 'javascript' library, the visualizations are inherently interactive and are well suited for integration
with 'Shiny' apps. While there are several 'htmlwidgets' focused on network visualization, they tend to underperform on
medium to large sized graphs. 'Sigma.js' was designed for larger network visualizations and this package aims to
make those strengths available to 'R' users.
Author: Ian Kloo [aut, cre]
Maintainer: Ian Kloo <iankloo@gmail.com>
Diff between sigmaNet versions 1.0.3 dated 2018-01-24 and 1.1.0 dated 2018-04-23
sigmaNet-1.0.3/sigmaNet/inst/htmlwidgets/lib/sigma-1.2.0 |only sigmaNet-1.1.0/sigmaNet/DESCRIPTION | 10 sigmaNet-1.1.0/sigmaNet/MD5 | 17 sigmaNet-1.1.0/sigmaNet/NAMESPACE | 1 sigmaNet-1.1.0/sigmaNet/R/sigmaAttrs.R | 45 sigmaNet-1.1.0/sigmaNet/R/sigmaFromIgraph.R | 11 sigmaNet-1.1.0/sigmaNet/inst/doc/getting-started.html | 3566 +++++++-------- sigmaNet-1.1.0/sigmaNet/inst/htmlwidgets/lib/sigma-1.2.1 |only sigmaNet-1.1.0/sigmaNet/inst/htmlwidgets/sigmaNet.js | 31 sigmaNet-1.1.0/sigmaNet/inst/htmlwidgets/sigmaNet.yaml | 4 sigmaNet-1.1.0/sigmaNet/man/addListener.Rd |only 11 files changed, 1904 insertions(+), 1781 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb],
Dryden Ian [cph]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Morpho versions 2.5.1 dated 2017-04-21 and 2.6 dated 2018-04-23
Morpho-2.5.1/Morpho/R/deform.grid.r |only Morpho-2.6/Morpho/DESCRIPTION | 16 Morpho-2.6/Morpho/MD5 | 98 ++-- Morpho-2.6/Morpho/NAMESPACE | 11 Morpho-2.6/Morpho/R/CVA.r | 3 Morpho-2.6/Morpho/R/ComputeTransform.r | 32 - Morpho-2.6/Morpho/R/Morpho-package.R | 6 Morpho-2.6/Morpho/R/ProcGPA.r | 4 Morpho-2.6/Morpho/R/applyTransform.r | 9 Morpho-2.6/Morpho/R/calcTang_U_s.r | 4 Morpho-2.6/Morpho/R/check.lm.r | 8 Morpho-2.6/Morpho/R/data2platonic.r |only Morpho-2.6/Morpho/R/deformGrid2d.r | 19 Morpho-2.6/Morpho/R/deformGrid3d.r |only Morpho-2.6/Morpho/R/fiducials.r | 16 Morpho-2.6/Morpho/R/fixLMmirror.r | 44 + Morpho-2.6/Morpho/R/fixLMtps.r | 2 Morpho-2.6/Morpho/R/line2plane.r | 4 Morpho-2.6/Morpho/R/mesh2ply.r | 5 Morpho-2.6/Morpho/R/place.patch.r | 589 ++++++++++++-------------- Morpho-2.6/Morpho/R/plot.normals.r | 18 Morpho-2.6/Morpho/R/pls2B.r | 140 +++++- Morpho-2.6/Morpho/R/procSym.r | 4 Morpho-2.6/Morpho/R/retrodeform.r | 2 Morpho-2.6/Morpho/R/rot.proc.r | 4 Morpho-2.6/Morpho/R/rotmesh.onto.r | 6 Morpho-2.6/Morpho/R/rotonto.r | 34 + Morpho-2.6/Morpho/R/showPC.r | 25 + Morpho-2.6/Morpho/R/slider3d.r | 46 +- Morpho-2.6/Morpho/R/symmetrize.r | 2 Morpho-2.6/Morpho/R/virtualMeshScan.r |only Morpho-2.6/Morpho/inst/NEWS.Rd | 46 ++ Morpho-2.6/Morpho/inst/extdata/SCP1_Endo.fcsv |only Morpho-2.6/Morpho/man/Morpho-package.Rd | 4 Morpho-2.6/Morpho/man/applyTransform.Rd | 11 Morpho-2.6/Morpho/man/computeTransform.Rd | 6 Morpho-2.6/Morpho/man/data2platonic.Rd |only Morpho-2.6/Morpho/man/deformGrid2d.Rd | 9 Morpho-2.6/Morpho/man/deformGrid3d.Rd | 21 Morpho-2.6/Morpho/man/fixLMmirror.Rd | 8 Morpho-2.6/Morpho/man/getOuterViewpoints.Rd |only Morpho-2.6/Morpho/man/getPCscores.Rd |only Morpho-2.6/Morpho/man/getPLSCommonShape.Rd |only Morpho-2.6/Morpho/man/getVisibleVertices.Rd |only Morpho-2.6/Morpho/man/plotNormals.Rd | 6 Morpho-2.6/Morpho/man/pls2B.Rd | 11 Morpho-2.6/Morpho/man/plsCoVar.Rd | 3 Morpho-2.6/Morpho/man/plsCoVarCommonShape.Rd |only Morpho-2.6/Morpho/man/read.fcsv.Rd | 4 Morpho-2.6/Morpho/man/rotmesh.onto.Rd | 4 Morpho-2.6/Morpho/man/rotonto.Rd | 4 Morpho-2.6/Morpho/man/showPC.Rd | 2 Morpho-2.6/Morpho/man/slider3d.Rd | 3 Morpho-2.6/Morpho/man/virtualMeshScan.Rd |only Morpho-2.6/Morpho/src/createL.cpp | 5 Morpho-2.6/Morpho/tests/testthat/test-CVA.r | 2 56 files changed, 821 insertions(+), 479 deletions(-)
Title: Linear Regression Based on Linear Structure Between Variables
Description: Linear regression based on a recursive structural equation model
(explicit multiples correlations) found by a M.C.M.C. algorithm. It permits to face
