Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Description: GEE solver for correlated nominal or ordinal multinomial responses using a local odds ratios parameterization.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
Diff between multgee versions 1.3 dated 2013-06-21 and 1.4 dated 2013-12-03
DESCRIPTION | 15 +++++++-------- MD5 | 20 ++++++++++---------- NEWS | 8 +++++++- R/intrinsic.pars.R | 49 ++++++++++++++++++++++++++++++++++++++++++------- R/nomLORgee.R | 17 ++++++++--------- R/ordLORgee.R | 24 ++++++++++++------------ inst/CITATION | 8 +++++--- man/intrinsic.pars.Rd | 22 ++++++++++++---------- man/multgee-package.Rd | 6 +++--- man/nomLORgee.Rd | 22 +++++++++++----------- man/ordLORgee.Rd | 26 ++++++++++++-------------- 11 files changed, 129 insertions(+), 88 deletions(-)
Title: A wrapper algorithm for all-relevant feature selection
Description: Boruta is an all-relevant feature selection wrapper algorithm.
It finds relevant features by comparing original attributes'
importance with importance achievable at random, estimated
using their permuted copies.
Author: Miron Bartosz Kursa [aut, cre],
Witold Remigiusz Rudnicki [aut]
Maintainer: Miron Bartosz Kursa
Diff between Boruta versions 2.1.0 dated 2013-04-25 and 3.0.0 dated 2013-12-03
DESCRIPTION | 27 +- MD5 | 20 + NAMESPACE | 4 R/Boruta.R | 435 ++++++++++++++++++++++--------------------- R/TentativeRoughFix.R | 67 +++--- R/plot.Boruta.R | 92 ++++----- inst/NEWS | 15 + man/Boruta.Rd | 64 ++---- man/TentativeRoughFix.Rd | 4 man/getImpFerns.Rd |only man/getImpRf.Rd |only man/getSelectedAttributes.Rd | 2 12 files changed, 383 insertions(+), 347 deletions(-)
Title: Multiple Testing for Hypotheses with Hierarchical or Group
Structure
Description: Performs multiple testing corrections that take specific structure of hypotheses into account.
Author: Kris Sankaran
Maintainer: Kris Sankaran
Diff between structSSI versions 1.0.4 dated 2013-08-13 and 1.0.5 dated 2013-12-03
DESCRIPTION | 11 ++-- MD5 | 30 +++++------ NAMESPACE | 11 +++- R/hFDR.adjust.R | 7 -- R/pi0.tst.R | 1 R/plotAdjustedHypothesesTree.R | 5 - R/plotUnadjustedHypothesesTree.R | 102 ++++++++++++++++++--------------------- R/treePValues.R | 77 ++++++++++++++--------------- R/tree_definition.R | 7 +- man/hFDR.adjust.Rd | 8 --- man/hypothesesTree.rd | 4 - man/plot-methods.Rd | 2 man/structSSI-package.Rd | 7 -- man/treePValues.Rd | 2 tests/testGBHProcedures.R | 3 - tests/testHierarchicalMethods.R | 8 +-- 16 files changed, 137 insertions(+), 148 deletions(-)
Title: R Transcription Factor Binding Site identification tool
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Melissa Hubisz
Diff between rtfbs versions 0.2 dated 2012-03-30 and 0.3 dated 2013-12-03
rtfbs-0.2/rtfbs/aclocal.m4 |only rtfbs-0.2/rtfbs/tests/.Rhistory |only rtfbs-0.2/rtfbs/tests/input.fas |only rtfbs-0.2/rtfbs/tests/pwm.meme |only rtfbs-0.3/rtfbs/ChangeLog | 4 rtfbs-0.3/rtfbs/DESCRIPTION | 25 rtfbs-0.3/rtfbs/LICENSE |only rtfbs-0.3/rtfbs/MD5 | 171 rtfbs-0.3/rtfbs/R/tfbs.R | 34 rtfbs-0.3/rtfbs/build |only rtfbs-0.3/rtfbs/configure | 6350 ++++++++++++++++++++++----------- rtfbs-0.3/rtfbs/inst/doc/vignette.R |only rtfbs-0.3/rtfbs/inst/doc/vignette.pdf |binary rtfbs-0.3/rtfbs/man/rtfbs-package.Rd | 15 rtfbs-0.3/rtfbs/man/score.ms.Rd | 16 rtfbs-0.3/rtfbs/man/simulate.ms.Rd | 4 rtfbs-0.3/rtfbs/man/split.ms.Rd | 4 rtfbs-0.3/rtfbs/src/Makevars.in | 134 rtfbs-0.3/rtfbs/src/Makevars.win | 134 rtfbs-0.3/rtfbs/src/bed.h | 4 rtfbs-0.3/rtfbs/src/bgc_hmm.c |only rtfbs-0.3/rtfbs/src/bgc_hmm.h |only rtfbs-0.3/rtfbs/src/category_map.c | 18 rtfbs-0.3/rtfbs/src/category_map.h | 1 rtfbs-0.3/rtfbs/src/em.c | 74 rtfbs-0.3/rtfbs/src/em.h | 4 rtfbs-0.3/rtfbs/src/fit_column.c | 9 rtfbs-0.3/rtfbs/src/fit_em.c | 55 rtfbs-0.3/rtfbs/src/fit_feature.c | 2 rtfbs-0.3/rtfbs/src/gff.c | 283 - rtfbs-0.3/rtfbs/src/gff.h | 17 rtfbs-0.3/rtfbs/src/hashtable.c | 2 rtfbs-0.3/rtfbs/src/hashtable.h | 2 rtfbs-0.3/rtfbs/src/hmm.c | 4 rtfbs-0.3/rtfbs/src/list_of_lists.c | 2 rtfbs-0.3/rtfbs/src/list_of_lists.h | 8 rtfbs-0.3/rtfbs/src/lists.c | 13 rtfbs-0.3/rtfbs/src/lists.h | 7 rtfbs-0.3/rtfbs/src/local_alignment.c | 5 rtfbs-0.3/rtfbs/src/maf.c | 31 rtfbs-0.3/rtfbs/src/maf_block.c | 110 rtfbs-0.3/rtfbs/src/maf_block.h | 17 rtfbs-0.3/rtfbs/src/markov_matrix.c | 35 rtfbs-0.3/rtfbs/src/memory_handler.c | 50 rtfbs-0.3/rtfbs/src/misc.c | 63 rtfbs-0.3/rtfbs/src/misc.h | 23 rtfbs-0.3/rtfbs/src/motif.c | 26 rtfbs-0.3/rtfbs/src/msa.c | 133 rtfbs-0.3/rtfbs/src/msa.h | 15 rtfbs-0.3/rtfbs/src/multi_msa.c | 102 rtfbs-0.3/rtfbs/src/multi_msa.h | 45 rtfbs-0.3/rtfbs/src/numerical_opt.c | 4 rtfbs-0.3/rtfbs/src/numerical_opt.h | 5 rtfbs-0.3/rtfbs/src/phast_cons.c | 65 rtfbs-0.3/rtfbs/src/phast_cons.h | 11 rtfbs-0.3/rtfbs/src/phylo_fit.c | 93 rtfbs-0.3/rtfbs/src/phylo_fit.h | 1 rtfbs-0.3/rtfbs/src/phylo_hmm.c | 4 rtfbs-0.3/rtfbs/src/phylo_hmm.h | 2 rtfbs-0.3/rtfbs/src/phylo_p.c | 16 rtfbs-0.3/rtfbs/src/phylo_p_print.c | 4 rtfbs-0.3/rtfbs/src/prob_matrix.c | 16 rtfbs-0.3/rtfbs/src/prob_vector.c | 8 rtfbs-0.3/rtfbs/src/rph_bgc_hmm.c |only rtfbs-0.3/rtfbs/src/rph_gff.c | 82 rtfbs-0.3/rtfbs/src/rph_hmm.c | 9 rtfbs-0.3/rtfbs/src/rph_init.c | 16 rtfbs-0.3/rtfbs/src/rph_msa.c | 116 rtfbs-0.3/rtfbs/src/rph_phyloFit.c | 69 rtfbs-0.3/rtfbs/src/rph_phyloP.c | 4 rtfbs-0.3/rtfbs/src/rph_tfbs.c | 208 - rtfbs-0.3/rtfbs/src/rph_tree_model.c | 15 rtfbs-0.3/rtfbs/src/rph_trees.c | 4 rtfbs-0.3/rtfbs/src/rph_util.c | 4 rtfbs-0.3/rtfbs/src/rph_wig.c |only rtfbs-0.3/rtfbs/src/stringsplus.c | 14 rtfbs-0.3/rtfbs/src/subst_distrib.c | 32 rtfbs-0.3/rtfbs/src/subst_mods.c | 99 rtfbs-0.3/rtfbs/src/subst_mods.h | 21 rtfbs-0.3/rtfbs/src/sufficient_stats.c | 31 rtfbs-0.3/rtfbs/src/sufficient_stats.h | 6 rtfbs-0.3/rtfbs/src/tfbs.c | 24 rtfbs-0.3/rtfbs/src/tfbs.h | 8 rtfbs-0.3/rtfbs/src/tree_likelihoods.c | 48 rtfbs-0.3/rtfbs/src/tree_likelihoods.h | 5 rtfbs-0.3/rtfbs/src/tree_model.c | 806 +++- rtfbs-0.3/rtfbs/src/tree_model.h | 42 rtfbs-0.3/rtfbs/src/trees.c | 35 rtfbs-0.3/rtfbs/src/vector.c | 3 rtfbs-0.3/rtfbs/src/vector.h | 15 rtfbs-0.3/rtfbs/src/version | 2 rtfbs-0.3/rtfbs/src/wig.c |only rtfbs-0.3/rtfbs/src/wig.h |only rtfbs-0.3/rtfbs/vignettes |only 94 files changed, 6804 insertions(+), 3194 deletions(-)
Title: Provides access to databases through the JDBC interface
Description: RJDBC is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between RJDBC versions 0.2-1 dated 2012-12-02 and 0.2-2 dated 2013-12-03
DESCRIPTION | 10 ++--- MD5 | 15 ++++---- NAMESPACE | 4 +- NEWS | 12 ++++++ R/class.R | 73 +++++++++++++++++++++++++++++++++++------- inst/java/RJDBC.jar |binary man/JDBC.Rd | 3 + man/JDBCConnection-methods.Rd | 16 ++++++++- test.sh |only 9 files changed, 107 insertions(+), 26 deletions(-)
Title: Low-level R to Java interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between rJava versions 0.9-4 dated 2013-03-12 and 0.9-5 dated 2013-12-03
rJava-0.9-4/rJava/inst/javadoc/resources/inherit.gif |only rJava-0.9-5/rJava/DESCRIPTION | 10 rJava-0.9-5/rJava/MD5 | 142 rJava-0.9-5/rJava/NEWS | 15 rJava-0.9-5/rJava/R/jinit.R | 18 rJava-0.9-5/rJava/R/zzz.R.in | 3 rJava-0.9-5/rJava/configure | 4943 ++++----- rJava-0.9-5/rJava/configure.ac | 43 rJava-0.9-5/rJava/inst/java/ArrayWrapper.class |binary rJava-0.9-5/rJava/inst/java/NotComparableException.class |binary rJava-0.9-5/rJava/inst/java/RJavaArrayTools.class |binary rJava-0.9-5/rJava/inst/java/RJavaArrayTools_Test.class |binary rJava-0.9-5/rJava/inst/java/RJavaTools_Test.class |binary rJava-0.9-5/rJava/inst/java/RectangularArraySummary.class |binary rJava-0.9-5/rJava/inst/java/boot/RJavaClassLoader$RJavaObjectInputStream.class |binary rJava-0.9-5/rJava/inst/java/boot/RJavaClassLoader.class |binary rJava-0.9-5/rJava/inst/java/boot/RJavaClassLoader.java | 14 rJava-0.9-5/rJava/inst/javadoc/ArrayDimensionException.html | 440 rJava-0.9-5/rJava/inst/javadoc/ArrayWrapper.html | 1335 +- rJava-0.9-5/rJava/inst/javadoc/ArrayWrapper_Test.html | 499 rJava-0.9-5/rJava/inst/javadoc/DummyPoint.html | 635 - rJava-0.9-5/rJava/inst/javadoc/FlatException.html | 445 rJava-0.9-5/rJava/inst/javadoc/NotAnArrayException.html | 471 rJava-0.9-5/rJava/inst/javadoc/NotComparableException.html | 529 - rJava-0.9-5/rJava/inst/javadoc/ObjectArrayException.html | 447 rJava-0.9-5/rJava/inst/javadoc/PrimitiveArrayException.html | 447 rJava-0.9-5/rJava/inst/javadoc/RJavaArrayIterator.html | 930 - rJava-0.9-5/rJava/inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 451 rJava-0.9-5/rJava/inst/javadoc/RJavaArrayTools.html | 5022 ++++------ rJava-0.9-5/rJava/inst/javadoc/RJavaArrayTools_Test.html | 494 rJava-0.9-5/rJava/inst/javadoc/RJavaClassLoader.html | 1284 +- rJava-0.9-5/rJava/inst/javadoc/RJavaComparator.html | 485 rJava-0.9-5/rJava/inst/javadoc/RJavaImport.html | 835 - rJava-0.9-5/rJava/inst/javadoc/RJavaTools.html | 1487 +- rJava-0.9-5/rJava/inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 409 rJava-0.9-5/rJava/inst/javadoc/RJavaTools_Test.TestException.html | 447 rJava-0.9-5/rJava/inst/javadoc/RJavaTools_Test.html | 737 - rJava-0.9-5/rJava/inst/javadoc/RectangularArrayBuilder.html | 1132 +- rJava-0.9-5/rJava/inst/javadoc/RectangularArrayBuilder_Test.html | 499 rJava-0.9-5/rJava/inst/javadoc/RectangularArrayExamples.html | 1071 -- rJava-0.9-5/rJava/inst/javadoc/RectangularArraySummary.html | 739 - rJava-0.9-5/rJava/inst/javadoc/TestException.html | 445 rJava-0.9-5/rJava/inst/javadoc/allclasses-frame.html | 116 rJava-0.9-5/rJava/inst/javadoc/allclasses-noframe.html | 116 rJava-0.9-5/rJava/inst/javadoc/constant-values.html | 282 rJava-0.9-5/rJava/inst/javadoc/deprecated-list.html | 274 rJava-0.9-5/rJava/inst/javadoc/help-doc.html | 389 rJava-0.9-5/rJava/inst/javadoc/index-all.html | 2147 ++-- rJava-0.9-5/rJava/inst/javadoc/index.html | 82 rJava-0.9-5/rJava/inst/javadoc/overview-tree.html | 299 rJava-0.9-5/rJava/inst/javadoc/package-frame.html | 130 rJava-0.9-5/rJava/inst/javadoc/package-summary.html | 494 rJava-0.9-5/rJava/inst/javadoc/package-tree.html | 300 rJava-0.9-5/rJava/inst/javadoc/resources/background.gif |only rJava-0.9-5/rJava/inst/javadoc/resources/tab.gif |only rJava-0.9-5/rJava/inst/javadoc/resources/titlebar.gif |only rJava-0.9-5/rJava/inst/javadoc/resources/titlebar_end.gif |only rJava-0.9-5/rJava/inst/javadoc/serialized-form.html | 463 rJava-0.9-5/rJava/inst/javadoc/stylesheet.css | 501 rJava-0.9-5/rJava/inst/jri |only rJava-0.9-5/rJava/src/Makevars.win | 2 rJava-0.9-5/rJava/src/Rglue.c | 2 rJava-0.9-5/rJava/src/config.h.in | 9 rJava-0.9-5/rJava/src/init.c | 54 rJava-0.9-5/rJava/src/java/ArrayWrapper.class |binary rJava-0.9-5/rJava/src/java/NotComparableException.class |binary rJava-0.9-5/rJava/src/java/RJavaArrayTools.class |binary rJava-0.9-5/rJava/src/java/RJavaArrayTools_Test.class |binary rJava-0.9-5/rJava/src/java/RJavaClassLoader$RJavaObjectInputStream.class |binary rJava-0.9-5/rJava/src/java/RJavaClassLoader.class |binary rJava-0.9-5/rJava/src/java/RJavaClassLoader.java | 14 rJava-0.9-5/rJava/src/java/RJavaTools_Test.class |binary rJava-0.9-5/rJava/src/java/RectangularArraySummary.class |binary rJava-0.9-5/rJava/src/jvm-w32/config.h |only rJava-0.9-5/rJava/src/rJava.h | 6 75 files changed, 15743 insertions(+), 16840 deletions(-)
Title: R/Cassandra interface
Description: This packages provides a direct interface (without the
use of Java) to the most basic functionality of Apache
Cassanda such as login, updates and queries.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between RCassandra versions 0.1-2.1 dated 2013-03-23 and 0.1-3 dated 2013-12-03
DESCRIPTION | 12 +++--- MD5 | 8 ++-- NEWS | 9 ++++ man/RC.insert.Rd | 33 ++++++++++++---- src/cass.c | 110 +++++++++++++++++++++++++++++++++++++++++++------------ 5 files changed, 131 insertions(+), 41 deletions(-)
Title: Read and write PNG images
Description: This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between png versions 0.1-6 dated 2013-08-02 and 0.1-7 dated 2013-12-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ src/write.c | 10 +++++----- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: netClass: An R Package for Network-Based Biomarker Discovery
Description: netClass is an R package for network-based feature (gene)
selection for biomarkers discovery via integrating biological
information. This package adapts the following 5 algorithms
for classifying and predicting gene expression data using prior
knowledge: 1) average gene expression of pathway (aep); 2)
pathway activities classification (PAC); 3) Hub network
Classification (hubc); 4) filter via top ranked genes (FrSVM);
5) network smoothed t-statistic (stSVM).
