Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD),
and forecasting time-series using fuzzy rule-based ensemble (FRBE).
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 1.2 dated 2015-06-18 and 1.3 dated 2016-04-22
lfl-1.2/lfl/R/tnorm.R |only lfl-1.2/lfl/man/tnorm.Rd |only lfl-1.2/lfl/tests/testthat/test-tnorm.R |only lfl-1.3/lfl/DESCRIPTION | 12 ++--- lfl-1.3/lfl/MD5 | 60 ++++++++++++++++----------- lfl-1.3/lfl/NAMESPACE | 1 lfl-1.3/lfl/R/algebra.R |only lfl-1.3/lfl/R/compose.R |only lfl-1.3/lfl/R/fire.R | 2 lfl-1.3/lfl/R/is.algebra.R |only lfl-1.3/lfl/R/mult.R |only lfl-1.3/lfl/R/pbld.R | 4 - lfl-1.3/lfl/R/rbcoverage.R | 2 lfl-1.3/lfl/R/reduce.R | 15 +++++- lfl-1.3/lfl/R/searchrules.R | 10 +++- lfl-1.3/lfl/man/aggregate.Rd | 2 lfl-1.3/lfl/man/algebra.Rd |only lfl-1.3/lfl/man/compose.Rd |only lfl-1.3/lfl/man/fcut.Rd | 11 ++-- lfl-1.3/lfl/man/fire.Rd | 12 ++--- lfl-1.3/lfl/man/fsets.Rd | 4 - lfl-1.3/lfl/man/lcut.Rd | 4 - lfl-1.3/lfl/man/mult.Rd |only lfl-1.3/lfl/man/pbld.Rd | 2 lfl-1.3/lfl/man/perceive.Rd | 2 lfl-1.3/lfl/man/rbcoverage.Rd | 10 ++-- lfl-1.3/lfl/man/reduce.Rd | 8 +-- lfl-1.3/lfl/man/searchrules.Rd | 4 - lfl-1.3/lfl/src/algebra.cpp |only lfl-1.3/lfl/src/algebra.h |only lfl-1.3/lfl/src/common.h | 12 +++++ lfl-1.3/lfl/src/mult.cpp |only lfl-1.3/lfl/src/mult.h |only lfl-1.3/lfl/src/reduce.cpp | 2 lfl-1.3/lfl/tests/testthat/test-algebra.R |only lfl-1.3/lfl/tests/testthat/test-compose.R |only lfl-1.3/lfl/tests/testthat/test-fire.R | 12 ++--- lfl-1.3/lfl/tests/testthat/test-is.algebra.R |only lfl-1.3/lfl/tests/testthat/test-mult.R |only lfl-1.3/lfl/tests/testthat/test-rbcoverage.R | 10 ++-- 40 files changed, 120 insertions(+), 81 deletions(-)
Title: Short Term Forecasting via GMDH-Type Neural Network Algorithms
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to make short term forecasting for a univariate time series.
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH versions 1.3 dated 2016-03-07 and 1.4 dated 2016-04-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/fcast.R | 15 ++++++++------- man/GMDH.Rd | 4 ++-- man/fcast.Rd | 6 ++++-- 5 files changed, 22 insertions(+), 19 deletions(-)
Title: Functional Data Analysis and Partial Differential Equations;
Statistical Analysis of Functional and Spatial Data, Based on
Regression with Partial Differential Regularizations
Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization.
Author: Eardi Lila [aut, cre],
Laura M. Sangalli [aut],
Jim Ramsay [aut],
Luca Formaggia [aut]
Maintainer: Eardi Lila <el425@cam.ac.uk>
Diff between fdaPDE versions 0.1-2 dated 2016-03-09 and 0.1-3 dated 2016-04-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/fdaPDE.smoothing.R | 16 +++++++++++++--- R/mesh.2D.R | 4 ++-- src/mesh_objects_imp.h | 4 ++-- src/mixedFERegression.h | 3 +-- src/mixedFERegression_imp.h | 7 ++++--- 7 files changed, 32 insertions(+), 22 deletions(-)
Title: Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Description: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. eRah outputs a table with compound names, matching scores and the integrated area of the compound for each sample.
