Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by
Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data.
Functions include methods for searching by sequences by taxonomic names,
ids, collectors, and institutions; as well as a function for searching
for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.8.0 dated 2018-10-26 and 0.8.6 dated 2018-12-14
DESCRIPTION | 13 +- MD5 | 54 ++++++++--- NEWS.md | 10 ++ R/bold_seq.R | 13 ++ R/zzz.R | 9 + README.md | 116 ++++++++++++++++++++----- inst/doc/bold_vignette.Rmd | 161 +++++++++++++++++++++-------------- inst/doc/bold_vignette.html | 161 +++++++++++++++++++++-------------- man/bold_seq.Rd | 9 + tests/fixtures |only tests/testthat/helper-bold.R |only tests/testthat/test-bold_identify.R | 33 ++++--- tests/testthat/test-bold_seq.R | 33 ++++--- tests/testthat/test-bold_seqspec.R | 40 ++++---- tests/testthat/test-bold_specimens.R | 40 ++++---- tests/testthat/test-bold_tax_id.R | 106 ++++++++++++++--------- tests/testthat/test-bold_tax_name.R | 36 ++++--- vignettes/bold_vignette.Rmd | 161 +++++++++++++++++++++-------------- 18 files changed, 646 insertions(+), 349 deletions(-)
Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input
data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
Brent Thorne [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between ggspatial versions 1.0.2 dated 2018-10-27 and 1.0.3 dated 2018-12-14
DESCRIPTION | 18 +++- MD5 | 40 +++++------ NAMESPACE | 8 ++ R/annotation-map-tile.R | 33 +++++---- R/annotation-north-arrow.R | 65 +++++++++++------ R/annotation-scale.R | 98 +++++++++++++++------------ R/df-spatial.R | 23 +++++- R/geom-spatial.R | 28 +++++++ R/layer-spatial-raster.R | 44 +++++++++--- inst/doc/ggspatial.html | 4 - man/annotation_north_arrow.Rd | 30 +++++--- man/annotation_scale.Rd | 43 ++++++----- man/layer_spatial.Raster.Rd | 7 + man/stat_spatial_identity.Rd | 16 ++++ tests/testthat/rosm.cache |only tests/testthat/test-annotation-north-arrow.R | 26 +++++++ tests/testthat/test-annotation-scale.R | 37 ++++++++++ tests/testthat/test-df_spatial.R | 8 ++ tests/testthat/test-geom_spatial.R | 39 ++++++++++ tests/testthat/test-layer-spatial-raster.R | 71 +++++++++++++++++++ tests/testthat/test-layer-spatial.R | 11 +++ 21 files changed, 499 insertions(+), 150 deletions(-)
Title: Toolkit for Bezier Curves and Splines
Description: The bezier package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between bezier versions 1.1 dated 2014-07-18 and 1.1.2 dated 2018-12-14
DESCRIPTION | 17 +++++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 8 ++++++++ R/bezierArcLength.R | 2 +- R/bezierCurveFit.R | 31 ++++++++++++++++++++----------- R/pointsOnBezier.R | 8 ++++++++ man/bezier-package.Rd | 4 ++-- man/bezierArcLength.Rd | 4 ++-- man/bezierCurveFit.Rd | 9 ++++++--- 9 files changed, 64 insertions(+), 35 deletions(-)
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction data set.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.14 dated 2018-03-23 and 0.2.17 dated 2018-12-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 27 +++++++++++++++++++++++++++ R/rglobi.R | 4 +++- README.md | 3 ++- build/vignette.rds |binary 6 files changed, 41 insertions(+), 11 deletions(-)
Title: Tool-Kit for Dynamic Materials Model and Thermal Processing Maps
Description: Provides a simple approach for constructing dynamic materials
modeling suggested by Prasad and Gegel <doi:10.1007/BF02664902>. It
can easily generate various processing-maps based on this model as well. The
calculation result in this package contains full materials constants, information
about power dissipation efficiency factor, and rheological properties, can
be exported completely also, through which further analysis and customized
plots will be applicable as well.