highly correlated variables. Variable selection is included (by lasso,
elastic net, etc.). It also provides some graphical tools for basic
statistics.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY <corregeous@correg.org>
Diff between CorReg versions 1.2.1 dated 2017-05-03 and 1.2.8 dated 2018-04-23
DESCRIPTION | 8 - MD5 | 40 +++++---- NAMESPACE | 4 NEWS | 1 R/BoxPlot.R | 8 + R/Hist.R | 4 R/Interpretor.R | 2 R/Is.Numeric.R |only R/Numeric_Only.R |only R/Terminator.R | 12 +- R/naive_model.R |only R/newtheta.R | 2 R/purge_values.R |only R/recursive_tree.R | 91 +++++++++++++-------- R/report_MSE.R |only R/zzz.R |only build/vignette.rds |binary inst/doc/CorReg.html | 212 +++++++++++++++++++++++++++----------------------- man/BoxPlot.Rd | 6 - man/Hist.Rd | 4 man/Numeric_Only.Rd |only man/naive_model.Rd |only man/purge_values.Rd |only man/recursive_tree.Rd | 6 + man/report_MSE.Rd |only src/cleancolZ.cpp | 2 26 files changed, 236 insertions(+), 166 deletions(-)
Title: Tomoka Ohta D Statistics
Description: Calculate's Tomoka Ohta's partitioning of linkage disequilibrium,
deemed D-statistics, for pairs of loci. Beissinger et al. (2016) <doi:10.1038/hdy.2015.81>.
Author: Paul F. Petrowski <pfpetrowski@mail.missouri.edu> & Timothy M. Beissinger <timbeissinger@gmail.com>
Maintainer: Paul F. Petrowski <pfpetrowski@mail.missouri.edu>
Diff between ohtadstats versions 1.0 dated 2018-03-01 and 1.1.0 dated 2018-04-23
ohtadstats-1.0/ohtadstats/R/ohtadstat.R |only ohtadstats-1.0/ohtadstats/man/ohtadstat.Rd |only ohtadstats-1.1.0/ohtadstats/DESCRIPTION | 10 ++++++---- ohtadstats-1.1.0/ohtadstats/MD5 | 13 +++++++------ ohtadstats-1.1.0/ohtadstats/NAMESPACE | 2 +- ohtadstats-1.1.0/ohtadstats/R/dstat.R |only ohtadstats-1.1.0/ohtadstats/R/dwrapper.R | 6 +++--- ohtadstats-1.1.0/ohtadstats/README.md |only ohtadstats-1.1.0/ohtadstats/man/dstat.Rd |only ohtadstats-1.1.0/ohtadstats/man/dwrapper.Rd | 4 ++-- 10 files changed, 19 insertions(+), 16 deletions(-)
Title: New and Extended Plots, Methods, and Panel Functions for
'lattice'
Description: Extensions to 'lattice', providing new high-level
functions, methods for existing functions, panel functions, and a theme.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>),
Deepayan Sarkar [ctb, cph] (lattice),
Brian Ripley [ctb] (stats::plot.acf)
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between tactile versions 0.1.0 dated 2017-11-15 and 0.2.0 dated 2018-04-23
DESCRIPTION | 11 MD5 | 106 +++--- NAMESPACE | 68 ++-- NEWS.md | 16 - R/imports-lattice.R | 13 R/panel.ci.R |only README.md | 12 build/vignette.rds |binary inst/CITATION |only inst/doc/new-high-level-functions.R | 68 ++-- inst/doc/new-high-level-functions.Rmd | 30 + inst/doc/new-high-level-functions.html | 472 +++++++++++++++++++++--------- inst/doc/new-methods.R | 78 ++-- inst/doc/new-methods.Rmd | 13 inst/doc/new-methods.html | 516 +++++++++++++++++++++++---------- inst/doc/new-panel-functions.R |only inst/doc/new-panel-functions.Rmd |only inst/doc/new-panel-functions.html |only inst/doc/tactile-theme.R | 58 +-- inst/doc/tactile-theme.Rmd | 120 +++---- inst/doc/tactile-theme.html | 454 +++++++++++++++++++++-------- man/bubbleplot.Rd | 130 ++++---- man/bwplot2.Rd | 112 +++---- man/diag.panel.splom.density.Rd | 146 ++++----- man/dont_plot.Rd | 38 +- man/feldspar.Rd | 96 +++--- man/get_fun.Rd | 30 - man/grid_wrap.Rd | 40 +- man/make_bubbles.Rd | 42 +- man/panel.bubbleplot.Rd | 60 +-- man/panel.ci.Rd |only man/panel.qqmathci.Rd | 158 +++++----- man/panel.ternaryplot.Rd | 130 ++++---- man/panel.ternaryplot.clip.Rd | 50 +-- man/panel.ternaryplot.density.Rd | 82 ++--- man/panel.ternaryplot.grid.Rd | 54 +-- man/panel.ternaryplot.response.Rd | 80 ++--- man/panel.ternaryplot.scales.Rd | 88 ++--- man/panel.ternaryplot.xyplot.Rd | 52 +-- man/prepanel.ci.Rd |only man/qqmath.zoo.Rd | 82 ++--- man/require_pkg.Rd | 36 +- man/rescale.Rd | 54 +-- man/seq_pal.Rd | 36 +- man/setup_key.Rd | 60 +-- man/tactile-package.Rd | 60 +-- man/tactile.theme.Rd | 84 ++--- man/ternaryplot.Rd | 212 ++++++------- man/updateList.Rd | 46 +- man/xyplot.Arima.Rd | 102 +++--- man/xyplot.acf.Rd | 80 ++--- man/xyplot.forecast.Rd | 130 ++++---- man/xyplot.lm.Rd | 120 +++---- man/xyz_to_xy.Rd | 36 +- vignettes/new-high-level-functions.Rmd | 30 + vignettes/new-methods.Rmd | 13 vignettes/new-panel-functions.Rmd |only vignettes/tactile-theme.Rmd | 120 +++---- 58 files changed, 2715 insertions(+), 2009 deletions(-)
