Title: Clustering via the Mean Shift Algorithm
Description: Clustering of vector data and functional data using the mean shift algorithm (multi-core processing is supported) or its blurring version.
Author: Mattia Ciollaro and Daren Wang
Maintainer: Mattia Ciollaro <mattiaciollaro@gmail.com>
Diff between MeanShift versions 1.0-2 dated 2016-02-06 and 1.1-1 dated 2016-04-23
DESCRIPTION | 14 ++++++++------ MD5 | 29 ++++++++++++++++++++++------- NAMESPACE | 4 +++- R/blurredmeanshift.R | 18 +++++++++--------- R/ext_functional.R |only README.md |only build/partial.rdb |binary build/vignette.rds |only inst |only man/MeanShift-package.Rd | 2 +- man/bmsClustering.Rd | 3 ++- man/msClustering.Rd | 8 +++----- man/projectCurveWavelets.Rd |only vignettes |only 14 files changed, 48 insertions(+), 30 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 0.1-3 dated 2016-04-22 and 0.1-4 dated 2016-04-23
fdaPDE-0.1-3/fdaPDE/README.md |only fdaPDE-0.1-4/fdaPDE/DESCRIPTION | 8 ++++---- fdaPDE-0.1-4/fdaPDE/MD5 | 15 ++++++++------- fdaPDE-0.1-4/fdaPDE/R/fdaPDE.checkParameters.R | 4 ++-- fdaPDE-0.1-4/fdaPDE/src/matrix_assembler_imp.h | 3 +++ fdaPDE-0.1-4/fdaPDE/src/mesh_objects_imp.h | 4 ++-- fdaPDE-0.1-4/fdaPDE/src/mixedFERegression.h | 1 - fdaPDE-0.1-4/fdaPDE/src/mixedFERegression_imp.h | 4 +++- fdaPDE-0.1-4/fdaPDE/tests/testcovariatesO1.R |only fdaPDE-0.1-4/fdaPDE/tests/testcovariatesO2.R |only 10 files changed, 22 insertions(+), 17 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>
Diff between Rdsdp versions 1.0.4 dated 2015-09-11 and 1.0.4-1 dated 2016-04-23
DESCRIPTION | 6 - MD5 | 4 src/dsdp/make.include | 274 +++++++++++++++++++++++++------------------------- 3 files changed, 142 insertions(+), 142 deletions(-)
Title: R interface to the CSDP semidefinite programming library
Description: R interface to the CSDP semidefinite programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if required. An existing installation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.
Author: Hector Corrada Bravo (CSDP by Brian Borchers)
Maintainer: Hector Corrada Bravo <hcorrada@gmail.com>
Diff between Rcsdp versions 0.1.53 dated 2014-04-12 and 0.1.53-1 dated 2016-04-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Csdp/lib/Makefile | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer
data in a number of formats usable in R, downloading a zip with all data from a
Quandl database, and the ability to search. This R package uses the Quandl API.
For more information go to https://www.quandl.com/docs/api. For more help on the
package itself go to https://www.quandl.com/help/r.
Author: Raymond McTaggart [aut, cre],
Gergely Daroczi [aut],
Clement Leung [aut],
Quandl Inc. [cph]
Maintainer: Raymond McTaggart <ray@quandl.com>
Diff between Quandl versions 2.7.0 dated 2015-09-17 and 2.8.0 dated 2016-04-23
ChangeLog | 6 ++ DESCRIPTION | 19 +++++---- LICENSE | 2 MD5 | 40 ++++++++++--------- NAMESPACE | 3 - R/Quandlapi.R | 34 ++++++++++++++++ R/Quandldatabase.R | 6 -- R/Quandldatatable.R |only README.md | 56 ++++++++++++++++----------- man/Quandl.Rd | 2 man/Quandl.api_key.Rd | 2 man/Quandl.auth.Rd | 2 man/Quandl.database.bulk_download_to_file.Rd | 2 man/Quandl.database.bulk_download_url.Rd | 2 man/Quandl.dataset.get.Rd | 2 man/Quandl.datatable.Rd |only man/Quandl.search.Rd | 2 man/metaData.Rd | 2 man/quandl.api.Rd | 2 tests/testthat/test-api.r | 13 +++++- tests/testthat/test-database.r | 27 ------------- tests/testthat/test-datatable-helper.r |only tests/testthat/test-datatable.r |only 23 files changed, 134 insertions(+), 90 deletions(-)
Title: In-Process Version of MonetDB for R
Description: An in-process version of MonetDB, a relational database focused on analytical tasks. Similar to SQLite, the database runs entirely inside the R shell, with the main difference that queries complete much faster thanks to MonetDB's columnar architecture.
Author: MonetDB Development Team
Maintainer: Hannes Muehleisen <hannes@cwi.nl>
Diff between MonetDBLite versions 0.2.0 dated 2016-03-11 and 0.2.2 dated 2016-04-23
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Title: Estimating Time-Varying Mixed Graphical Models
Description: Estimation of time-varying Mixed Graphical model using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.1-4 dated 2016-01-07 and 1.1-5 dated 2016-04-23
DESCRIPTION | 12 - MD5 | 35 +++- NAMESPACE | 7 R/RcppExports.R | 14 - R/calc.EBIC.R |only R/f_VARreshape.R |only R/mgmfit.R | 362 +++------------------------------------------- R/mgmfit_core.R |only R/mgmsampler.R | 5 R/node.est.R |only R/tv.mgmfit.R |only R/tv.mgmsampler.R |only R/tv_var.mgm.R |only R/var.mgm.R |only man/confusion.Rd | 98 ++++++------ man/mgm-internal.Rd |only man/mgm-package.Rd | 91 ++++------- man/mgmfit.Rd | 192 ++++++++++++------------ man/mgmsampler.Rd | 153 ++++++++++--------- man/print.mgm.Rd | 68 +++----- man/tv.mgmfit.Rd |only man/tv.mgmsampler.Rd |only man/tv_var.mgm.Rd |only man/var.mgm.Rd |only src/mMRFSampler_Ccore.cpp | 23 ++ 25 files changed, 380 insertions(+), 680 deletions(-)
Title: Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School
Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary
school.