Author: Xavier Domingo-Almenara, Alexandre Perera, Maria Vinaixa, Sara Samino, Marta Diaz, Lourdes Ibanez, Xavier Correig, Jesus Brezmes, Oscar Yanes
Maintainer: Xavier Domingo-Almenara <xavier.domingo@urv.cat>
Diff between erah versions 1.0.0 dated 2016-04-15 and 1.0.1 dated 2016-04-22
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS |only inst/doc/eRahManual.pdf |binary 4 files changed, 6 insertions(+), 5 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with both continuous and discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.26 dated 2015-12-21 and 2.27 dated 2016-04-22
BDgraph-2.26/BDgraph/build |only BDgraph-2.26/BDgraph/inst |only BDgraph-2.26/BDgraph/vignettes |only BDgraph-2.27/BDgraph/DESCRIPTION | 12 - BDgraph-2.27/BDgraph/MD5 | 36 +-- BDgraph-2.27/BDgraph/R/bdgraph.R | 169 +++++++++++++----- BDgraph-2.27/BDgraph/R/plotcoda.R | 8 BDgraph-2.27/BDgraph/man/BDgraph-package.Rd | 4 BDgraph-2.27/BDgraph/src/gcgm_DMH_bd.cpp |only BDgraph-2.27/BDgraph/src/gcgm_DMH_bd_multi_update.cpp |only BDgraph-2.27/BDgraph/src/gcgm_DMH_rj.cpp |only BDgraph-2.27/BDgraph/src/gcgm_bd.cpp | 15 - BDgraph-2.27/BDgraph/src/gcgm_bd_multi_update.cpp | 12 - BDgraph-2.27/BDgraph/src/gcgm_rj.cpp | 12 - BDgraph-2.27/BDgraph/src/ggm_DMH_bd.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_bd_multi_update.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_rj.cpp |only BDgraph-2.27/BDgraph/src/ggm_bd.cpp | 26 +- BDgraph-2.27/BDgraph/src/ggm_bd_multi_update.cpp | 17 - BDgraph-2.27/BDgraph/src/ggm_rj.cpp | 16 - BDgraph-2.27/BDgraph/src/matrix.cpp | 68 ++++++- BDgraph-2.27/BDgraph/src/matrix.h | 8 22 files changed, 280 insertions(+), 123 deletions(-)
Title: Advanced Data Analysis of Immune Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor and
Immunoglobulin repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 2.2.1.7 dated 2015-12-22 and 2.2.1.11 dated 2016-04-22
DESCRIPTION | 10 - MD5 | 22 +-- R/docdata.R | 254 +++++++++++++++++++++++++++++++++++++--------- R/io.R | 2 R/parsing.R | 138 ++++++++++++++++++------ R/plots.R | 39 +++++-- README.md | 4 build/vignette.rds |binary inst/doc/tcrvignette.html | 24 ++-- man/parse.folder.Rd | 3 man/segments.alphabets.Rd | 26 ++++ man/vis.heatmap.Rd | 6 - 12 files changed, 405 insertions(+), 123 deletions(-)
Title: Multidimensional Scaling
Description: Provides the following approaches for multidimensional scaling (MDS) based on stress minimization by means of majorization (smacof): basic MDS on symmetric dissimilarity matrices,
MDS with external constraints on the configuration, individual difference scaling (idioscal, indscal, and friends), MDS with spherical restrictions, and unfolding. The MDS type can be ratio, interval, ordinal, and monotone splines.