Title: Spanish version of orloca package
Description: Help and demo in Spanish of the orloca package. (Ayuda y demo en espanol del paquete orloca.) Objetos y metodos para manejar y resolver el problema de localizacion de suma minima, tambien conocido como problema de Fermat-Weber. El problema de localizacion de suma minima busca un punto tal que la suma ponderada de las distancias a los puntos de demanda se minimice. Vease "The Fermat-Weber location problem revisited" por Brimberg, Mathematical Programming, 1, pag. 71-76, 1995. <DOI: 10.1007/BF01592245>. Los algoritmos generales de optimizacion global se usan para resolver el problema, junto con el metodo adhoc Weiszfeld, ver "Sur le point pour lequel la Somme des distance de n points donnes est minimum", por Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pag. . 355-386, 1937.
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between orloca.es versions 4.3 dated 2017-11-01 and 4.5 dated 2018-04-23
DESCRIPTION | 16 +++++++++------- MD5 | 26 +++++++++++++++----------- build |only inst |only man/andalucia-data.Rd | 18 ++++++++++-------- man/as-methods.Rd | 2 +- man/contour.loca.p.Rd | 4 +++- man/loca.p.Rd | 24 +++++++++++++++--------- man/orloca.es-package.Rd | 35 ++++++++++++++++++++--------------- man/persp.loca.p.Rd | 20 +++++++++++--------- man/plot.Rd | 2 ++ man/rloca.p.Rd | 6 +++++- man/zsum.Rd | 23 ++++++++++------------- man/zsumgra.Rd | 5 +++++ vignettes |only 15 files changed, 106 insertions(+), 75 deletions(-)
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between fbati versions 1.0-1.1 dated 2016-07-10 and 1.0-3 dated 2018-04-23
DESCRIPTION | 10 +- MD5 | 41 +++++----- NAMESPACE | 9 ++ R/cgFbatCode.R | 214 +++++++++++++++++++++++++++---------------------------- R/datamatrix.R | 4 - R/fbatge.R | 108 +++++++++++++-------------- R/fbati.R | 2 R/ibat.R | 2 R/merge.R | 4 - src/cgFbat.cpp | 100 +++++++++++++++---------- src/fbatdist.cpp | 2 src/fbatge.cpp | 2 src/fbati.cpp | 2 src/fbati.h | 7 + src/fbati_init.c |only src/fbatmeev.cpp | 6 - src/joint.cpp | 4 - src/nuclify.cpp | 20 ++--- src/nuclify.h | 4 - src/random.cpp | 4 - src/rmatrix.cpp | 6 + src/rvector.cpp | 6 + 22 files changed, 298 insertions(+), 259 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.1.9 dated 2018-03-13 and 1.2.0 dated 2018-04-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 7 ++++--- R/Nodesig_function.R | 2 +- man/nodiv-package.Rd | 4 ++-- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: A Self-Describing Dataset Format and Interface
Description: Defines a compact data format that includes metadata.
The function fold() creates the format by converting
from data.frame, and unfold() converts back. The predictability
of the folded format supports reusability of data processing tools,
while the presence of embedded metadata improves portability,
interpretability, and efficiency.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between fold versions 0.2.5 dated 2018-01-07 and 0.2.6 dated 2018-04-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/meta.R | 11 ++++++----- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: NMF-EM Algorithm
Description: Provides a version of the Expectation-Maximization algorithm for
mix-models, reducing the numbers of parameters to estimate using
Non-negative Matrix Factorization methods.
For more explanations, see pre-print of Carel and Alquier (2017) <arXiv:1709.03346>.