Author: Yupeng Cun
Maintainer: Yupeng Cun
Diff between netClass versions 1.2 dated 2013-09-18 and 1.2.1 dated 2013-12-03
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- man/cv.aep.Rd | 4 ++-- vignettes |only 4 files changed, 9 insertions(+), 8 deletions(-)
Title: iPlots - interactive graphics for R
Description: Interactive plots for R
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between iplots versions 1.1-6 dated 2013-07-30 and 1.1-7 dated 2013-12-03
DESCRIPTION | 6 +- MD5 | 10 +-- NAMESPACE | 1 NEWS | 14 ++++ R/iplots.R | 149 +++++++++++++++++++++++---------------------------- inst/java/iplots.jar |binary 6 files changed, 91 insertions(+), 89 deletions(-)
Title: Dissimilarity-based functions for ecological analysis
Description: Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.
Author: Sarah Goslee and Dean Urban
Maintainer: Sarah Goslee
Diff between ecodist versions 1.2.7 dated 2012-03-22 and 1.2.9 dated 2013-12-03
ecodist-1.2.7/ecodist/R/zzz.R |only ecodist-1.2.9/ecodist/DESCRIPTION | 15 +++++------- ecodist-1.2.9/ecodist/MD5 | 27 ++++++++++------------ ecodist-1.2.9/ecodist/R/crosstab.R | 35 +++++++++++++++++++++++++---- ecodist-1.2.9/ecodist/R/nmdsmin.R | 1 ecodist-1.2.9/ecodist/data/bump.rda |binary ecodist-1.2.9/ecodist/data/graze.rda |binary ecodist-1.2.9/ecodist/data/permresults.rda |binary ecodist-1.2.9/ecodist/man/crosstab.Rd | 30 +++++++++++++++++------- ecodist-1.2.9/ecodist/man/mantel.Rd | 3 +- ecodist-1.2.9/ecodist/man/mgram.Rd | 4 ++- ecodist-1.2.9/ecodist/man/nmds.Rd | 3 +- ecodist-1.2.9/ecodist/man/permresults.Rd | 7 ++++- ecodist-1.2.9/ecodist/man/pmgram.Rd | 4 +-- ecodist-1.2.9/ecodist/src/Makevars | 1 15 files changed, 88 insertions(+), 42 deletions(-)
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output.
Description: This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between Cairo versions 1.5-2 dated 2012-11-05 and 1.5-3 dated 2013-12-03
DESCRIPTION | 24 --- MD5 | 12 - NEWS | 6 R/zzz.R | 8 - configure | 363 +++++++++++++++++++++++++++++++--------------------------- src/cairogd.c | 9 + src/cairogd.h | 2 7 files changed, 224 insertions(+), 200 deletions(-)
Title: Explorer of World Population Prospects
Description: A shiny interface for exploring data in wpp2008-wpp2012 packages.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
Diff between wppExplorer versions 1.1-1 dated 2013-10-09 and 1.1-2 dated 2013-12-03
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/wpp.R | 8 ++++++++ man/wppExplorer-package.Rd | 4 ++-- tests/run_tests.R | 3 ++- tests/test_functions.R | 12 ++++++++++++ 7 files changed, 38 insertions(+), 13 deletions(-)
Title: A Hydraulics Package to Compute Open-Channel Flow over Weirs
Description: This hydraulics package provides computational support for flow over weirs, such as sharp-crested, broad-crested, and embankments. Initially, the package supports broad- and sharp-crested weirs.
Author: William Asquith
Maintainer: William Asquith
Diff between weirs versions 0.21 dated 2010-10-05 and 0.23 dated 2013-12-03
ChangeLog | 3 +++ DESCRIPTION | 14 ++++++-------- MD5 |only NAMESPACE |only R/zzz.R | 11 +++++------ 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Flexible Randomization-Based Inference
Description: The 'randomizationInference' package allows the user to conduct randomization-based inference for a wide variety of experimental scenarios. The package leverages a potential outcomes framework to output randomization-based p-values and null intervals for any estimand of interest, according to the specified null and alternative hypotheses. The package also creates visualizations of randomization distributions and can test multiple test statistics simultaneously.