Various tools and extensions like jackknife MDS, permutation tests, gravity models, inverse MDS, unidimensional scaling, classical scaling, and Procrustes.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Ingwer Borg [ctb], Patrick J. F. Groenen [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between smacof versions 1.8-10 dated 2016-02-02 and 1.8-13 dated 2016-04-22
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NAMESPACE | 3 ++- R/dissWeights.R |only R/plot.smacof.R | 32 +++++++++++++++++++++++--------- R/smacofConstraint.R | 2 +- R/smacofIndDiff.R | 2 +- R/smacofSphere.R | 2 +- R/smacofSym.R | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 22 ++++++++++++++++++++++ inst/doc/smacof.pdf |binary man/dissWeights.Rd |only man/plot.smacof.rd | 7 +++++-- 14 files changed, 74 insertions(+), 32 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.20.5 dated 2016-04-12 and 0.20.7 dated 2016-04-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/export_functions.r | 2 +- R/methods_class_dimVar.r | 38 +++++++++++++++++++++----------------- R/methods_class_sdcProblem.r | 5 ++++- R/methods_multiple_classes.r | 4 +++- inst/doc/sdcTable.pdf |binary 7 files changed, 39 insertions(+), 30 deletions(-)
Title: Fitting Distributions to Given Data or Known Quantiles
Description: Collection of functions for fitting distributions to given data or
by known quantiles. Two main functions fit.perc() and fit.cont() provide
users a GUI that allows to choose a most appropriate distribution without
any knowledge of the R syntax. Note, this package is a part of the 'rrisk'
project.
Author: Natalia Belgorodski [aut] (STAT-UP Statistical Consulting),
Matthias Greiner [aut, cre] (Federal Institute for Risk Assessment,
Germany),
Kristin Tolksdorf [aut] (Federal Institute for Risk Assessment,
Germany),
Katharina Schueller [aut] (STAT-UP Statistical Consulting),
Matthias Flor [ctb] (Federal Institute for Risk Assessment, Germany),
Lutz Göhring [ctb] (Lutz Göhring Consulting)
Maintainer: Matthias Greiner <matthias.greiner@bfr.bund.de>
Diff between rriskDistributions versions 2.1 dated 2015-05-19 and 2.1.1 dated 2016-04-22
rriskDistributions-2.1.1/rriskDistributions/DESCRIPTION | 19 rriskDistributions-2.1.1/rriskDistributions/MD5 | 70 +- rriskDistributions-2.1.1/rriskDistributions/NAMESPACE | 86 +-- rriskDistributions-2.1.1/rriskDistributions/R/rriskDistributions-package.R | 124 ++-- rriskDistributions-2.1.1/rriskDistributions/R/rriskDistributions_functions.R |only rriskDistributions-2.1.1/rriskDistributions/README.md | 78 +- rriskDistributions-2.1.1/rriskDistributions/man/fit.cont.Rd | 97 +-- rriskDistributions-2.1.1/rriskDistributions/man/fit.perc.Rd | 154 ++--- rriskDistributions-2.1.1/rriskDistributions/man/get.beta.par.Rd | 251 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.cauchy.par.Rd | 249 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.chisq.par.Rd | 241 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.chisqnc.par.Rd | 249 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.exp.par.Rd | 260 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.f.par.Rd | 245 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.gamma.par.Rd | 251 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.gompertz.par.Rd | 258 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.hyper.par.Rd | 213 +++---- rriskDistributions-2.1.1/rriskDistributions/man/get.lnorm.par.Rd | 273 +++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.logis.par.Rd | 228 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.nbinom.par.Rd | 247 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.norm.par.Rd | 251 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.norm.sd.Rd | 231 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.pert.par.Rd | 251 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.pois.par.Rd | 245 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.t.par.Rd | 245 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.tnorm.par.Rd | 232 ++++---- rriskDistributions-2.1.1/rriskDistributions/man/get.triang.par.Rd | 246 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/get.unif.par.Rd | 137 ++--- rriskDistributions-2.1.1/rriskDistributions/man/get.weibull.par.Rd | 260 ++++----- rriskDistributions-2.1.1/rriskDistributions/man/plotDiagnostics.perc.Rd | 126 ++-- rriskDistributions-2.1.1/rriskDistributions/man/rriskDistributions-package.Rd | 137 ++--- rriskDistributions-2.1.1/rriskDistributions/man/rriskFitdist.cont.Rd | 179 +++--- rriskDistributions-2.1.1/rriskDistributions/man/rriskFitdist.perc.Rd | 139 ++--- rriskDistributions-2.1.1/rriskDistributions/man/rriskMLEdist.Rd | 190 +++--- rriskDistributions-2.1.1/rriskDistributions/man/rriskMMEdist.Rd | 131 ++-- rriskDistributions-2.1.1/rriskDistributions/man/useFitdist.Rd | 93 +-- rriskDistributions-2.1/rriskDistributions/R/rriskDistributions_functions_v1.9.1.R |only 37 files changed, 3400 insertions(+), 3286 deletions(-)
More information about rriskDistributions at CRAN
Permanent link
Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses
and geolocating them to country, city, timezone and other geographic ranges. For
individual connectors, see the package index.