Author: ZHANG_Chen Developer [aut, com, cre]
Maintainer: ZHANG_Chen Developer <447974102@qq.com>
Diff between TPMplt versions 0.1.1 dated 2018-12-02 and 0.1.2 dated 2018-12-14
DESCRIPTION | 8 +-- MD5 | 40 +++++++++++---- NAMESPACE | 6 ++ R/DMMprocess.R | 47 +++++++++++++++++- R/TCorrect.R |only README.md | 47 +++++++++++++++--- inst/doc/TPMplt-vignette.R | 10 +++ inst/doc/TPMplt-vignette.Rmd | 52 +++++++++++++++++++- inst/doc/TPMplt-vignette.html | 108 ++++++++++++++++++++++++++++-------------- man/AllPF.Rd |only man/Dvec.Rd |only man/TCorrect.Rd |only man/basicPF.Rd |only man/chrgen1.Rd |only man/chrgen2.Rd |only vignettes/TPMplt-vignette.Rmd | 52 +++++++++++++++++++- vignettes/img/Img10.png |only vignettes/img/Img11.png |only vignettes/img/Img12.png |only vignettes/img/Img13.png |only vignettes/img/Img3.png |binary vignettes/img/Img4.png |only vignettes/img/Img5.png |only vignettes/img/Img6.png |only vignettes/img/Img7.png |only vignettes/img/Img8.png |only vignettes/img/Img9.png |only vignettes/img/demo_figs1.png |binary vignettes/img/demo_figs2.png |binary vignettes/img/demo_figs3.png |only 30 files changed, 306 insertions(+), 64 deletions(-)
Title: A XML-Based Testing Framework for Automated Component Tests of R
Packages
Description: This provides a framework for R packages developed for
a regulatory environment. It is based on the 'testthat' unit testing system and provides the adapter
functionalities for XML-based test case definition as well as for standardized
reporting of the test results.
Author: Sebastian Wolf [aut, cre],
Matthias Pfeifer [aut, ctb],
Sergej Potapov [ctb],
Roche [cph, fnd]
Maintainer: Sebastian Wolf <sebastian@mail-wolf.de>
Diff between RTest versions 1.2.1 dated 2018-12-11 and 1.2.2 dated 2018-12-14
DESCRIPTION | 14 - MD5 | 59 ++++-- NAMESPACE | 19 +- R/RTestCase.R | 31 ++- R/RTestCase.test-adapter.R | 200 ++++++++++++++++++++++ R/RTestCollection.R | 12 - R/utils.R | 59 ++++++ R/utils.examples.R |only R/utils.test.R | 80 ++++++++ build/vignette.rds |binary inst/ChangeLog.txt | 16 + inst/doc/RTest-test-adapter.R |only inst/doc/RTest-test-adapter.Rmd |only inst/doc/RTest-test-adapter.pdf |only inst/doc/RTest.R | 96 +--------- inst/doc/RTest.Rmd | 286 +++++++++++++++++++++++--------- inst/doc/RTest.pdf |binary inst/xml-templates/RTest_TC-01.xml | 1 inst/xml-templates/RTest_TC-02.xml |only inst/xml-templates/RTest_TC-fail.xml |only inst/xml-templates/RTest_TC-generic.xml |only inst/xsd/RTest.xsd | 257 +++++++++++++++++++++++++--- man/RTest.execute.Rd |only man/arguments_creator.Rd |only man/example_data_frame.Rd |only man/example_image.Rd |only man/example_list.Rd |only man/example_variable.Rd |only man/example_vector.Rd |only man/exec.Rd | 9 - man/generic.Rd |only man/get_existence_of_fun.Rd |only man/show-RTestCollection-method.Rd | 3 man/test.RTest.funct_01.Rd | 8 man/test_returnValue_any.Rd |only vignettes/RTest-test-adapter.Rmd |only vignettes/RTest.Rmd | 286 +++++++++++++++++++++++--------- vignettes/RTest_TC-generic.xml |only vignettes/general_principle.jpg |only vignettes/report.jpg |only vignettes/report_generic.jpg |only vignettes/test_fun.jpg |only 42 files changed, 1121 insertions(+), 315 deletions(-)
Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for
feature selection in high-dimensional regressions proposed in
Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>,
with support for multi-step adaptive MCP-net (MSAMNet) and
multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Qing-Song Xu [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between msaenet versions 2.9 dated 2018-05-14 and 3.0 dated 2018-12-14