Author: Eleonora Feist [ctb] (contributed as student in the initial phase
--2008),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Anja Hueller [ctb] (contributed as student in the initial phase --2008)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTeach versions 2.6 dated 2016-04-23 and 2.6.1 dated 2016-04-23
DESCRIPTION | 14 +++++++------- MD5 | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-)
Title: Estimation and Testing Classes Based on Package 'distr'
Description: Evaluation (S4-)classes based on package distr for evaluating procedures
(estimators/tests) at data/simulation in a unified way.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTEst versions 2.5 dated 2013-09-13 and 2.6 dated 2016-04-23
DESCRIPTION | 39 +++++++++++++++++++++++++-------------- MD5 | 22 +++++++++++----------- NAMESPACE | 4 +++- R/summary-methods.R | 2 +- inst/CITATION | 1 - inst/NEWS | 9 +++++++++ man/0distrTEst-package.Rd | 17 +++++++++-------- man/Evaluation-class.Rd | 2 +- man/EvaluationList-class.Rd | 2 +- man/distrTEst-internals.Rd | 2 +- man/distrTEstoptions.Rd | 2 +- man/numericorNULL-class.Rd | 2 +- 12 files changed, 63 insertions(+), 41 deletions(-)
Title: Distribution Classes for Distributions from Rmetrics
Description: S4-distribution classes based on package distr for distributions from packages
'fBasics' and 'fGarch'.
Author: Peter Ruckdeschel [cre, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrRmetrics versions 2.5 dated 2013-09-13 and 2.6 dated 2016-04-23
DESCRIPTION | 24 +++++++++++++----------- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + inst/CITATION | 1 - inst/NEWS | 11 +++++++++++ man/0distrRmetrics-package.Rd | 20 ++++++++++---------- man/SNorm-class.Rd | 2 +- man/SNorm.Rd | 2 +- man/SNormParameter-class.Rd | 2 +- man/SSTd-class.Rd | 2 +- man/SSTd.Rd | 2 +- man/SSTdParameter-class.Rd | 2 +- man/STd.Rd | 2 +- 13 files changed, 54 insertions(+), 41 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.5 dated 2016-03-28 and 0.3.6 dated 2016-04-23
DESCRIPTION | 10 +-- MD5 | 36 +++++------ NEWS | 9 ++ R/chordDiagram.R | 2 R/genomic.R | 9 +- R/global.R | 6 + R/link.R | 72 ++++++++++++++-------- R/plot.R | 8 +- inst/doc/circlize.R | 8 +- inst/doc/circlize.Rnw | 7 +- inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.Rnw | 2 inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary vignettes/circlize.Rnw | 7 +- vignettes/interesting_graphics.Rnw | 2 19 files changed, 110 insertions(+), 68 deletions(-)
Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful
and 'ready-to-publish' survival curves with the 'number at risk' table.
Other functions are also available for visual examinations of cox model assumptions.
Author: Alboukadel Kassambara [aut, cre],
Marcin Kosinski [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between survminer versions 0.2.0 dated 2016-02-18 and 0.2.1 dated 2016-04-23
DESCRIPTION | 30 ++--- MD5 | 18 ++- NAMESPACE | 10 + NEWS.md | 28 ++++ R/ggcoxfunctional.R |only R/ggcoxzph.R |only R/ggsurvplot.R | 80 +++++++++++-- R/theme_classic2.R |only README.md | 285 +++++-------------------------------------------- man/ggcoxfunctional.Rd |only man/ggcoxzph.Rd |only man/ggsurvplot.Rd | 13 +- man/theme_classic2.Rd |only 13 files changed, 167 insertions(+), 297 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-71 dated 2016-04-01 and 0.1-72 dated 2016-04-23
DESCRIPTION | 12 ++--- MD5 | 13 ++++-- NAMESPACE | 13 +++--- NEWS | 3 + R/ICA.BinCont.R |only R/plot_ICABinCont.R |only R/summary_ICABinCont.R |only man/ICABinCont.Rd |only man/plot.ICABinCont.Rd |only man/summary.gen.Rd | 106 ++++++++++++++++++++++++------------------------- 10 files changed, 80 insertions(+), 67 deletions(-)
Title: Utilities for Start-Up Messages
Description: Provides utilities to create or suppress start-up messages.