Author: Oliver Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb],
Maxmind, Inc. [cph], Pascal Gloor [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between rgeolocate versions 0.5.0 dated 2015-10-12 and 0.7.0 dated 2016-04-22
rgeolocate-0.5.0/rgeolocate/R/telize.R |only rgeolocate-0.5.0/rgeolocate/man/telize.Rd |only rgeolocate-0.7.0/rgeolocate/DESCRIPTION | 16 + rgeolocate-0.7.0/rgeolocate/MD5 | 42 ++-- rgeolocate-0.7.0/rgeolocate/NAMESPACE | 3 rgeolocate-0.7.0/rgeolocate/NEWS | 23 ++ rgeolocate-0.7.0/rgeolocate/R/maxmind.R | 14 + rgeolocate-0.7.0/rgeolocate/README.md | 9 rgeolocate-0.7.0/rgeolocate/build/vignette.rds |binary rgeolocate-0.7.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.Rmd | 15 - rgeolocate-0.7.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.html | 75 ++++--- rgeolocate-0.7.0/rgeolocate/inst/extdata/GeoLite2-Country.mmdb |binary rgeolocate-0.7.0/rgeolocate/man/db_ip.Rd | 2 rgeolocate-0.7.0/rgeolocate/man/ip_api.Rd | 2 rgeolocate-0.7.0/rgeolocate/man/maxmind.Rd | 14 + rgeolocate-0.7.0/rgeolocate/man/rgeolocate.Rd | 2 rgeolocate-0.7.0/rgeolocate/src/RcppExports.cpp | 4 rgeolocate-0.7.0/rgeolocate/src/maxmind.cpp | 95 +++++++--- rgeolocate-0.7.0/rgeolocate/src/maxmind.h | 24 +- rgeolocate-0.7.0/rgeolocate/src/rgeolocate.cpp | 2 rgeolocate-0.7.0/rgeolocate/tests/testthat/test_ip_api.R | 38 ++-- rgeolocate-0.7.0/rgeolocate/tests/testthat/test_maxmind.R | 15 - rgeolocate-0.7.0/rgeolocate/vignettes/Introduction_to_rgeolocate.Rmd | 15 - 23 files changed, 258 insertions(+), 152 deletions(-)
Title: Multidimensional Iterative Proportional Fitting and Alternative
Models
Description: An implementation of the iterative proportional fitting (IPFP),
maximum likelihood, minimum chi-square and weighted least squares procedures
for updating a N-dimensional array with respect to given target marginal
distributions (which, in turn can be multi-dimensional). The package also
provides an application of the IPFP to simulate multivariate Bernoulli
distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>
Diff between mipfp versions 2.2.1 dated 2015-09-19 and 3.0 dated 2016-04-22
DESCRIPTION | 8 - MD5 | 46 +++-- NAMESPACE | 15 + R/deprecated.R |only R/ipfp_multi_dim.R | 132 ++++------------ R/models.R | 220 ++++++--------------------- R/s3_mipfp.R |only R/utils.R | 352 ++++++++++++++++++++++++++++++++++++-------- man/CompareMaxDev.Rd |only man/ComputeA.Rd |only man/Corr2Odds.Rd | 166 ++++++++++---------- man/Corr2PairProbs.Rd | 4 man/Estimate.Rd |only man/GetConfInt.Rd | 26 ++- man/GetLinInd.Rd | 2 man/Ipfp.Rd | 65 ++------ man/IpfpCov.Rd | 33 ++-- man/ObtainModelEstimates.Rd | 89 +++-------- man/Odds2Corr.Rd | 2 man/RMultBinary.Rd | 4 man/Vector2Array.Rd | 2 man/coef.mipfp.Rd |only man/confint.mipfp.Rd |only man/error.margins.Rd |only man/flat.Rd |only man/gof.estimates.Rd |only man/mipfp-package.Rd | 48 +++--- man/spnamur.Rd | 88 +++++------ man/summary.mipfp.Rd |only man/vcov.mipfp.Rd |only 30 files changed, 669 insertions(+), 633 deletions(-)
Title: Elastic Functional Data Analysis