DESCRIPTION | 8 - MD5 | 88 +++++++-------- NEWS.md | 6 + R/aenet.R | 134 ++++++++++++---------- R/amnet.R | 194 +++++++++++++++++---------------- R/asnet.R | 194 +++++++++++++++++---------------- R/msaenet-eval.R | 8 - R/msaenet-inspect.R | 152 +++++++++++++------------- R/msaenet-package.R | 6 - R/msaenet-sim.R | 226 +++++++++++++++++++------------------- R/msaenet-tune-glmnet.R | 163 +++++++++++++-------------- R/msaenet-tune-ncvreg.R | 228 +++++++++++++++++++-------------------- R/msaenet-utils.R | 49 ++++---- R/msaenet.R | 195 +++++++++++++++++---------------- R/msamnet.R | 257 +++++++++++++++++++++++--------------------- R/msasnet.R | 257 +++++++++++++++++++++++--------------------- R/plot-msaenet.R | 228 ++++++++++++++++++++++----------------- R/predict-msaenet.R | 34 +++-- R/print-msaenet.R | 52 ++++---- README.md | 4 build/vignette.rds |binary inst/doc/msaenet.R | 14 +- inst/doc/msaenet.Rmd | 14 +- inst/doc/msaenet.html | 88 +++++++++------ man/aenet.Rd | 22 ++- man/amnet.Rd | 26 +++- man/asnet.Rd | 26 +++- man/coef.msaenet.Rd | 10 + man/msaenet-package.Rd | 5 man/msaenet.Rd | 22 ++- man/msaenet.fn.Rd | 10 + man/msaenet.fp.Rd | 10 + man/msaenet.nzv.Rd | 10 + man/msaenet.nzv.all.Rd | 10 + man/msaenet.sim.binomial.Rd | 9 - man/msaenet.sim.cox.Rd | 5 man/msaenet.sim.gaussian.Rd | 9 - man/msaenet.sim.poisson.Rd | 9 - man/msaenet.tp.Rd | 10 + man/msamnet.Rd | 28 +++- man/msasnet.Rd | 28 +++- man/plot.msaenet.Rd | 15 +- man/predict.msaenet.Rd | 12 +- man/print.msaenet.Rd | 10 + vignettes/msaenet.Rmd | 14 +- 45 files changed, 1572 insertions(+), 1327 deletions(-)
Title: Finding Convergence Clubs
Description: Functions for clustering regions that form convergence clubs, according to the definition of Phillips and Sul (2009) <doi:10.1002/jae.1080>.
Author: Roberto Sichera [aut, cre, cph],
Pietro Pizzuto [aut]
Maintainer: Roberto Sichera <roberto.sichera@unipa.it>
Diff between ConvergenceClubs versions 1.4.2 dated 2018-12-06 and 1.4.3 dated 2018-12-14
DESCRIPTION | 8 - MD5 | 42 +++---- NAMESPACE | 56 +++++----- R/dim.convergence.clubs.R | 40 +++---- R/print.convergence.clubs.R | 20 +-- R/summary.convergence.clubs.R | 15 +- README.md | 23 +--- man/ConvergenceClubs-package.Rd | 90 ++++++++-------- man/GDP.Rd | 46 ++++---- man/club.Rd | 92 ++++++++-------- man/computeH.Rd | 100 +++++++++--------- man/coreG.Rd | 118 ++++++++++----------- man/dim.convergence.clubs.Rd | 40 +++---- man/estimateMod.Rd | 100 +++++++++--------- man/filteredGDP.Rd | 50 ++++----- man/findClubs.Rd | 214 +++++++++++++++++++------------------- man/mergeClubs.Rd | 202 ++++++++++++++++++------------------ man/mergeDivergent.Rd | 150 +++++++++++++-------------- man/plot.convergence.clubs.Rd | 216 +++++++++++++++++++-------------------- man/print.convergence.clubs.Rd | 32 ++--- man/ps_andrews_hac.Rd | 56 +++++----- man/summary.convergence.clubs.Rd | 32 ++--- 22 files changed, 873 insertions(+), 869 deletions(-)
More information about ConvergenceClubs at CRAN
Permanent link
Title: Interpolate Data for Smooth Animations
Description: In order to create smooth animation between states of data,
tweening is necessary. This package provides a range of functions for
creating tweened data that can be used as basis for animation. Furthermore
it adds a number of vectorized interpolaters for common R data
types such as numeric, date and colour.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tweenr versions 1.0.0 dated 2018-09-27 and 1.0.1 dated 2018-12-14
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/tween_components.R | 3 +-- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Cancer Registry Data Analysis and Visualisation
Description: Tools for basic and advance cancer statistics and graphics.