Author: Peter Ruckdeschel [cre, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between startupmsg versions 0.9 dated 2013-09-13 and 0.9.3 dated 2016-04-23
DESCRIPTION | 26 ++++++++++++++------------ MD5 | 8 ++++---- inst/NEWS | 1 + man/StartupUtilities.Rd | 2 +- man/myStartupUtilities.Rd | 2 +- 5 files changed, 21 insertions(+), 18 deletions(-)
Title: Diverse Basic Statistical and Graphical Functions
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé <mx.herve@gmail.com>
Diff between RVAideMemoire versions 0.9-54 dated 2016-03-28 and 0.9-55 dated 2016-04-23
RVAideMemoire-0.9-54/RVAideMemoire/R/multtest.R |only RVAideMemoire-0.9-54/RVAideMemoire/man/multtest.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/DESCRIPTION | 8 +- RVAideMemoire-0.9-55/RVAideMemoire/MD5 | 27 ++++++---- RVAideMemoire-0.9-55/RVAideMemoire/NAMESPACE | 10 ++- RVAideMemoire-0.9-55/RVAideMemoire/NEWS | 7 ++ RVAideMemoire-0.9-55/RVAideMemoire/R/MVA.scores.R | 2 RVAideMemoire-0.9-55/RVAideMemoire/R/coord.proj.R |only RVAideMemoire-0.9-55/RVAideMemoire/R/loc.slp.R |only RVAideMemoire-0.9-55/RVAideMemoire/R/multtest.cor.R |only RVAideMemoire-0.9-55/RVAideMemoire/R/multtest.gp.R |only RVAideMemoire-0.9-55/RVAideMemoire/R/zzz.R | 2 RVAideMemoire-0.9-55/RVAideMemoire/man/MVA.cor.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/man/MVA.load.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/man/MVA.scoreplot.Rd | 2 RVAideMemoire-0.9-55/RVAideMemoire/man/MVA.scores.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/man/RVAideMemoire-package.Rd | 4 - RVAideMemoire-0.9-55/RVAideMemoire/man/coord.proj.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/man/loc.slp.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/man/multtest.cor.Rd |only RVAideMemoire-0.9-55/RVAideMemoire/man/multtest.gp.Rd |only 21 files changed, 41 insertions(+), 21 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.8 dated 2016-01-09 and 3.1.11 dated 2016-04-23
RandomFields-3.1.11/RandomFields/DESCRIPTION | 8 RandomFields-3.1.11/RandomFields/MD5 | 113 +- RandomFields-3.1.11/RandomFields/NAMESPACE | 32 RandomFields-3.1.11/RandomFields/R/Class.R | 5 RandomFields-3.1.11/RandomFields/R/D.H.R | 70 + RandomFields-3.1.11/RandomFields/R/Methods-RFsp.R | 403 ------- RandomFields-3.1.11/RandomFields/R/Methods-aux.R | 86 + RandomFields-3.1.11/RandomFields/R/RFempvario-Methods-plots.R | 311 ++--- RandomFields-3.1.11/RandomFields/R/RFempvario.R | 91 + RandomFields-3.1.11/RandomFields/R/RFfit.R | 56 - RandomFields-3.1.11/RandomFields/R/RMmodels-Methods-plots.R | 138 +- RandomFields-3.1.11/RandomFields/R/RMmodelsSpecial.R | 8 RandomFields-3.1.11/RandomFields/R/auxiliary.R | 16 RandomFields-3.1.11/RandomFields/R/basic.fctns.R | 2 RandomFields-3.1.11/RandomFields/R/bigdata.R | 2 RandomFields-3.1.11/RandomFields/R/convert.R | 6 RandomFields-3.1.11/RandomFields/R/internal_use.R | 216 ++-- RandomFields-3.1.11/RandomFields/R/nicht.nachladbar.R | 29 RandomFields-3.1.11/RandomFields/R/rf-plots.R | 523 +++++----- RandomFields-3.1.11/RandomFields/R/rf.R | 4 RandomFields-3.1.11/RandomFields/man/Changings.Rd | 1 RandomFields-3.1.11/RandomFields/man/RFempVariog-class.Rd | 28 RandomFields-3.1.11/RandomFields/man/RFfit-class.Rd | 88 - RandomFields-3.1.11/RandomFields/man/RFfractaldim.Rd | 10 RandomFields-3.1.11/RandomFields/man/RFgridDataFrame-class.Rd | 16 RandomFields-3.1.11/RandomFields/man/RFinterpolate.Rd | 5 RandomFields-3.1.11/RandomFields/man/RFoptions.Rd | 129 +- RandomFields-3.1.11/RandomFields/man/RFpointsDataFrame-class.Rd | 17 RandomFields-3.1.11/RandomFields/man/RFsimulate.Rd | 41 RandomFields-3.1.11/RandomFields/man/RFsimulateAdvanced.Rd | 2 RandomFields-3.1.11/RandomFields/man/RFsp-class.Rd | 12 RandomFields-3.1.11/RandomFields/man/RFspatialGridDataFrame-class.Rd | 37 RandomFields-3.1.11/RandomFields/man/RFspatialPointsDataFrame-class.Rd | 18 RandomFields-3.1.11/RandomFields/man/RMmodel-class.Rd | 45 RandomFields-3.1.11/RandomFields/man/papers.S02.Rd | 2 RandomFields-3.1.11/RandomFields/man/papers.SBS14.Rd | 2 RandomFields-3.1.11/RandomFields/man/papers.SS11.Rd | 2 RandomFields-3.1.11/RandomFields/man/papers.jss14.Rd | 4 RandomFields-3.1.11/RandomFields/man/plot-method.Rd | 148 +- RandomFields-3.1.11/RandomFields/src/Brown.cc | 4 RandomFields-3.1.11/RandomFields/src/KeyInfo.cc | 5 RandomFields-3.1.11/RandomFields/src/Primitive.cc | 7 RandomFields-3.1.11/RandomFields/src/RF.h | 12 RandomFields-3.1.11/RandomFields/src/Userinterfaces.h | 13 RandomFields-3.1.11/RandomFields/src/extremes.cc | 11 RandomFields-3.1.11/RandomFields/src/gauss.cc | 3 RandomFields-3.1.11/RandomFields/src/getNset.cc | 132 +- RandomFields-3.1.11/RandomFields/src/nugget.cc | 2 RandomFields-3.1.11/RandomFields/src/operator.cc | 3 RandomFields-3.1.11/RandomFields/src/plusmalS.cc | 219 ++-- RandomFields-3.1.11/RandomFields/src/rf_interfaces.cc | 5 RandomFields-3.1.11/RandomFields/src/sequential.cc | 3 RandomFields-3.1.11/RandomFields/src/tbm.cc | 2 RandomFields-3.1.11/RandomFields/src/userinterfaces.cc | 38 RandomFields-3.1.11/RandomFields/src/variogramAndCo.cc | 4 RandomFields-3.1.11/RandomFields/src/variogramAndCo.h | 4 RandomFields-3.1.11/RandomFields/src/xport.cc | 2 RandomFields-3.1.8/RandomFields/man/RFsp2conventional.Rd |only 58 files changed, 1625 insertions(+), 1570 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 0.1.2 dated 2016-03-25 and 0.1.3 dated 2016-04-23
GetoptLong-0.1.2/GetoptLong/inst/tests |only GetoptLong-0.1.3/GetoptLong/DESCRIPTION | 12 ++-- GetoptLong-0.1.3/GetoptLong/MD5 | 26 +++++----- GetoptLong-0.1.3/GetoptLong/NAMESPACE | 8 +-- GetoptLong-0.1.3/GetoptLong/NEWS | 7 ++ GetoptLong-0.1.3/GetoptLong/R/0_global.R | 5 + GetoptLong-0.1.3/GetoptLong/R/GetoptLong.R | 9 ++- GetoptLong-0.1.3/GetoptLong/inst/doc/GetoptLong.pdf |binary GetoptLong-0.1.3/GetoptLong/inst/doc/variable_interpolation.pdf |binary GetoptLong-0.1.3/GetoptLong/man/qq.options.rd | 1 GetoptLong-0.1.3/GetoptLong/man/qqcat.rd | 2 GetoptLong-0.1.3/GetoptLong/tests/test-all.R | 4 - GetoptLong-0.1.3/GetoptLong/tests/testthat |only 13 files changed, 45 insertions(+), 29 deletions(-)
Title: Implementation of a Machine Learning Framework for Predicting
Drugs Side Effects
Description: An implementation of a Machine Learning Framework for prediction of new drugs Side Effects.
Firstly drugs are clustered with respect to their features description and secondly predictions are made, according to Bayesian scores.
Moreover it can perform protein enrichment considering the proteins clustered together in the first step of the algorithm.
This last tool is of extreme interest for biologist and drug discovery purposes, given the fact that it can be used either as a validation of the clusters obtained, as well as for the possible discovery of new interactions between certain side effects and non targeted pathways.
Clustering of the drugs in the feature space can be done using K-Means, PAM or K-Seeds (a novel clustering algorithm proposed by the author).
Author: Giovanna Maria Dimitri
Maintainer: Giovanna Maria Dimitri <gmd43@cam.ac.uk>
Diff between DrugClust versions 0.1 dated 2016-01-19 and 0.2 dated 2016-04-23
DESCRIPTION | 8 MD5 | 56 - R/DrugClustKMeans.R | 12 R/DrugClustKSeeds.R | 16 R/DrugClustPAM.R | 12 R/VariousFunctions.R | 1174 +++++++++++++++++++++------------------ man/AUC.Rd | 7 man/AUPR.Rd | 7 man/CreateFolds.Rd | 7 man/DrugClustKMeans.Rd | 11 man/DrugClustKMeansEnrichment.Rd | 7 man/DrugClustKSeeds.Rd | 11 man/DrugClustKSeedsEnrichment.Rd | 7 man/DrugClustPAM.Rd | 11 man/DrugClustPAMEnrichment.Rd | 7 man/Enrichment_Proteins.Rd | 6 man/InitFeatures.Rd | 7 man/InitSideEffect.Rd | 5 man/KMeansClusteringAlgorithm.Rd | 6 man/KMeansModel.Rd | 6 man/KSeedsClusters.Rd | 10 man/KSeedsScores.Rd | 16 man/PAM.Rd | 4 man/PAM_Model.Rd | 6 man/PredictionKMeans.Rd | 6 man/PredictionKSeeds.Rd | 27 man/Prediction_PAM.Rd | 6 man/RandomSeedGenerator.Rd | 11 man/SeedSelection.Rd | 9 29 files changed, 928 insertions(+), 550 deletions(-)
Title: Simulation Classes Based on Package 'distr'
Description: S4-classes for setting up a coherent framework for simulation within the distr
family of packages.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrSim versions 2.5.2 dated 2013-09-12 and 2.6 dated 2016-04-23
DESCRIPTION | 36 ++++++++++++++++++++++++------------ MD5 | 28 ++++++++++++++-------------- NAMESPACE | 5 ++++- inst/CITATION | 1 - inst/NEWS | 8 ++++++++ man/0distrSim-package.Rd | 17 +++++++++-------- man/Contsimulation-class.Rd | 2 +- man/Dataclass-class.Rd | 2 +- man/Dataclass.Rd | 2 +- man/SeqDataFrame-class.Rd | 2 +- man/Simulation-class.Rd | 2 +- man/cload.Rd | 2 +- man/distrSimMASK.Rd | 2 +- man/distrSimoptions.Rd | 2 +- man/vectororNULL-class.Rd | 2 +- 15 files changed, 68 insertions(+), 45 deletions(-)
Title: Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School
Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary
school.