Author: Joseph J. Lee and Tirthankar Dasgupta
Maintainer: Joseph J. Lee
Diff between randomizationInference versions 1.0.0 dated 2013-09-10 and 1.0.1 dated 2013-12-03
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- R/blockRand.R | 20 +++++++++++++------- man/anovaF.Rd | 4 ++-- man/constEffect.Rd | 2 +- man/diffMeans.Rd | 2 +- man/diffMeansVector.Rd | 2 +- man/randInterval.Rd | 6 +++--- man/randTest.Rd | 2 +- man/randomizationInference-package.Rd | 10 +++++----- man/withinBlockEffects.Rd | 2 +- man/zeroEffect.Rd | 2 +- 12 files changed, 46 insertions(+), 40 deletions(-)
More information about randomizationInference at CRAN
Permanent link
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos
Maintainer: Peter Solymos
Diff between mefa versions 3.2-4 dated 2013-10-07 and 3.2-5 dated 2013-12-03
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- build/vignette.rds |binary demo/mefa.R | 7 ++++--- inst/ChangeLog | 5 +++++ inst/doc/mefa.R | 20 +++++++------------- inst/doc/mefa.Rnw | 16 ++++++---------- inst/doc/mefa.pdf |binary vignettes/mefa.Rnw | 16 ++++++---------- 9 files changed, 41 insertions(+), 49 deletions(-)
Title: Logic Regression
Description: Routines for Logic Regression
Author: Charles Kooperberg
Maintainer: Charles Kooperberg
Diff between LogicReg versions 1.5.4 dated 2013-04-26 and 1.5.5 dated 2013-12-03
DESCRIPTION | 11 +++++------ MD5 | 6 +++--- R/LogicReg.R | 22 ++++++++++++++-------- man/logreg.Rd | 2 +- 4 files changed, 23 insertions(+), 18 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Description: The package provides a comparatively comprehensive implementation of the theory of L-moments. Implementations for L-moment and probability-weighted moment (PWM) estimation, and parameter estimation for numerous familiar and not-so-familiar distributions are provided. L-moment estimation for the same distributions from parameters. L-moments are linear functions of order statistics and are linearly related to PWMs. L-moments are analogous to product moments; however, L-moments have many advantages including unbiasedness, robustness, and consistency. L-moments can outperform maximum likelihood for small to moderate samples. The lmomco package historically was originally oriented around circa 1996-FORTRAN algorithms by Hosking, and the nomenclature parallels those of the Hosking library. The Hosking algorithms later became available in the lmom package. However, vast extensions, components, concepts, L-moment curiosities, and research topics are added to aid and expand the breadth of L-moment applications. Such extensions the Sen weighted mean, Gini mean difference, plotting positions, and conditional probability adjustments. L-moment ratio diagrams are supported. Computations of L-moments for right-tail and left-tail censoring by known or unknown censoring threshold (via Hosking) and also by indicator variable (via Wang et al.) also are available. Asymmetric trimmed L-moments are supported as are numerical integration dynamically compute trajectories of select TL-moment ratios for the construction of TL-moment ratio diagrams. L-moments have been extended into multivariate space; the sample L-comoments are implemented and might have considerable application in copula theory because L-comoments measure asymmetric association and higher comoments or comovements of variables. The package supports exact analytical boot-strap estimates of order statistics, L-moments, and variances-covariances of L-moments. The package provides the Harri-Coble Tau34-squared Test for Normality using sample L-skew and L-kurtosis. Support for the following distributions, with moment type shown as "L" (L-moments) or "TL" (trimmed L-moments) and additional support for right-tail censoring ([RC]) include, is available: Asymmetric Exponential Power (L), Cauchy (TL), Eta-Mu (L), Exponential (L), Gamma (L), Generalized Extreme Value (L), Generalized Lambda (L & TL), Generalized Logistic (L), Generalized Normal (L), Generalized Pareto (L[RC] & TL), Gumbel (L), Kappa (L), Kappa-Mu (L), Kumaraswamy (L), Laplace (L), Normal (L), 3-parameter log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse Gumbel (L[RC]), Rice/Rician (L), Truncated Exponential (L), Wakeby (L), and Weibull (L).
Author: William Asquith
Maintainer: William Asquith
Diff between lmomco versions 1.7.8 dated 2013-07-05 and 1.7.9 dated 2013-12-03
DESCRIPTION | 58 ++++------------------------------ MD5 | 33 +++++++++++-------- NAMESPACE | 23 +++++++------ NEWS | 34 +++++++++++++++++++ R/paraep4.R | 5 +- R/parln3.R | 10 +++++ R/pp.f.R |only R/quaaep4kapmix.R |only data/TX38lgtrmFlow.RData |only inst/ERRATA_FOR_ISBN9781463508418.txt | 49 +++++++++++++++++++++++++++- man/TX38lgtrmFlow.Rd |only man/are.paraep4.valid.Rd | 2 + man/cdfaep4.Rd | 2 + man/lmomaep4.Rd | 2 + man/paraep4.Rd | 4 +- man/parln3.Rd | 17 +++++++++ man/pdfaep4.Rd | 2 + man/pp.f.Rd |only man/pp.median.Rd |only man/quaaep4.Rd | 2 + man/quaaep4kapmix.Rd |only 21 files changed, 160 insertions(+), 83 deletions(-)
Title: Probabilistic Population Projection
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
Diff between bayesPop versions 4.2-1 dated 2013-10-10 and 4.2-2 dated 2013-12-03
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NAMESPACE | 3 ++- man/bayesPop-package.Rd | 4 ++-- man/expressions.Rd | 4 ++-- man/get.pop.Rd |only 7 files changed, 20 insertions(+), 14 deletions(-)
Title: SMACOF for Multidimensional Scaling.