Calculates age-specific rate, age-standardized rate, estimated annual
percentage rate with standards error. Creates graphics across variable and
time, such as age-specific trends and period-cohort trends.
Author: Mathieu Laversanne [aut, cre],
Cancer Surveillance Unit [cph]
Maintainer: Mathieu Laversanne <laversannem@iarc.fr>
Diff between Rcan versions 1.3.62 dated 2018-12-10 and 1.3.63 dated 2018-12-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/csu_eapc.R | 9 +++++---- R/helper.r | 7 ++++--- build/partial.rdb |binary inst/testdata/csu_asr_test1.rds |binary inst/testdata/csu_eapc_test1.rds |binary man/csu_eapc.Rd | 6 +++++- tests/testthat/test-Rcan.R | 35 ++++++++++++++++------------------- 10 files changed, 44 insertions(+), 41 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Davide Vega, Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from this libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 2.0.0 dated 2018-12-06 and 2.0.1 dated 2018-12-14
DESCRIPTION | 8 MD5 | 82 ++++---- src/include/core/attributes/AttributeStore.h | 2 src/include/core/attributes/MainMemoryAttributeStore.h | 2 src/include/core/attributes/Text.h | 1 src/include/core/attributes/Value.h | 1 src/include/core/datastructures/containers/Attributed.h | 2 src/include/core/datastructures/containers/DefaultEQ.h | 2 src/include/core/datastructures/containers/DefaultLT.h | 2 src/include/core/datastructures/containers/LabeledSharedPtrSortedRandomSet.h | 2 src/include/core/datastructures/containers/LabeledUniquePtrSortedRandomSet.h | 2 src/include/core/datastructures/containers/PtrSortedRandomSet.h | 2 src/include/core/datastructures/containers/SharedPtrEQ.h | 2 src/include/core/datastructures/containers/SharedPtrLT.h | 2 src/include/core/datastructures/containers/SharedPtrSortedRandomSet.h | 2 src/include/core/datastructures/containers/SortedRandomSet.h | 2 src/include/core/datastructures/containers/SortedRandomSetEntry.h | 2 src/include/core/datastructures/containers/UniquePtrEQ.h | 2 src/include/core/datastructures/containers/UniquePtrLT.h | 2 src/include/core/datastructures/containers/UniquePtrSortedRandomSet.h | 2 src/include/core/datastructures/objects/NamedObject.h | 2 src/include/core/datastructures/objects/Object.h | 2 src/include/core/datastructures/observers/GenericObserver.h | 5 src/include/core/datastructures/observers/Observer.h | 2 src/include/core/datastructures/observers/ObserverStore.h | 2 src/include/core/datastructures/observers/Subject.h | 2 src/include/mnet/community/glouvain.h | 2 src/include/mnet/community/modularity.h | 95 ++++++++++ src/include/mnet/datastructures/graphs/MultilayerNetwork.h | 3 src/include/mnet/datastructures/layers/SimpleGraphLayer.h | 6 src/include/net/community/Community.h | 5 src/include/net/datastructures/graphs/Graph.h | 3 src/include/net/datastructures/stores/AttributeStoreWrapper.h | 1 src/include/net/datastructures/stores/EdgeStore.h | 2 src/include/net/datastructures/stores/GenericEdgeStore.h | 2 src/include/net/datastructures/stores/GenericSimpleEdgeStore.h | 2 src/include/net/datastructures/stores/MultiEdgeStore.h | 1 src/include/net/datastructures/stores/SimpleEdgeStore.h | 2 src/include/net/datastructures/stores/VertexStore.h | 4 src/infomap/infomap/InfomapBase.cpp | 14 - src/lib/infomap/infomap/InfomapBase.cpp | 14 - src/multinet/mnet/datastructures/graphs/AttributedTwoModeNetwork.cpp | 6 42 files changed, 223 insertions(+), 78 deletions(-)
Title: Maximal Information-Based Nonparametric Exploration for Variable
Analysis
Description: Wrapper for 'minepy' implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family). Detailed information of the ANSI C implementation of
'minepy' can be found at <http://minepy.readthedocs.io/en/latest>.