Author: Lena Carel [aut, cre]
Maintainer: Lena Carel <lena.carel@gmail.com>
Diff between nmfem versions 1.0.1 dated 2018-04-11 and 1.0.2 dated 2018-04-23
DESCRIPTION | 6 ++-- MD5 | 8 +++--- R/nmfem_mult.R | 48 +++++++++++++++++++------------------- inst/doc/NMFEM_for_travelers.html | 4 +-- man/nmfem_mult.Rd | 2 - 5 files changed, 34 insertions(+), 34 deletions(-)
Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric
baseline hazard with the Expectation-Maximization algorithm. Supported data formats
include clustered failures with left truncation and recurrent events in gap-time
or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable
and the Power Variance Family are supported.
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <t.a.balan@lumc.nl>
Diff between frailtyEM versions 0.8.3 dated 2018-02-05 and 0.8.7 dated 2018-04-23
frailtyEM-0.8.3/frailtyEM/README.md |only frailtyEM-0.8.7/frailtyEM/DESCRIPTION | 10 frailtyEM-0.8.7/frailtyEM/MD5 | 79 frailtyEM-0.8.7/frailtyEM/NAMESPACE | 131 - frailtyEM-0.8.7/frailtyEM/NEWS.md | 417 +-- frailtyEM-0.8.7/frailtyEM/R/RcppExports.R | 72 frailtyEM-0.8.7/frailtyEM/R/autoplot.emfrail.R | 762 +++--- frailtyEM-0.8.7/frailtyEM/R/ca_test_cph.R | 872 +++---- frailtyEM-0.8.7/frailtyEM/R/ca_test_fit.R | 256 +- frailtyEM-0.8.7/frailtyEM/R/em_fit.R | 1113 ++++----- frailtyEM-0.8.7/frailtyEM/R/emfrail.R | 1714 +++++++-------- frailtyEM-0.8.7/frailtyEM/R/emfrail_arguments.R | 306 +- frailtyEM-0.8.7/frailtyEM/R/emfrail_aux.R | 404 +-- frailtyEM-0.8.7/frailtyEM/R/emfrail_methods.R | 154 - frailtyEM-0.8.7/frailtyEM/R/fast_Estep.R | 108 frailtyEM-0.8.7/frailtyEM/R/plot.emfrail.R | 630 ++--- frailtyEM-0.8.7/frailtyEM/R/predict.emfrail.R | 668 ++--- frailtyEM-0.8.7/frailtyEM/R/print.emfrail.R | 108 frailtyEM-0.8.7/frailtyEM/R/print.emfrail_summary.R | 435 +-- frailtyEM-0.8.7/frailtyEM/R/summary.emfrail.R | 870 +++---- frailtyEM-0.8.7/frailtyEM/build/vignette.rds |binary frailtyEM-0.8.7/frailtyEM/inst/doc/frailtyEM_manual.R | 400 +-- frailtyEM-0.8.7/frailtyEM/inst/doc/frailtyEM_manual.Rnw | 1615 +++++++------- frailtyEM-0.8.7/frailtyEM/inst/doc/frailtyEM_manual.pdf |binary frailtyEM-0.8.7/frailtyEM/man/Estep.Rd | 64 frailtyEM-0.8.7/frailtyEM/man/autoplot.emfrail.Rd | 182 - frailtyEM-0.8.7/frailtyEM/man/ca_test.Rd | 72 frailtyEM-0.8.7/frailtyEM/man/dist_to_pars.Rd | 44 frailtyEM-0.8.7/frailtyEM/man/emfrail.Rd | 445 +-- frailtyEM-0.8.7/frailtyEM/man/emfrail_control.Rd | 142 - frailtyEM-0.8.7/frailtyEM/man/emfrail_dist.Rd | 84 frailtyEM-0.8.7/frailtyEM/man/emfrail_pll.Rd | 170 - frailtyEM-0.8.7/frailtyEM/man/fast_Estep.Rd | 66 frailtyEM-0.8.7/frailtyEM/man/laplace_transform.Rd | 52 frailtyEM-0.8.7/frailtyEM/man/logLik.emfrail.Rd | 64 frailtyEM-0.8.7/frailtyEM/man/plot.emfrail.Rd | 152 - frailtyEM-0.8.7/frailtyEM/man/predict.emfrail.Rd | 248 +- frailtyEM-0.8.7/frailtyEM/man/residuals.emfrail.Rd | 58 frailtyEM-0.8.7/frailtyEM/man/summary.emfrail.Rd | 197 - frailtyEM-0.8.7/frailtyEM/vignettes/frailtyEM_manual.Rnw | 1615 +++++++------- frailtyEM-0.8.7/frailtyEM/vignettes/mybib.bib | 977 ++++---- 41 files changed, 8046 insertions(+), 7710 deletions(-)
Title: Rubik's Cube Solving
Description: Functions for visualizing, animating, solving and
analyzing the Rubik's cube. Includes data structures for
solvable and unsolvable cubes, random moves and random
state scrambles and cubes, 3D displays and animations
using 'OpenGL', patterned cube generation, and lightweight
solvers. See Rokicki, T. (2008) <arXiv:0803.3435> for the
Kociemba solver.