Description: This package provides the following approaches of multidimensional scaling (MDS) based on stress minimization by means of majorization (smacof): Simple smacof on symmetric dissimilarity matrices, smacof for rectangular matrices (unfolding models), smacof with constraints on the configuration, three-way smacof for individual differences (including constraints for idioscal, indscal, and identity), and spherical smacof (primal and dual algorithm). Each of these approaches is implemented in a metric and nonmetric manner including primary, secondary, and tertiary approaches for tie handling. Jackknife and permutation tests are included as well.
Author: Jan de Leeuw, Patrick Mair
Maintainer: Jan de Leeuw
Diff between smacof versions 1.2-1 dated 2011-11-29 and 1.2-3 dated 2013-12-03
smacof-1.2-1/smacof/COPYRIGHTS |only smacof-1.2-1/smacof/inst/doc/colwavelength.png |only smacof-1.2-1/smacof/inst/doc/dplot.pdf |only smacof-1.2-1/smacof/inst/doc/ekmanLuv.pdf |only smacof-1.2-1/smacof/inst/doc/ekmanbasic.pdf |only smacof-1.2-1/smacof/inst/doc/ekmansphere.pdf |only smacof-1.2-1/smacof/inst/doc/globe.png |only smacof-1.2-1/smacof/inst/doc/inddiffconfid.pdf |only smacof-1.2-1/smacof/inst/doc/inddiffconfuc.pdf |only smacof-1.2-1/smacof/inst/doc/inddiffresid.pdf |only smacof-1.2-1/smacof/inst/doc/inddiffresuc.pdf |only smacof-1.2-1/smacof/inst/doc/jconfbfast.pdf |only smacof-1.2-1/smacof/inst/doc/kinshipconstr.pdf |only smacof-1.2-1/smacof/inst/doc/kinshipstressr.pdf |only smacof-1.2-1/smacof/inst/doc/kinshipstressu.pdf |only smacof-1.2-1/smacof/inst/doc/kinshipsym.pdf |only smacof-1.2-1/smacof/inst/doc/plotje.pdf |only smacof-1.2-1/smacof/inst/doc/shepbfast.pdf |only smacof-1.2-1/smacof/inst/doc/smacof.Rnw |only smacof-1.2-1/smacof/inst/doc/smacof.bib |only smacof-1.2-1/smacof/inst/doc/smacof.pdf |only smacof-1.2-1/smacof/inst/doc/spectrum.gif |only smacof-1.2-1/smacof/inst/doc/spectrum.png |only smacof-1.2-3/smacof/DESCRIPTION | 14 + smacof-1.2-3/smacof/MD5 | 100 ++++++------ smacof-1.2-3/smacof/NAMESPACE | 2 smacof-1.2-3/smacof/R/smacofRect.R | 3 smacof-1.2-3/smacof/data/EW_eng.rda |binary smacof-1.2-3/smacof/data/EW_ger.rda |binary smacof-1.2-3/smacof/data/bread.rda |binary smacof-1.2-3/smacof/data/breakfast.rda |binary smacof-1.2-3/smacof/data/csrranking.rda |binary smacof-1.2-3/smacof/data/ekman.rda |binary smacof-1.2-3/smacof/data/helm.rda |binary smacof-1.2-3/smacof/data/kinshipdelta.rda |binary smacof-1.2-3/smacof/data/kinshipscales.rda |binary smacof-1.2-3/smacof/data/partypref.rda |binary smacof-1.2-3/smacof/data/perception.rda |binary smacof-1.2-3/smacof/data/rect_constr.rda |binary smacof-1.2-3/smacof/data/rectangles.rda |binary smacof-1.2-3/smacof/data/stardist.rda |binary smacof-1.2-3/smacof/data/trading.rda |binary smacof-1.2-3/smacof/data/winedat.rda |binary smacof-1.2-3/smacof/data/wish.rda |binary smacof-1.2-3/smacof/data/wish_ger.rda |binary smacof-1.2-3/smacof/inst/COPYRIGHTS |only smacof-1.2-3/smacof/inst/doc/vignettes |only smacof-1.2-3/smacof/man/jackknife.smacofB.Rd | 147 +++++++++--------- smacof-1.2-3/smacof/man/plot.smacof.rd | 188 +++++++++++++----------- smacof-1.2-3/smacof/man/smacofConstraint.rd | 17 +- smacof-1.2-3/smacof/man/smacofRect.Rd | 10 - smacof-1.2-3/smacof/man/smacofSphere.dual.rd | 6 smacof-1.2-3/smacof/man/smacofSym.Rd | 4 53 files changed, 264 insertions(+), 227 deletions(-)
Title: Sample Generation by Replacement
Description: The library for Sample Generation by Replacement simulations. The package can be used to perform fake data analysis according to the sample generation by replacement approach. It includes functions for making simple inferences about discrete/ordinal fake data. The package allows to study the implications of fake data for empirical results.