Author: Michele Filosi [aut, cre],
Roberto Visintainer [aut],
Davide Albanese [aut],
Samantha Riccadonna [ctb],
Giuseppe Jurman [ctb],
Cesare Furlanello [ctb]
Maintainer: Michele Filosi <michele.filosi@gmail.com>
Diff between minerva versions 1.4.7 dated 2017-07-21 and 1.5 dated 2018-12-14
minerva-1.4.7/minerva/src/minerva_init.c |only minerva-1.5/minerva/DESCRIPTION | 26 +- minerva-1.5/minerva/MD5 | 25 +- minerva-1.5/minerva/NAMESPACE | 16 - minerva-1.5/minerva/NEWS | 8 minerva-1.5/minerva/R/RcppExports.R |only minerva-1.5/minerva/R/mine.R | 253 ++++++++++++++++++++++++- minerva-1.5/minerva/R/mine_onemeasure.R |only minerva-1.5/minerva/R/minerva-package.R |only minerva-1.5/minerva/README.md | 8 minerva-1.5/minerva/build |only minerva-1.5/minerva/man/mine.Rd | 227 +++++++++++----------- minerva-1.5/minerva/man/mine_compute.Rd |only minerva-1.5/minerva/man/mine_compute_cstats.Rd |only minerva-1.5/minerva/man/mine_compute_pstats.Rd |only minerva-1.5/minerva/man/mine_stat.Rd |only minerva-1.5/minerva/src/RcppExports.cpp |only minerva-1.5/minerva/src/mine_int.cpp |only minerva-1.5/minerva/tests/testthat/testthat.R | 15 + 19 files changed, 442 insertions(+), 136 deletions(-)
Title: Density Estimation and Random Number Generation with
Distribution Element Trees
Description: Density estimation for possibly large data sets and conditional/unconditional random number generation or bootstrapping with distribution element trees. The function 'det.construct' translates a dataset into a distribution element tree. To evaluate the probability density based on a previously computed tree at arbitrary query points, the function 'det.query' is available. The functions 'det1' and 'det2' provide density estimation and plotting for one- and two-dimensional datasets. Conditional/unconditional smooth bootstrapping from an available distribution element tree can be performed by 'det.rnd'. For more details on distribution element trees, see: Meyer, D.W. (2016) <arXiv:1610.00345> or Meyer, D.W., Statistics and Computing (2017) <doi:10.1007/s11222-017-9751-9> and Meyer, D.W. (2017) <arXiv:1711.04632> or Meyer, D.W., Journal of Computational and Graphical Statistics (2018) <doi:10.1080/10618600.2018.1482768>.
Author: Daniel Meyer
Maintainer: Daniel Meyer <meyerda@ethz.ch>
Diff between detpack versions 1.1.1 dated 2018-04-26 and 1.1.2 dated 2018-12-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ R/detpack.R | 2 +- R/detrnd.R | 6 +++--- man/detpack.Rd | 2 +- 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Tools for Developing Binary Logistic Regression Models
Description: Tools designed to make it easier for beginner and intermediate users to build and validate
binary logistic regression models. Includes bivariate analysis, comprehensive regression output,
model fit statistics, variable selection procedures, model validation techniques and a 'shiny'
app for interactive model building.