Author: Alec Stephenson.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between cubing versions 1.0-4 dated 2018-04-14 and 1.0-5 dated 2018-04-23
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- R/solver.R | 12 ++++++------ inst/doc/cubingintro.Rnw | 2 +- inst/doc/cubingintro.pdf |binary src/cubing_init.c | 35 ++++++++++++++++++++++++++++++----- src/header.h | 2 +- vignettes/cubingintro.Rnw | 2 +- 8 files changed, 53 insertions(+), 28 deletions(-)
Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with
corresponding random forest for conditional transformation models
as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>)
and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between trtf versions 0.3-0 dated 2018-01-08 and 0.3-1 dated 2018-04-23
DESCRIPTION | 14 MD5 | 34 R/methods.R | 22 R/trees_forests.R | 4 inst/NEWS.Rd | 12 inst/sim/2d.R | 2 inst/sim/artificial_simfun.R | 23 inst/sim/friedman.R | 2 inst/sim/lognormal_2d.R | 2 inst/sim/lognormal_friedman.R | 2 inst/sim/plots.R | 68 + man/traforest.Rd | 7 tests/GBSG2-Ex.R | 2 tests/GBSG2-Ex.Rout.save | 103 +- tests/regtest-traforest.R | 2 tests/regtest-traforest.Rout.save | 1423 +++++++++++++++++++------------------- tests/regtest-trafotree.R | 2 tests/regtest-trafotree.Rout.save | 89 +- 18 files changed, 951 insertions(+), 862 deletions(-)
Title: SciViews - Manage GUIs in R
Description: The SciViews svGUI package eases the management of Graphical User
Interfaces (GUI) in R. It is independent from any particular GUI widgets (Tk,
Gtk2, native, ...). It centralizes info about GUI elements currently used,
and it dispatches GUI calls to the particular toolkits in use in function of
the context (is R run at the terminal, within a Tk application, a HTML page?).
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svGUI versions 0.9-55 dated 2014-03-02 and 1.0.0 dated 2018-04-23
svGUI-0.9-55/svGUI/NEWS |only svGUI-0.9-55/svGUI/R/dontAsk.R |only svGUI-0.9-55/svGUI/R/guiAdd.R |only svGUI-0.9-55/svGUI/man/dontAsk.Rd |only svGUI-0.9-55/svGUI/man/guiAdd.Rd |only svGUI-1.0.0/svGUI/DESCRIPTION | 26 +++-- svGUI-1.0.0/svGUI/MD5 | 39 +++++--- svGUI-1.0.0/svGUI/NAMESPACE | 44 ++++++--- svGUI-1.0.0/svGUI/R/dont_ask.R |only svGUI-1.0.0/svGUI/R/gui.R | 107 +++++++++++++++-------- svGUI-1.0.0/svGUI/R/gui_add.R |only svGUI-1.0.0/svGUI/R/setUI.R | 148 ++++++++++++++++++++++----------- svGUI-1.0.0/svGUI/R/svGUI-internal.R | 58 ++++++------ svGUI-1.0.0/svGUI/R/svGUI-package.R |only svGUI-1.0.0/svGUI/TODO | 2 svGUI-1.0.0/svGUI/build |only svGUI-1.0.0/svGUI/inst/CITATION | 4 svGUI-1.0.0/svGUI/inst/doc |only svGUI-1.0.0/svGUI/man/dont_ask.Rd |only svGUI-1.0.0/svGUI/man/gui.Rd | 75 ++++++---------- svGUI-1.0.0/svGUI/man/gui_add.Rd |only svGUI-1.0.0/svGUI/man/setUI.Rd | 136 ++++++++++++++++-------------- svGUI-1.0.0/svGUI/man/svGUI-package.Rd | 101 +++++++++++++++++----- svGUI-1.0.0/svGUI/tests |only svGUI-1.0.0/svGUI/vignettes |only 25 files changed, 450 insertions(+), 290 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 0.1.3 dated 2017-12-27 and 0.2.0 dated 2018-04-23
DESCRIPTION | 6 +-- LICENSE | 2 - MD5 | 26 ++++++------- NEWS.md | 9 ++++ R/RcppExports.R | 4 ++ README.md | 2 - build/vignette.rds |binary inst/doc/RcppThread.Rmd | 9 +++- inst/doc/RcppThread.html | 8 +++- inst/include/RcppThread/ThreadPool.hpp | 65 +++++++++++++++++++-------------- src/RcppExports.cpp | 10 +++++ src/test.cpp | 22 ++++++++++- tests/testthat/tests.R | 1 vignettes/RcppThread.Rmd | 9 +++- 14 files changed, 119 insertions(+), 54 deletions(-)
Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Description: Tools to create a layout for figures made of multiple panels, and
to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap'
plots, grobs, and PNG, JPEG, SVG and TIFF images.
Author: Johannes Graumann [cre, aut],
Richard Cotton [ctb]
Maintainer: Johannes Graumann <johannes.graumann@mpi-bn.mpg.de>
Diff between multipanelfigure versions 0.10.7 dated 2018-04-03 and 1.0.0 dated 2018-04-23
DESCRIPTION | 16 +++++++-------- MD5 | 35 +++++++++++++++++----------------- R/assertions.R | 6 +++++ R/capture_base_plot.R | 3 ++ R/fill_panel.R | 3 ++ R/grob_dimensions.R | 3 ++ R/methods.R | 3 ++ R/multi_panel_figure.R | 3 ++ R/save_multi_panel_figure.R | 3 ++ inst/CITATION |only inst/doc/panel-positioning.html | 4 +-- inst/doc/scaling-clipping-images.html | 4 +-- man/assert_is_multipanelfigure.Rd | 5 ++++ man/capture_base_plot.Rd | 5 ++++ man/fill_panel.Rd | 5 ++++ man/grob_dimensions.Rd | 5 ++++ man/multi_panel_figure.Rd | 5 ++++ man/print.multipanelfigure.Rd | 5 ++++ man/save_multi_panel_figure.Rd | 5 ++++ 19 files changed, 89 insertions(+), 29 deletions(-)
More information about multipanelfigure at CRAN
Permanent link
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC).