Author: Eleonora Feist [ctb] (contributed as student in the initial phase
--2008),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Anja Hueller [ctb] (contributed as student in the initial phase --2008)
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTeach versions 2.5 dated 2013-09-13 and 2.6 dated 2016-04-23
DESCRIPTION | 37 ++++++++++++++++++++++++------------- MD5 | 20 ++++++++++---------- NAMESPACE | 5 +++++ R/AllGeneric.R | 10 +++++----- R/illustLLN.R | 37 +++++++++++++++++++++++++++++++++++-- inst/CITATION | 2 +- inst/NEWS | 14 ++++++++++++++ man/0distrTeach-package.Rd | 17 +++++++++-------- man/IllustCLT.Rd | 10 +++++++++- man/IllustLLN.Rd | 2 +- man/plotCLT.Rd | 2 +- 11 files changed, 114 insertions(+), 42 deletions(-)
Title: Object Oriented Implementation of Distributions
Description: S4-classes and methods for distributions.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005),
R Core Team [ctb, cph] (for source file ks.c/ routines 'pKS2' and
'pKolmogorov2x')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distr versions 2.5.3 dated 2014-08-09 and 2.6 dated 2016-04-23
DESCRIPTION | 45 MD5 | 241 +-- NAMESPACE | 204 +- R/0distrOptions.R | 2 R/AllGenerics.R | 14 R/Convpow.R | 2 R/DiscreteDistribution.R | 127 - R/Distribution.R | 3 R/EmpiricalDistribution.R |only R/Truncate.R | 1 R/internalUtils.R | 30 R/internals-qqplot.R | 183 +- R/makeAbscontDistribution.R | 2 R/plot-methods.R | 155 +- R/plot-methods_LebDec.R | 96 + R/qqbounds.R | 18 R/qqplot.R | 48 R/solve.R | 2 inst/CITATION | 2 inst/NEWS | 1650 ++++++++++++------------ inst/doc/newDistributions.R | 1 inst/doc/newDistributions.Rnw | 13 inst/doc/newDistributions.pdf |binary man/0distr-package.Rd | 174 +- man/AbscontDistribution-class.Rd | 2 man/AbscontDistribution.Rd | 2 man/Arcsine-class.Rd | 2 man/Beta-class.Rd | 2 man/BetaParameter-class.Rd | 2 man/Binom-class.Rd | 2 man/BinomParameter-class.Rd | 2 man/Cauchy-class.Rd | 2 man/CauchyParameter-class.Rd | 2 man/Chisq-class.Rd | 2 man/ChisqParameter-class.Rd | 2 man/CompoundDistribution-class.Rd | 2 man/CompoundDistribution.Rd | 2 man/ConvPow.Rd | 9 man/DExp-class.Rd | 2 man/Dirac-class.Rd | 2 man/DiracParameter-class.Rd | 2 man/DiscreteDistribution-class.Rd | 2 man/DiscreteDistribution.Rd | 3 man/Distribution-class.Rd | 2 man/EmpiricalDistribution.Rd |only man/EuclideanSpace-class.Rd | 2 man/Exp-class.Rd | 2 man/ExpOrGammaOrChisq-class.Rd | 2 man/ExpParameter-class.Rd | 2 man/FParameter-class.Rd | 2 man/Fd-class.Rd | 2 man/GammaParameter-class.Rd | 2 man/Gammad-class.Rd | 2 man/Geom-class.Rd | 2 man/GeomParameter-class.Rd | 2 man/Hyper-class.Rd | 2 man/HyperParameter-class.Rd | 2 man/Integer-class.Rd | 2 man/Lattice-class.Rd | 2 man/LatticeDistribution-class.Rd | 2 man/LatticeDistribution.Rd | 2 man/Lnorm-class.Rd | 2 man/LnormParameter-class.Rd | 2 man/Logis-class.Rd | 2 man/LogisParameter-class.Rd | 2 man/MakeAbscontDistribution.Rd | 2 man/Naturals-class.Rd | 2 man/Nbinom-class.Rd | 2 man/NbinomParameter-class.Rd | 2 man/Norm-class.Rd | 2 man/NormParameter-class.Rd | 2 man/OptionalParameter-class.Rd | 2 man/Parameter-class.Rd | 2 man/Pois-class.Rd | 2 man/PoisParameter-class.Rd | 2 man/PosDefSymmMatrix-class.Rd | 2 man/PosDefSymmMatrix.Rd | 2 man/Reals-class.Rd | 2 man/RtoDPQ.LC.Rd | 2 man/RtoDPQ.Rd | 2 man/RtoDPQ.d.Rd | 2 man/TParameter-class.Rd | 2 man/Td-class.Rd | 2 man/UniNormParameter-class.Rd | 2 man/Unif-class.Rd | 2 man/UnifParameter-class.Rd | 2 man/UnivarLebDecDistribution-class.Rd | 2 man/UnivarLebDecDistribution.Rd | 2 man/UnivarMixingDistribution-class.Rd | 2 man/UnivarMixingDistribution.Rd | 2 man/UnivariateDistribution-class.Rd | 2 man/Weibull-class.Rd | 2 man/WeibullParameter-class.Rd | 2 man/distrARITH.Rd | 2 man/distrMASK.Rd | 2 man/distroptions.Rd | 2 man/flat.LCD.Rd | 2 man/flat.mix.Rd | 2 man/getLabel.Rd | 2 man/getLow.Rd | 2 man/igamma.Rd | 2 man/internalClassUnions-class.Rd | 2 man/internalGenerics.Rd | 2 man/internals-qqplot.Rd | 22 man/internals.Rd | 20 man/operators-methods.Rd | 7 man/options.Rd | 2 man/p-methods.Rd | 19 man/plot-methods.Rd | 30 man/q-methods.Rd | 26 man/qqbounds.Rd | 2 man/qqplot.Rd | 329 ++-- man/rSpace-class.Rd | 2 man/solve-methods.Rd | 2 man/sqrt-methods.Rd | 2 src/ks.c | 10 tests/Examples |only tests/doSvUnit.R | 146 +- tests/unitTests/runit.dontrunMinimum.R | 38 tests/unitTests/runit.dontrunOperatorsMethods.R | 42 tests/unitTests/runit.dontrunQQPlot.R | 136 - vignettes/newDistributions-exam1.pdf |only vignettes/newDistributions.Rnw | 13 123 files changed, 2240 insertions(+), 1785 deletions(-)