Author: Aravind Hebbali [aut, cre] (<https://orcid.org/0000-0001-9220-9669>)
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between blorr versions 0.1.0 dated 2018-05-11 and 0.2.0 dated 2018-12-14
DESCRIPTION | 23 MD5 | 72 +- NAMESPACE | 10 NEWS.md | 20 R/blr-backward-elimination.R | 12 R/blr-forward-selection.R | 12 R/blr-gains-table.R | 140 ---- R/blr-lorenz-curve.R | 45 - R/blr-multi-model-fit-stats.R | 16 R/blr-plots-data.R |only R/blr-roc-curve.R | 38 - R/blr-stepwise-backward-regression.R | 11 R/blr-stepwise-forward-regression.R | 10 R/blr-stepwise-regression.R | 11 R/blr-stepwise-selection.R | 12 R/zzz.R | 19 README.md | 109 ++- build/vignette.rds |binary inst/application/ui.R | 2 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 1173 +++++++++++++++++++++-------------- man/blr_gains_table.Rd | 12 man/blr_ks_chart.Rd | 2 man/blr_prep_dcrate_data.Rd |only man/blr_prep_kschart_data.Rd |only man/blr_prep_lchart_gmean.Rd |only man/blr_prep_lorenz_data.Rd |only man/blr_prep_roc_data.Rd |only man/blr_roc_curve.Rd | 10 man/blr_step_aic_backward.Rd | 6 man/blr_step_aic_both.Rd | 6 man/blr_step_aic_forward.Rd | 6 man/blr_step_p_backward.Rd | 5 man/blr_step_p_both.Rd | 5 man/blr_step_p_forward.Rd | 5 tools/README-kschart-1.png |binary tools/README-lift-1.png |binary tools/README-roc-1.png |binary tools/README-unnamed-chunk-2-1.png |binary vignettes/introduction.Rmd | 2 40 files changed, 1029 insertions(+), 767 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.4.3 dated 2018-08-22 and 0.4.4 dated 2018-12-14
DESCRIPTION | 8 MD5 | 29 +- R/plot.stslist.surv.R | 4 R/seqprec.states.check.R |only R/seqprecarity.R | 28 ++ R/seqprecorr.R | 407 ++++++++++++++++++++---------------------- R/seqprecstart.R | 53 +---- R/seqsplot.R | 35 +-- R/seqsurv.R | 13 + inst/CITATION | 8 inst/NEWS | 27 ++ inst/NEWS.Rd | 35 +++ man/TraMineRextras-package.Rd | 2 man/plot.stslist.surv.Rd | 10 - man/seqprecarity.Rd | 44 ++-- man/seqprecstart.Rd | 16 + 16 files changed, 383 insertions(+), 336 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective base
version, if available. Package developers can make use of new functions or
arguments by selectively importing specific backports to
support older installations.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.1.2 dated 2017-12-13 and 1.1.3 dated 2018-12-14
.aspell |only DESCRIPTION | 35 ++++++++++++++++++++--------------- MD5 | 20 +++++++++++++++----- NAMESPACE | 4 ++++ NEWS.md | 5 +++++ R/URLencode.R |only R/capture.output.R |only R/import.R | 11 ++++++----- R/warningCondition.R |only R/zzz.R | 2 +- man/URLencode.Rd |only man/backports-package.Rd |only man/capture.output.Rd |only man/warningCondition.Rd |only tests/test_URLencode.R |only tests/test_capture.output.R |only tests/test_warningCondition.R |only 17 files changed, 51 insertions(+), 26 deletions(-)
Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full polynomial,
shifted and rotated squared differences, rising ridge surfaces, basic
squared differences). The package provides plotting functions for 3d
wireframe surfaces, interactive 3d plots, and contour plots. Calculates
many surface parameters (a1 to a4, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schönbrodt [cre, aut],
Sarah Humberg [aut]
Maintainer: Felix Schönbrodt <felix@nicebread.de>
Diff between RSA versions 0.9.12 dated 2018-07-03 and 0.9.13 dated 2018-12-14
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 + R/RSA.R | 12 ++++++++++-- R/demoRSA.R | 44 +++++++++++++++++++++++--------------------- R/imports.R | 2 +- R/plot.RSA.R | 4 ++++ R/print.RSA.R | 2 +- inst/News.Rd | 23 +++++++++++++++++++++++ man/RSA.Rd | 11 ++++++----- man/RSA.ST.Rd | 4 ++-- man/aictab.Rd | 4 ++-- man/demoRSA.Rd | 10 +++++----- man/movieRSA.Rd | 4 ++-- man/plotRSA.Rd | 41 +++++++++++++++++++++-------------------- 15 files changed, 120 insertions(+), 80 deletions(-)
Title: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Description: Reference-free method for conducting EWAS while deconvoluting DNA methylation
arising as mixtures of cell types. The older method
(Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to
surrogate variable analysis (SVA and ISVA), except that it makes additional use
of a biological mixture assumption.