Description: Functions to support functional data analysis using the square root velocity framework.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.6.0 dated 2016-01-15 and 1.6.1 dated 2016-04-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 ++++- R/curve_karcher_mean.R | 9 ++++++--- README.md | 2 +- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: Item Focused Trees for the Identification of Items in
Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of
items and variables that induce Differential Item Functioning (DIF) based on the
Rasch Model or the Logistic Regression Approach for DIF detection.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Diff between DIFtree versions 2.0.1 dated 2016-01-21 and 2.0.2 dated 2016-04-22
DESCRIPTION | 8 ++--- MD5 | 12 +++---- R/DIFtree.R | 6 +-- R/DIFtree.default.R | 27 +++++++++------- R/tree_Rasch.R | 78 ++++++++++++++++++++++++------------------------- man/DIFtree.Rd | 9 +++-- man/summary.DIFtree.Rd | 4 +- 7 files changed, 74 insertions(+), 70 deletions(-)
Title: Exploring Genomic Relations at the Gene and SNP Level Through
Enrichment, Similarity and Network Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list more interpretable by comprehensively utilising ontology and network information to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, and 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs. Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene and SNP level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.0 dated 2016-04-07 and 1.0.1 dated 2016-04-22
XGR-1.0.0/XGR/R/xPrioritiser.r |only XGR-1.0.0/XGR/R/xPrioritiserGenes.r |only XGR-1.0.0/XGR/R/xPrioritiserManhattan.r |only XGR-1.0.0/XGR/R/xPrioritiserPathways.r |only XGR-1.0.0/XGR/R/xPrioritiserSNPs.r |only XGR-1.0.0/XGR/README.md |only XGR-1.0.0/XGR/inst/AS.txt |only XGR-1.0.0/XGR/inst/CITATIONS.md |only XGR-1.0.0/XGR/inst/HTML.md |only XGR-1.0.0/XGR/inst/INSTALLATION.md |only XGR-1.0.0/XGR/inst/SLE.txt |only XGR-1.0.0/XGR/inst/Spondyloarthritis.txt |only XGR-1.0.0/XGR/inst/xPrioritiser.html |only XGR-1.0.0/XGR/inst/xPrioritiserGenes.html |only XGR-1.0.0/XGR/inst/xPrioritiserManhattan.html |only XGR-1.0.0/XGR/inst/xPrioritiserPathways.html |only XGR-1.0.0/XGR/inst/xPrioritiserSNPs.html |only XGR-1.0.0/XGR/man/xPrioritiser.Rd |only XGR-1.0.0/XGR/man/xPrioritiserGenes.Rd |only XGR-1.0.0/XGR/man/xPrioritiserManhattan.Rd |only XGR-1.0.0/XGR/man/xPrioritiserPathways.Rd |only XGR-1.0.0/XGR/man/xPrioritiserSNPs.Rd |only XGR-1.0.0/XGR/vignettes |only XGR-1.0.1/XGR/DESCRIPTION | 19 +++---- XGR-1.0.1/XGR/MD5 | 67 ++++++++----------------- XGR-1.0.1/XGR/NAMESPACE | 11 ---- XGR-1.0.1/XGR/R/xCircos.r | 69 +++++++++++++++----------- XGR-1.0.1/XGR/R/xDAGsim.r | 2 XGR-1.0.1/XGR/R/xEnrichViewer.r | 4 - XGR-1.0.1/XGR/R/xSocialiser.r | 2 XGR-1.0.1/XGR/R/xSocialiserGenes.r | 2 XGR-1.0.1/XGR/R/xSocialiserSNPs.r | 2 XGR-1.0.1/XGR/R/xSubneterSNPs.r | 4 - XGR-1.0.1/XGR/inst/NEWS |only XGR-1.0.1/XGR/inst/xCircos.html | 24 ++++----- XGR-1.0.1/XGR/inst/xDAGsim.html | 4 - XGR-1.0.1/XGR/inst/xSocialiser.html | 4 - XGR-1.0.1/XGR/inst/xSocialiserGenes.html | 4 - XGR-1.0.1/XGR/inst/xSocialiserSNPs.html | 4 - XGR-1.0.1/XGR/inst/xSubneterSNPs.html | 5 + XGR-1.0.1/XGR/man/xCircos.Rd | 22 ++++---- XGR-1.0.1/XGR/man/xDAGsim.Rd | 4 - XGR-1.0.1/XGR/man/xSocialiser.Rd | 4 - XGR-1.0.1/XGR/man/xSocialiserGenes.Rd | 4 - XGR-1.0.1/XGR/man/xSocialiserSNPs.Rd | 4 - XGR-1.0.1/XGR/man/xSubneterSNPs.Rd | 5 + 46 files changed, 125 insertions(+), 145 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.4 dated 2016-03-01 and 1.5 dated 2016-04-22