Author: Haiming Zhou <zhouh@niu.edu> and Timothy Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between spBayesSurv versions 1.1.2 dated 2018-01-11 and 1.1.3 dated 2018-04-23
spBayesSurv-1.1.2/spBayesSurv/man/b_spline.Rd |only spBayesSurv-1.1.2/spBayesSurv/man/predict.b_spline.Rd |only spBayesSurv-1.1.2/spBayesSurv/vignettes/Leukemia-LDDPM-copula-Map.pdf |only spBayesSurv-1.1.2/spBayesSurv/vignettes/Leukemia-LDDPM-copula-age.pdf |only spBayesSurv-1.1.2/spBayesSurv/vignettes/Leukemia-LDDPM-copula-trace.pdf |only spBayesSurv-1.1.2/spBayesSurv/vignettes/Leukemia-PH-copula-Map.pdf |only spBayesSurv-1.1.2/spBayesSurv/vignettes/Leukemia-PH-copula-age.pdf |only spBayesSurv-1.1.2/spBayesSurv/vignettes/Leukemia-PH-copula-trace.pdf |only spBayesSurv-1.1.3/spBayesSurv/DESCRIPTION | 13 spBayesSurv-1.1.3/spBayesSurv/MD5 | 114 spBayesSurv-1.1.3/spBayesSurv/NAMESPACE | 9 spBayesSurv-1.1.3/spBayesSurv/R/GetCurves.R | 84 spBayesSurv-1.1.3/spBayesSurv/R/SpatDensReg.R | 180 spBayesSurv-1.1.3/spBayesSurv/R/SuperSurvRegBayes.R | 150 spBayesSurv-1.1.3/spBayesSurv/R/anovaDDP.R | 593 spBayesSurv-1.1.3/spBayesSurv/R/bspline.R |only spBayesSurv-1.1.3/spBayesSurv/R/frailtyGAFT.R | 1219 + spBayesSurv-1.1.3/spBayesSurv/R/indeptCoxph.R | 730 - spBayesSurv-1.1.3/spBayesSurv/R/spCopulaCoxph.R | 932 - spBayesSurv-1.1.3/spBayesSurv/R/spCopulaDDP.R | 749 - spBayesSurv-1.1.3/spBayesSurv/R/survregbayes.R | 463 spBayesSurv-1.1.3/spBayesSurv/R/survregbayes2.R | 1424 +- spBayesSurv-1.1.3/spBayesSurv/R/wrappers.R | 63 spBayesSurv-1.1.3/spBayesSurv/build/vignette.rds |binary spBayesSurv-1.1.3/spBayesSurv/inst/CITATION | 10 spBayesSurv-1.1.3/spBayesSurv/inst/doc/spBayesSurv.Rnw | 993 - spBayesSurv-1.1.3/spBayesSurv/inst/doc/spBayesSurv.pdf |binary spBayesSurv-1.1.3/spBayesSurv/man/GetCurves.Rd | 42 spBayesSurv-1.1.3/spBayesSurv/man/SpatDensReg.Rd | 81 spBayesSurv-1.1.3/spBayesSurv/man/SuperSurvRegBayes.Rd | 104 spBayesSurv-1.1.3/spBayesSurv/man/anovaDDP.Rd | 66 spBayesSurv-1.1.3/spBayesSurv/man/baseline.Rd | 54 spBayesSurv-1.1.3/spBayesSurv/man/bspline.Rd |only spBayesSurv-1.1.3/spBayesSurv/man/cox.snell.survregbayes.Rd |only spBayesSurv-1.1.3/spBayesSurv/man/frailtyGAFT.Rd | 126 spBayesSurv-1.1.3/spBayesSurv/man/frailtyprior.Rd | 51 spBayesSurv-1.1.3/spBayesSurv/man/indeptCoxph.Rd | 79 spBayesSurv-1.1.3/spBayesSurv/man/predict.bspline.Rd |only spBayesSurv-1.1.3/spBayesSurv/man/spCopulaCoxph.Rd | 91 spBayesSurv-1.1.3/spBayesSurv/man/spCopulaDDP.Rd | 82 spBayesSurv-1.1.3/spBayesSurv/man/survregbayes.Rd | 560 spBayesSurv-1.1.3/spBayesSurv/man/survregbayes2.Rd | 2 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_AFT_BP.cpp | 48 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_AH_BP.cpp | 48 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_LDTFP_tools.cpp | 5 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_PH_BP.cpp | 48 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_PO_BP.cpp | 48 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_SpatDens.cpp | 124 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_frailtyLDTFP.cpp | 9 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_frailty_GRF_LDTFP.cpp | 9 spBayesSurv-1.1.3/spBayesSurv/src/spSurv_nonfrailtyLDTFP.cpp | 9 spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-GAFT-CAR-Map.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-GAFT-CAR-age.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-GAFT-CAR-trace.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-CAR-Cox-Snell.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-CAR-Map.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-CAR-age.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-CAR-trace.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-GRF-Cox-Snell.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-GRF-Map.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-GRF-age.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/Leukemia-PO-GRF-trace.pdf |binary spBayesSurv-1.1.3/spBayesSurv/vignettes/bibliography.bib | 6567 +++++----- spBayesSurv-1.1.3/spBayesSurv/vignettes/spBayesSurv.Rnw | 993 - 64 files changed, 9229 insertions(+), 7743 deletions(-)
Title: Regularized PQL for Joint Selection in GLMMs
Description: Performs joint selection in Generalized Linear Mixed Models (GLMMs) using penalized likelihood methods. Specifically, the Penalized Quasi-Likelihood (PQL) is used as a loss function, and penalties are then "added on" to perform simultaneous fixed and random effects selection. Regularized PQL avoids the need for integration (or approximations such as the Laplace's method) during the estimation process, and so the full solution path for model selection can be constructed relatively quickly.