Author: Massimiliano Pastore & Luigi Lombardi
Maintainer: Massimiliano Pastore
Diff between sgr versions 1.0.2 dated 2013-08-17 and 1.0.3 dated 2013-12-03
sgr-1.0.2/sgr/sgr-Ex.R |only sgr-1.0.3/sgr/DESCRIPTION | 9 ++++----- sgr-1.0.3/sgr/MD5 | 20 +++++++++++--------- sgr-1.0.3/sgr/R/formule.bias.R |only sgr-1.0.3/sgr/man/amse.Rd |only sgr-1.0.3/sgr/man/arb.Rd |only sgr-1.0.3/sgr/man/dgBetaD.Rd | 2 +- sgr-1.0.3/sgr/man/model.fake.par.Rd | 2 +- sgr-1.0.3/sgr/man/pfake.Rd | 2 +- sgr-1.0.3/sgr/man/pfakebad.Rd | 2 +- sgr-1.0.3/sgr/man/pfakegood.Rd | 2 +- sgr-1.0.3/sgr/man/rdatagen.Rd | 2 +- sgr-1.0.3/sgr/man/sgr-package.Rd | 7 +++---- 13 files changed, 24 insertions(+), 24 deletions(-)
Title: Power Analysis and Sample Size Calculation
Description: The package allows for the Estimation of Sample-size and Power by Exploring Simulated Study Outcomes.
WE ARE AWARE A BUG ON THE LAST VERSION OF THE TOOL AND I WORKING TO SORT IT OUT.
A NEW VERSION WILL BE AVAILABLE BY THE END OF DECEMBER 2013.
WE ARE ALSO WORKING ON A WEB-BASED INTERFACE WHICH THAT WILL BE AVAILABLE AT www.espresso-research.org
Author: A. Gaye & Burton P.
Maintainer: Amadou Gaye
Diff between ESPRESSO versions 1.1 dated 2011-12-19 and 2.0 dated 2013-12-03
ESPRESSO-1.1/ESPRESSO/R/empirical.power.calc.R |only ESPRESSO-1.1/ESPRESSO/R/get.critical.results.R |only ESPRESSO-1.1/ESPRESSO/R/get.observed.data.R |only ESPRESSO-1.1/ESPRESSO/R/is.posdef.R |only ESPRESSO-1.1/ESPRESSO/R/make.cov.mat.R |only ESPRESSO-1.1/ESPRESSO/R/make.obs.env.R |only ESPRESSO-1.1/ESPRESSO/R/make.obs.geno.R |only ESPRESSO-1.1/ESPRESSO/R/make.posdef.R |only ESPRESSO-1.1/ESPRESSO/R/misclassify.R |only ESPRESSO-1.1/ESPRESSO/R/model.power.calc.R |only ESPRESSO-1.1/ESPRESSO/R/regr.analysis.R |only ESPRESSO-1.1/ESPRESSO/R/samplsize.calc.R |only ESPRESSO-1.1/ESPRESSO/R/sim.CC.data.R |only ESPRESSO-1.1/ESPRESSO/R/sim.LDgeno.data.R |only ESPRESSO-1.1/ESPRESSO/R/sim.LDsnps.R |only ESPRESSO-1.1/ESPRESSO/R/sim.QTL.data.R |only ESPRESSO-1.1/ESPRESSO/R/sim.env.data.R |only ESPRESSO-1.1/ESPRESSO/R/sim.env.sesp.R |only ESPRESSO-1.1/ESPRESSO/R/sim.geno.data.R |only ESPRESSO-1.1/ESPRESSO/R/sim.geno.sesp.R |only ESPRESSO-1.1/ESPRESSO/R/sim.interact.data.R |only ESPRESSO-1.1/ESPRESSO/R/sim.pheno.bin.R |only ESPRESSO-1.1/ESPRESSO/R/sim.pheno.qtl.R |only ESPRESSO-1.1/ESPRESSO/R/sim.subject.data.R |only ESPRESSO-1.1/ESPRESSO/R/skew.rnorm.R |only ESPRESSO-1.1/ESPRESSO/data |only ESPRESSO-1.1/ESPRESSO/man/empirical.power.calc.Rd |only ESPRESSO-1.1/ESPRESSO/man/env.params.Rd |only ESPRESSO-1.1/ESPRESSO/man/gen.params.Rd |only ESPRESSO-1.1/ESPRESSO/man/general.params.Rd |only ESPRESSO-1.1/ESPRESSO/man/get.critical.results.Rd |only ESPRESSO-1.1/ESPRESSO/man/get.observed.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/init.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/is.posdef.Rd |only ESPRESSO-1.1/ESPRESSO/man/make.cov.mat.Rd |only ESPRESSO-1.1/ESPRESSO/man/make.obs.env.Rd |only ESPRESSO-1.1/ESPRESSO/man/make.obs.geno.Rd |only ESPRESSO-1.1/ESPRESSO/man/make.posdef.Rd |only ESPRESSO-1.1/ESPRESSO/man/misclassify.Rd |only ESPRESSO-1.1/ESPRESSO/man/model.power.calc.Rd |only ESPRESSO-1.1/ESPRESSO/man/obs.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/regr.analysis.Rd |only ESPRESSO-1.1/ESPRESSO/man/samplsize.calc.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.CC.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.LDgeno.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.LDsnps.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.QTL.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.env.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.env.sesp.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.geno.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.geno.sesp.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.interact.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.pheno.bin.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.pheno.qtl.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.sesp.params.Rd |only ESPRESSO-1.1/ESPRESSO/man/sim.subject.data.Rd |only ESPRESSO-1.1/ESPRESSO/man/skew.rnorm.Rd |only ESPRESSO-2.0/ESPRESSO/DESCRIPTION | 14 - ESPRESSO-2.0/ESPRESSO/MD5 | 70 ------ ESPRESSO-2.0/ESPRESSO/NAMESPACE |only ESPRESSO-2.0/ESPRESSO/R/msg.R |only ESPRESSO-2.0/ESPRESSO/R/run.ESPRESSO.R |only ESPRESSO-2.0/ESPRESSO/man/ESPRESSO-package.Rd | 231 +--------------------- ESPRESSO-2.0/ESPRESSO/man/run.ESPRESSO.Rd |only 64 files changed, 26 insertions(+), 289 deletions(-)