Title: Bayesian Estimation of Mixtures of Multivariate Bernoulli
Distributions
Description: Fully Bayesian inference for estimating the number of clusters and related parameters to heterogeneous binary data.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between BayesBinMix versions 1.1 dated 2016-04-19 and 1.2 dated 2016-04-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/coupledMetropolis.R | 10 +++++++--- man/BayesBinMix-package.Rd | 8 +++++++- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Explorer of World Population Prospects
Description: Explore data in the 'wpp2015' (or 2012, 2010) package using a 'shiny' interface.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 1.8-0 dated 2016-04-16 and 1.8-1 dated 2016-04-23
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/wpp.R | 17 +++++++++++++---- inst/explore/README.html | 4 +++- inst/explore/server.R | 12 ++++++++++-- man/wppExplorer-package.Rd | 4 ++-- tests/testthat/test-indicators.R | 27 +++++++++++++++++++++++---- 8 files changed, 71 insertions(+), 25 deletions(-)
Title: Unit Testing for R
Description: A unit testing system designed to be fun, flexible and easy to
set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 1.0.1 dated 2016-04-21 and 1.0.2 dated 2016-04-23
DESCRIPTION | 6 +- MD5 | 16 +++---- NEWS.md | 5 ++ R/compare-time.R | 2 R/test-compiled-code.R | 32 ++++++++++++-- inst/include/testthat/testthat.h | 2 man/use_catch.Rd | 34 +++++++++++++-- src/test-catch.cpp | 4 + tests/test-catch.R | 87 +++++++++++++++++++++++++-------------- 9 files changed, 134 insertions(+), 54 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and 'iDigBio'. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.4.5 dated 2016-01-27 and 0.5.0 dated 2016-04-23
spocc-0.4.5/spocc/R/tbldf.R |only spocc-0.4.5/spocc/man/spocc_type_sum.Rd |only spocc-0.5.0/spocc/DESCRIPTION | 11 spocc-0.5.0/spocc/MD5 | 60 +- spocc-0.5.0/spocc/NAMESPACE | 14 spocc-0.5.0/spocc/NEWS.md | 25 + spocc-0.5.0/spocc/R/antweb_helpers.R | 4 spocc-0.5.0/spocc/R/as.antweb.R | 2 spocc-0.5.0/spocc/R/as.ecoengine.R | 2 spocc-0.5.0/spocc/R/ecoengine_helpers.R | 6 spocc-0.5.0/spocc/R/inat.R | 4 spocc-0.5.0/spocc/R/methods.r | 8 spocc-0.5.0/spocc/R/occ.r | 101 ++-- spocc-0.5.0/spocc/R/occ2df.R | 15 spocc-0.5.0/spocc/R/occ_names.R | 2 spocc-0.5.0/spocc/R/plugin_helpers.R | 26 - spocc-0.5.0/spocc/R/plugins.r | 99 ++- spocc-0.5.0/spocc/R/spocc-package.R | 13 spocc-0.5.0/spocc/R/zzz.r | 36 + spocc-0.5.0/spocc/README.md | 107 ++-- spocc-0.5.0/spocc/build/vignette.rds |binary spocc-0.5.0/spocc/inst/doc/spocc_vignette.Rmd | 418 ++++++++-------- spocc-0.5.0/spocc/inst/doc/spocc_vignette.html | 446 +++++++++--------- spocc-0.5.0/spocc/man/occ.Rd | 20 spocc-0.5.0/spocc/man/occ2df.Rd | 3 spocc-0.5.0/spocc/man/spocc-package.Rd | 6 spocc-0.5.0/spocc/man/spocc_objects.Rd | 6 spocc-0.5.0/spocc/tests/testthat/test-common_params.R | 16 spocc-0.5.0/spocc/tests/testthat/test-has_coords.R | 32 - spocc-0.5.0/spocc/tests/testthat/test-occ.R | 59 ++ spocc-0.5.0/spocc/tests/testthat/test-occ2df.R | 5 spocc-0.5.0/spocc/vignettes/spocc_vignette.Rmd | 418 ++++++++-------- 32 files changed, 1080 insertions(+), 884 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.0.14 dated 2015-12-15 and 0.1.0 dated 2016-04-23
DESCRIPTION | 6 ++-- MD5 | 32 ++++++++++++------------- configure.ac | 6 ++-- inst/CITATION | 3 +- inst/include/Error_utils.h | 25 ++++++++++++++++++- inst/include/Matrix_mult.h | 1 inst/include/Solve.h | 26 ++++++++++++++------ inst/include/utils.h | 23 +++++++++++------- src/Basic_utils.h | 4 +-- src/Error_utils.h | 25 ++++++++++++++++++- src/Makevars.in | 11 -------- src/Matrix_mult.h | 1 src/Solve.h | 26 ++++++++++++++------ src/matrix_mult.cc | 19 ++++++++++++++- src/solve.cc | 53 +++++++++++++++++++++++------------------ src/sqrt.cc | 57 +++++++++++++++++++++++---------------------- src/utils.h | 23 +++++++++++------- 17 files changed, 219 insertions(+), 122 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 3.0 dated 2016-04-08 and 3.2 dated 2016-04-23