Author: Francis K.C. Hui, Samuel Mueller, A.H. Welsh
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between rpql versions 0.5 dated 2016-10-07 and 0.6 dated 2018-04-23
DESCRIPTION | 13 - MD5 | 22 + NAMESPACE | 7 R/RcppExports.R |only R/auxilaryfunctions.R | 157 +++++++++----- R/rpql-main.R | 540 +++++++++++++++++++++++++++++-------------------- inst |only man/build.start.fit.Rd | 22 - man/gendat.glmm.Rd | 44 +-- man/rpql-package.Rd | 2 man/rpql.Rd | 150 ++++++++----- src |only 12 files changed, 576 insertions(+), 381 deletions(-)
Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest' algorithm used to impute mixed-type data sets by chaining tree ensembles, introduced by Stekhoven, D.J. and Buehlmann, P. (2012) <doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the lightning fast random jungle package 'ranger'. Between the iterative model fitting, we offer the option of using predictive mean matching. This firstly avoids imputation with values not already present in the original data (like a value 0.3334 in 0-1 coded variable). Secondly, predictive mean matching tries to raise the variance in the resulting conditional distributions to a realistic level. This would allow e.g. to do multiple imputation when repeating the call to missRanger().
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between missRanger versions 1.0.1 dated 2018-03-22 and 1.0.2 dated 2018-04-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++---- R/missRanger.R | 43 +++++++++++++++++++++++++++++-------------- README.md | 2 +- man/missRanger.Rd | 9 +++++++-- 6 files changed, 48 insertions(+), 30 deletions(-)
Title: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Description: Convert 'Ensembl' gene identifiers from Genotype-Tissue
Expression (GTEx) data to identifiers in other annotation systems,
including 'Entrez', 'HGNC', and 'UniProt'.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Gao Wang [aut],
Lei Sun [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between grex versions 1.7 dated 2017-11-05 and 1.8 dated 2018-04-23
grex-1.7/grex/TODO |only grex-1.8/grex/DESCRIPTION | 11 - grex-1.8/grex/MD5 | 29 +-- grex-1.8/grex/NEWS.md | 19 +- grex-1.8/grex/R/grex-datalist.R | 9 + grex-1.8/grex/R/grex-package.R | 7 grex-1.8/grex/R/sysdata.rda |binary grex-1.8/grex/build/vignette.rds |binary grex-1.8/grex/data/gtexv6.rda |binary grex-1.8/grex/data/gtexv6p.rda |binary grex-1.8/grex/data/gtexv7.rda |only grex-1.8/grex/inst/doc/grex.R | 9 - grex-1.8/grex/inst/doc/grex.Rmd | 17 + grex-1.8/grex/inst/doc/grex.html | 328 ++++++++++++++++++++++++++++++++------ grex-1.8/grex/man/grex-package.Rd | 4 grex-1.8/grex/man/gtexv7.Rd |only grex-1.8/grex/vignettes/grex.Rmd | 17 + 17 files changed, 350 insertions(+), 100 deletions(-)
Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions and
use them to create shells (skeletons which must be manually completed by
the user) of test files to be tested with the 'testthat' package.