DESCRIPTION | 6 - MD5 | 28 +++---- R/gui.R | 19 ++--- R/kde.R | 30 ++++---- R/plot.R | 161 +++++++++++++++++++++++++++------------------ man/KDE.Rd | 5 + man/KDEs.Rd | 5 + man/plot.GPA.Rd | 20 +++++ man/plot.INDSCAL.Rd | 20 +++++ man/plot.KDE.Rd | 9 +- man/plot.MDS.Rd | 25 +++++- man/plot.compositional.Rd | 6 + man/plot.distributional.Rd | 15 ++-- man/plot.minsorting.Rd | 7 + man/plot.ternary.Rd | 18 +++-- 15 files changed, 241 insertions(+), 133 deletions(-)
Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies using asymptotic chi-square or exact statistics. These tests were motivated to reveal evidence for causality based on functional dependencies. They include asymptotic functional chi-square tests, an exact functional test, a comparative functional chi-square test, and also a comparative chi-square test. The normalized non-constant functional chi-square test was used by Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed. They also provide a novel means to assess directional dependencies among categorical data not possible with classical Pearson's chi-square or Fisher's exact tests.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.2.3 dated 2016-04-01 and 2.2.4 dated 2016-04-22
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++++--- NEWS | 7 +++++++ build |only inst/doc |only man/FunChisq-package.Rd | 8 +++----- vignettes |only 7 files changed, 24 insertions(+), 14 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I
clinical trial design for finding the maximum tolerated dose (MTD). It can be
used to design both single-agent and drug-combination trials. The BOIN design
is motivated by the top priority and concern of clinicians when testing a new
drug, which is to effectively treat patients and minimize the chance of exposing
them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same
time. The BOIN design is algorithm-based and can be implemented in a simple
way similar to the traditional 3+3 design. The BOIN design yields an average
performance that is comparable to that of the continual reassessment method
(CRM, one of the best model-based designs) in terms of selecting the MTD, but
has a substantially lower risk of assigning patients to subtherapeutic or overly
toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 2.1 dated 2016-03-01 and 2.2 dated 2016-04-22
DESCRIPTION | 8 ++--- MD5 | 38 +++++++++++------------ NAMESPACE | 2 - R/BOIN.R | 2 - R/get.boundary.R | 10 +++--- R/get.oc.R | 9 +++-- R/get.oc.comb.R | 37 +++++++++++------------ R/get.oc.comb.phase12.R | 23 +++++++------- R/next.comb.R | 6 +-- R/next.subtrial.R | 72 +++++++++++++++++++++------------------------ R/select.mtd.R | 15 ++++++--- R/select.mtd.comb.R | 16 +++++----- man/get.boundary.Rd | 8 ++--- man/get.oc.Rd | 10 ++++-- man/get.oc.comb.Rd | 26 ++++++++-------- man/get.oc.comb.phase12.Rd | 22 ++++++------- man/next.comb.Rd | 6 +-- man/next.subtrial.Rd | 24 +++++---------- man/select.mtd.Rd | 12 +++++-- man/select.mtd.comb.Rd | 12 +++---- 20 files changed, 185 insertions(+), 173 deletions(-)