molaR-3.0/molaR/R/bgplot3d_XQuartz.R |only molaR-3.0/molaR/man/bgplot3d_XQuartz.Rd |only molaR-3.2/molaR/DESCRIPTION | 6 molaR-3.2/molaR/MD5 | 54 ++--- molaR-3.2/molaR/R/DNE.R | 47 +++- molaR-3.2/molaR/R/DNE3d.R | 280 ++++++++------------------- molaR-3.2/molaR/R/DNE_Legend.R | 35 +-- molaR-3.2/molaR/R/Directional_Bins.R | 9 molaR-3.2/molaR/R/OPC.R | 81 ++++--- molaR-3.2/molaR/R/OPC3d.R | 90 +++----- molaR-3.2/molaR/R/OPC_Legend.R | 98 ++++----- molaR-3.2/molaR/R/OPCr.R | 9 molaR-3.2/molaR/R/RFI.R | 8 molaR-3.2/molaR/R/RFI3d.R | 59 +---- molaR-3.2/molaR/R/RFI_Legend.R | 63 ++---- molaR-3.2/molaR/R/molaR_Batch.R | 261 +++++++++++++++---------- molaR-3.2/molaR/R/molaR_Clean.R | 113 +++++----- molaR-3.2/molaR/R/molaR_bgplot.R |only molaR-3.2/molaR/build/molaR.pdf |binary molaR-3.2/molaR/inst/doc/molaR_vignette.R | 2 molaR-3.2/molaR/inst/doc/molaR_vignette.Rmd | 2 molaR-3.2/molaR/man/DNE.Rd | 17 + molaR-3.2/molaR/man/DNE3d.Rd | 15 - molaR-3.2/molaR/man/DNE_Legend.Rd | 17 - molaR-3.2/molaR/man/OPC_Legend.Rd | 11 - molaR-3.2/molaR/man/RFI3d.Rd | 2 molaR-3.2/molaR/man/RFI_Legend.Rd | 10 molaR-3.2/molaR/man/molaR_Batch.Rd | 16 + molaR-3.2/molaR/man/molaR_bgplot.Rd |only molaR-3.2/molaR/vignettes/molaR_vignette.Rmd | 2 30 files changed, 629 insertions(+), 678 deletions(-)
Title: Add-in to Customize 'ggplot2' Themes
Description: Rstudio add-in that delivers a graphical interface for editing 'ggplot2' theme elements.
Author: Calli Gross [aut, cre],
Philipp Ottolinger [aut, ctb]
Maintainer: Calli Gross <ggthemeassist@icloud.com>
Diff between ggThemeAssist versions 0.1.0 dated 2016-03-09 and 0.1.4 dated 2016-04-23
ggThemeAssist-0.1.0/ggThemeAssist/R/buildTheme.R |only ggThemeAssist-0.1.0/ggThemeAssist/R/is.valid.R |only ggThemeAssist-0.1.4/ggThemeAssist/DESCRIPTION | 7 ggThemeAssist-0.1.4/ggThemeAssist/MD5 | 24 ggThemeAssist-0.1.4/ggThemeAssist/NAMESPACE | 16 ggThemeAssist-0.1.4/ggThemeAssist/R/constants.R | 457 +++-- ggThemeAssist-0.1.4/ggThemeAssist/R/constructThemeString.R | 149 - ggThemeAssist-0.1.4/ggThemeAssist/R/formatResult.R |only ggThemeAssist-0.1.4/ggThemeAssist/R/ggThemeAssist-package.R | 16 ggThemeAssist-0.1.4/ggThemeAssist/R/ggThemeAssist.R | 971 +++++++----- ggThemeAssist-0.1.4/ggThemeAssist/R/helpers.R | 155 + ggThemeAssist-0.1.4/ggThemeAssist/R/jsHelpers.R |only ggThemeAssist-0.1.4/ggThemeAssist/R/updateDefaults.R | 110 - ggThemeAssist-0.1.4/ggThemeAssist/inst/rstudio/addins.dcf | 8 ggThemeAssist-0.1.4/ggThemeAssist/man/ggThemeAssist.Rd | 56 15 files changed, 1232 insertions(+), 737 deletions(-)
Title: Tools for Functional Response Analysis
Description: Tools to support sensible statistics for functional response analysis.
Author: Daniel Pritchard [aut, cre],
Daniel Barrios-O'Neill [ctb],
Helene Bovy [ctb],
Rachel Paterson [ctb]
Maintainer: Daniel Pritchard <daniel@pritchard.co>
Diff between frair versions 0.4 dated 2014-02-11 and 0.5 dated 2016-04-23
frair-0.4/frair/man/fr_bdII.Rd |only frair-0.4/frair/man/fr_hassIIIr.Rd |only frair-0.4/frair/man/fr_real77.Rd |only frair-0.4/frair/man/fr_real77r.Rd |only frair-0.5/frair/DESCRIPTION | 31 ++++++--- frair-0.5/frair/MD5 | 87 +++++++++++++++---------- frair-0.5/frair/NAMESPACE | 46 +++++++++---- frair-0.5/frair/NEWS.md |only frair-0.5/frair/R/fr_bdII.R | 100 +++++------------------------ frair-0.5/frair/R/fr_bdaII.R |only frair-0.5/frair/R/fr_emdII.R |only frair-0.5/frair/R/fr_flexp.R |only frair-0.5/frair/R/fr_flexpnr.R |only frair-0.5/frair/R/fr_hassIII.R | 4 - frair-0.5/frair/R/fr_hassIIInr.R |only frair-0.5/frair/R/fr_hassIIIr.R | 98 +++++------------------------ frair-0.5/frair/R/fr_hollingsII.R | 4 - frair-0.5/frair/R/fr_real77.R | 99 +++++------------------------ frair-0.5/frair/R/fr_real77r.R | 101 +++++------------------------- frair-0.5/frair/R/fr_rogersII.R | 12 +-- frair-0.5/frair/R/fr_typeI.R | 4 - frair-0.5/frair/R/frair_boot.R | 13 ++- frair-0.5/frair/R/frair_boot_methods.R | 48 ++++++++------ frair-0.5/frair/R/frair_compare.R | 13 ++- frair-0.5/frair/R/frair_fit.R | 29 +++++++- frair-0.5/frair/R/frair_fit_methods.R | 14 +++- frair-0.5/frair/R/frair_responses.R | 57 +++++++++------- frair-0.5/frair/R/frair_utils.R | 9 +- frair-0.5/frair/data/bythotrephes.RData |only frair-0.5/frair/man/bythotrephes.Rd |only frair-0.5/frair/man/fr_emdII.Rd |only frair-0.5/frair/man/fr_flexp.Rd |only frair-0.5/frair/man/fr_flexpnr.Rd |only frair-0.5/frair/man/fr_hassIII.Rd | 14 ++-- frair-0.5/frair/man/fr_hassIIInr.Rd |only frair-0.5/frair/man/fr_hollingsII.Rd | 12 +-- frair-0.5/frair/man/fr_rogersII.Rd | 24 +++---- frair-0.5/frair/man/fr_typeI.Rd | 12 +-- frair-0.5/frair/man/frair-deprecated.Rd |only frair-0.5/frair/man/frair-package.Rd | 10 -- frair-0.5/frair/man/frair_boot.Rd | 14 ++-- frair-0.5/frair/man/frair_boot_methods.Rd | 24 ++++--- frair-0.5/frair/man/frair_compare.Rd | 38 ++++++----- frair-0.5/frair/man/frair_fit.Rd | 14 ++-- frair-0.5/frair/man/frair_fit_methods.Rd | 12 ++- frair-0.5/frair/man/frair_responses.Rd | 2 frair-0.5/frair/man/frair_test.Rd | 6 - frair-0.5/frair/man/gammarus.Rd | 8 +- frair-0.5/frair/tests |only 49 files changed, 412 insertions(+), 547 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It is best suited to data from a Freesurfer analysis (cortical
thickness, volumes, local gyrification index, surface area), but also works
with e.g., tractography data from FSL. It contains a graphical user
interface for graph visualization and data exploration.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 0.55.0 dated 2015-12-24 and 0.62.0 dated 2016-04-23
brainGraph-0.55.0/brainGraph/R/group_graph_diffs.R |only brainGraph-0.55.0/brainGraph/R/permute_vertex.R |only brainGraph-0.55.0/brainGraph/man/group.graph.diffs.Rd |only brainGraph-0.55.0/brainGraph/man/permute.vertex.Rd |only brainGraph-0.55.0/brainGraph/man/spatial.dist.Rd |only brainGraph-0.62.0/brainGraph/DESCRIPTION | 10 brainGraph-0.62.0/brainGraph/MD5 | 63 +++-- brainGraph-0.62.0/brainGraph/NAMESPACE | 15 - brainGraph-0.62.0/brainGraph/R/NBS.R |only brainGraph-0.62.0/brainGraph/R/SPM.R |only brainGraph-0.62.0/brainGraph/R/analysis_random_graphs.R |only brainGraph-0.62.0/brainGraph/R/dti_create_mats.R | 65 +++-- brainGraph-0.62.0/brainGraph/R/graph_efficiency.R | 6 brainGraph-0.62.0/brainGraph/R/make_empty_brainGraph.R |only brainGraph-0.62.0/brainGraph/R/part_coeff.R | 20 - brainGraph-0.62.0/brainGraph/R/permute_group.R | 4 brainGraph-0.62.0/brainGraph/R/plot_brainGraph_gui.R | 119 ++++++---- brainGraph-0.62.0/brainGraph/R/plot_brainGraph_list.R | 98 ++++++-- brainGraph-0.62.0/brainGraph/R/plot_global.R |only brainGraph-0.62.0/brainGraph/R/plot_perm_diffs.R | 5 brainGraph-0.62.0/brainGraph/R/plot_rich_norm.R | 14 - brainGraph-0.62.0/brainGraph/R/rich_club_coeff.R | 2 brainGraph-0.62.0/brainGraph/R/rich_club_norm.R | 2 brainGraph-0.62.0/brainGraph/R/set_brainGraph_attributes.R | 38 ++- brainGraph-0.62.0/brainGraph/R/spatial_dist.R | 37 ++- brainGraph-0.62.0/brainGraph/R/update_brainGraph_gui.R | 63 +++-- brainGraph-0.62.0/brainGraph/R/vertex_attr_dt.R | 4 brainGraph-0.62.0/brainGraph/R/within_module_degree_z_score.R | 14 - brainGraph-0.62.0/brainGraph/data/destrieux.scgm.rda |only brainGraph-0.62.0/brainGraph/man/NBS.Rd |only brainGraph-0.62.0/brainGraph/man/SPM.Rd |only brainGraph-0.62.0/brainGraph/man/analysis_random_graphs.Rd |only brainGraph-0.62.0/brainGraph/man/destrieux.scgm.Rd |only brainGraph-0.62.0/brainGraph/man/dti_create_mats.Rd | 27 +- brainGraph-0.62.0/brainGraph/man/edge_spatial_dist.Rd |only brainGraph-0.62.0/brainGraph/man/make_empty_brainGraph.Rd |only brainGraph-0.62.0/brainGraph/man/plot_brainGraph_list.Rd | 25 +- brainGraph-0.62.0/brainGraph/man/plot_global.Rd |only brainGraph-0.62.0/brainGraph/man/plot_rich_norm.Rd | 6 brainGraph-0.62.0/brainGraph/man/set.brainGraph.attributes.Rd | 5 brainGraph-0.62.0/brainGraph/man/update_brainGraph_gui.Rd | 11 brainGraph-0.62.0/brainGraph/man/vertex_spatial_dist.Rd |only 42 files changed, 440 insertions(+), 213 deletions(-)