Author: Rory Nolan [aut, cre],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between exampletestr versions 1.2.0 dated 2018-01-26 and 1.3.0 dated 2018-04-23
exampletestr-1.2.0/exampletestr/man/make_tests_shells_file.Rd |only exampletestr-1.3.0/exampletestr/DESCRIPTION | 10 exampletestr-1.3.0/exampletestr/MD5 | 26 - exampletestr-1.3.0/exampletestr/NAMESPACE | 2 exampletestr-1.3.0/exampletestr/NEWS.md | 9 exampletestr-1.3.0/exampletestr/R/exampletestr.R | 4 exampletestr-1.3.0/exampletestr/R/exemplar.R | 239 ++++++++-- exampletestr-1.3.0/exampletestr/build/vignette.rds |binary exampletestr-1.3.0/exampletestr/inst/doc/exampletestr.R | 2 exampletestr-1.3.0/exampletestr/inst/doc/exampletestr.Rmd | 4 exampletestr-1.3.0/exampletestr/inst/doc/exampletestr.html | 215 ++++---- exampletestr-1.3.0/exampletestr/man/extract_examples.Rd | 12 exampletestr-1.3.0/exampletestr/man/test-shells.Rd |only exampletestr-1.3.0/exampletestr/tests/testthat/test-exemplar.R | 122 ++++- exampletestr-1.3.0/exampletestr/vignettes/exampletestr.Rmd | 4 15 files changed, 452 insertions(+), 197 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.2-0 dated 2018-02-26 and 0.2-1 dated 2018-04-23
DESCRIPTION | 15 ++++++++------- MD5 | 30 ++++++++++++++++-------------- R/internal.R | 21 +++++++++++++-------- R/models.R | 2 +- R/tram.R | 40 ++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary inst/CITATION |only inst/NEWS.Rd | 11 +++++++++++ inst/doc/tram.R | 8 -------- inst/doc/tram.Rnw | 24 +++++++++--------------- inst/doc/tram.pdf |binary man/tram.Rd | 15 +++++++++++++-- tests/Coxph-Ex.Rout.save | 21 ++++++++++++++------- tests/Survreg-Ex.Rout.save | 22 +++++++++++----------- tests/bugfixes.R |only vignettes/mlt.bib | 9 +++++++++ vignettes/tram.Rnw | 24 +++++++++--------------- 17 files changed, 148 insertions(+), 94 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-42 dated 2017-12-21 and 0.1-43 dated 2018-04-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 7 ++----- 3 files changed, 8 insertions(+), 11 deletions(-)
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between relations versions 0.6-7 dated 2017-08-09 and 0.6-8 dated 2018-04-23
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 4 +--- build/partial.rdb |binary inst/NEWS.Rd | 6 ++++++ inst/doc/relations.pdf |binary 6 files changed, 18 insertions(+), 13 deletions(-)
Title: Cluster Ensembles
Description: CLUster Ensembles.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Walter Böhm [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between clue versions 0.3-54 dated 2017-08-09 and 0.3-55 dated 2018-04-23
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- R/predict.R | 4 ++-- build/partial.rdb |binary inst/doc/clue.pdf |binary 5 files changed, 12 insertions(+), 11 deletions(-)
More information about semantic.dashboard at CRAN
Permanent link
More information about ROI.plugin.qpoases at CRAN
Permanent link
More information about BoutrosLab.plotting.general at CRAN
Permanent link
Title: Utility Functions for Davidian Curves
Description: A Davidian curve defines a seminonparametric density, whose shape and flexibility can be tuned by
easy to estimate parameters. Since a special case of a Davidian curve is the standard normal density,
Davidian curves can be used for relaxing normality assumption in statistical applications (Zhang & Davidian, 2001)
<doi:10.1111/j.0006-341X.2001.00795.x>. This package provides the density function, the gradient of
the loglikelihood and a random generator for Davidian curves.
Author: Oğuzhan Öğreden
Maintainer: Oğuzhan Öğreden <oguzhan@oguzhanogreden.com>
Diff between dcurver versions 0.9.0 dated 2018-04-05 and 0.9.1 dated 2018-04-23
DESCRIPTION | 14 +++++----- MD5 | 20 ++++++++------- NEWS.md |only R/RcppExports.R | 16 +++++++++--- README.md | 13 ++++----- build |only man/dc_grad.Rd | 14 +++++++++- man/ddc.Rd | 2 - man/rdc.Rd | 2 - src/dcUtils.cpp | 71 +++++++++++++++++++++++++----------------------------- src/distFuncs.cpp | 17 +++--------- src/estFuncs.cpp | 22 ++++++++-------- 12 files changed, 99 insertions(+), 92 deletions(-)
Title: Asymptotic Classification Theory for Cognitive Diagnosis
Description: Cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; <doi:10.1007/s11336-009-9125-0>). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.
Author: Chia-Yi Chiu (Rutgers, the State University of New Jersey) and Wenchao
Ma (The University of Alabama)
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between ACTCD versions 1.1-0 dated 2016-12-17 and 1.2-0 dated 2018-04-23
DESCRIPTION | 16 ++++++++-------- MD5 | 11 ++++++----- NAMESPACE | 1 + R/alpha.R | 18 ++---------------- R/labeling.R | 4 +--- man/ACTCD-package.Rd | 2 +- src/ACTCD_init.c |only 7 files changed, 19 insertions(+), 33 deletions(-)
Title: Augmented and Penalized Minimization Method L0
Description: Fit linear, logistic and Cox models regularized with L0, lasso (L1), elastic-net (L1 and L2), or net (L1 and Laplacian) penalty, and their adaptive forms, such as adaptive lasso / elastic-net and net adjusting for signs of linked coefficients. It solves L0 penalty problem by simultaneously selecting regularization parameters and the number of non-zero coefficients. This augmented and penalized minimization method provides an approximation solution to the L0 penalty problem, but runs as fast as L1 regularization problem. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients. It could deal with very high dimensional data and has superior selection performance.
Author: Xiang Li, Shanghong Xie, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li <xli256@its.jnj.com>
Diff between APML0 versions 0.8 dated 2018-04-15 and 0.9 dated 2018-04-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/net_cox.R | 15 +++++++++------ man/APML0-package.Rd | 4 ++-- 4 files changed, 17 insertions(+), 14 deletions(-)