The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar
to non-negative matrix factorization, with additional constraints
and additional utilities.
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman <eahouseman@gmail.com>
Diff between RefFreeEWAS versions 2.1 dated 2017-02-25 and 2.2 dated 2018-12-14
DESCRIPTION | 22 - MD5 | 21 - NAMESPACE | 39 +- R/RefFreeCellMix.R | 437 ++++++++++++++++-------------- R/RefFreeEWAS.R | 50 +++ man/EstDimIC.Rd | 58 +-- man/EstDimRMT.Rd |only man/ImputeByMean.Rd |only man/RefFreeCellMix.Rd | 86 ++--- man/RefFreeCellMixArray.Rd | 79 ++--- man/RefFreeCellMixArrayWithCustomStart.Rd |only man/RefFreeCellMixInitialize.Rd | 54 +-- man/RefFreeCellMixInitializeBySVD.Rd |only man/SVDwithMissing.Rd |only 14 files changed, 477 insertions(+), 369 deletions(-)
Title: Parsimonious Gaussian Mixture Models
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.
Author: Paul D. McNicholas [aut, cre],
Aisha ElSherbiny [aut],
K. Raju Jampani [ctb],
Aaron F. McDaid [aut],
T. Brendan Murphy [aut],
Larry Banks [ctb]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between pgmm versions 1.2.2 dated 2018-03-18 and 1.2.3 dated 2018-12-14
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 12 +-- R/pgmmEM.R | 176 ++++++++++++++++++++++++++++------------------------------ man/pgmm.Rd | 4 - man/pgmmEM.Rd | 4 - src/aecm.c | 49 +++++++++++----- 7 files changed, 142 insertions(+), 116 deletions(-)
Title: Statistical Inference and Sure Independence Screening via Ball
Statistics
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence <doi:10.1214/17-AOS1579>, ball covariance, and ball correlation <doi:10.1080/01621459.2018.1462709>, are developed to analyze complex data. The ball divergence and ball covariance based distribution-free tests are implemented to detecting distribution difference and association in metric spaces <arXiv:1811.03750>. Furthermore, a generic non-parametric SIS procedure based on ball correlation and all of its variants are implemented to tackle the challenge in the context of ultra high dimensional data.
Author: Xueqin Wang, Wenliang Pan, Heping Zhang, Hongtu Zhu, Yuan Tian, Weinan Xiao, Chengfeng Liu, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between Ball versions 1.3.6 dated 2018-12-03 and 1.3.7 dated 2018-12-14
DESCRIPTION | 10 ++-- MD5 | 31 ++++++------- NEWS.md | 4 + R/Ball.R |only R/bcorsis.R | 31 ++++++------- R/bcov.R | 106 ++++++++++++++++++++++----------------------- R/bd.R | 82 +++++++++++++++++----------------- R/data.R | 44 ++++++++---------- R/wrap_c.R | 50 ++++++++++----------- inst/doc/Ball.html | 8 +-- man/bcorsis.Rd | 13 +++-- man/bcov.Rd | 8 +-- man/bcov.test.Rd | 36 ++++++++------- man/bd.Rd | 8 +-- man/bd.test.Rd | 40 ++++++++-------- tests/testthat/test_bcov.R | 20 ++++---- tests/testthat/test_bd.R | 26 +++++------ 17 files changed, 266 insertions(+), 251 deletions(-)