Title: Generation, reconstruction, simulation and analysis of
synchronous, asynchronous, and probabilistic Boolean networks
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, and probabilistic Boolean networks, and to
analyze and visualize attractors in Boolean networks
Author: Christoph Müssel, Martin Hopfensitz, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler
Diff between BoolNet versions 1.61 dated 2013-03-20 and 1.62 dated 2013-12-03
BoolNet-1.61/BoolNet/inst/doc/BoolNet_package_vignette.bib |only BoolNet-1.61/BoolNet/inst/doc/attractor1.pdf |only BoolNet-1.61/BoolNet/inst/doc/attractor2.pdf |only BoolNet-1.61/BoolNet/inst/doc/basinsize.pdf |only BoolNet-1.61/BoolNet/inst/doc/biotap_initval.png |only BoolNet-1.61/BoolNet/inst/doc/biotap_logic.png |only BoolNet-1.61/BoolNet/inst/doc/biotap_model.png |only BoolNet-1.61/BoolNet/inst/doc/biotap_sim_properties.png |only BoolNet-1.61/BoolNet/inst/doc/indegree.pdf |only BoolNet-1.61/BoolNet/inst/doc/indegree_kl.pdf |only BoolNet-1.61/BoolNet/inst/doc/pajek.png |only BoolNet-1.61/BoolNet/inst/doc/pbntransitions.pdf |only BoolNet-1.61/BoolNet/inst/doc/piecewisestategraph.pdf |only BoolNet-1.61/BoolNet/inst/doc/robustness.pdf |only BoolNet-1.61/BoolNet/inst/doc/sequence.pdf |only BoolNet-1.61/BoolNet/inst/doc/stategraph.pdf |only BoolNet-1.61/BoolNet/inst/doc/wiring.pdf |only BoolNet-1.61/BoolNet/inst/doc/wiring_biotap.pdf |only BoolNet-1.62/BoolNet/DESCRIPTION | 8 - BoolNet-1.62/BoolNet/MD5 | 62 ++++++------- BoolNet-1.62/BoolNet/R/loadNetwork.R | 5 - BoolNet-1.62/BoolNet/inst/NEWS.Rd | 13 ++ BoolNet-1.62/BoolNet/inst/doc/BoolNet_package_vignette.Snw | 7 + BoolNet-1.62/BoolNet/inst/doc/BoolNet_package_vignette.pdf |binary BoolNet-1.62/BoolNet/inst/doc/cellcycle.txt |only BoolNet-1.62/BoolNet/man/BoolNet-package.Rd | 4 BoolNet-1.62/BoolNet/man/plotStateGraph.Rd | 3 BoolNet-1.62/BoolNet/src/boolean_network.c | 6 - BoolNet-1.62/BoolNet/src/common.c | 6 - BoolNet-1.62/BoolNet/src/common.h | 8 - BoolNet-1.62/BoolNet/src/probabilistic_boolean_network.c | 6 - BoolNet-1.62/BoolNet/src/reconstruct_network.c | 22 ++-- BoolNet-1.62/BoolNet/vignettes |only 33 files changed, 83 insertions(+), 67 deletions(-)
Title: Clustering of variables
Description: Cluster analysis of a set of variables. Variables can be
quantitative, qualitative or a mixture of both.
Author: Marie Chavent and Vanessa Kuentz and Benoit Liquet and Jerome Saracco
Maintainer: Marie Chavent
Diff between ClustOfVar versions 0.7 dated 2012-09-19 and 0.8 dated 2013-12-03
ClustOfVar-0.7/ClustOfVar/R/ClustOfVar-internal.R |only ClustOfVar-0.7/ClustOfVar/R/tab.disjonctif.prop.R |only ClustOfVar-0.7/ClustOfVar/inst |only ClustOfVar-0.8/ClustOfVar/DESCRIPTION | 16 ClustOfVar-0.8/ClustOfVar/MD5 | 41 +- ClustOfVar-0.8/ClustOfVar/NAMESPACE | 21 - ClustOfVar-0.8/ClustOfVar/R/clusterscore.R | 27 - ClustOfVar-0.8/ClustOfVar/R/descript.R | 128 +++---- ClustOfVar-0.8/ClustOfVar/R/kmeansvar.R | 361 ++++++++++---------- ClustOfVar-0.8/ClustOfVar/R/mixedVarSim.R | 108 ++--- ClustOfVar-0.8/ClustOfVar/R/plot.hclustvar.R | 53 +- ClustOfVar-0.8/ClustOfVar/R/predict.clustvar.R |only ClustOfVar-0.8/ClustOfVar/R/recod.R | 175 +++++---- ClustOfVar-0.8/ClustOfVar/R/recodquant.R | 26 - ClustOfVar-0.8/ClustOfVar/R/summary.clustvar.R | 102 ++--- ClustOfVar-0.8/ClustOfVar/man/ClustOfVar-package.Rd | 64 +-- ClustOfVar-0.8/ClustOfVar/man/cutreevar.Rd | 116 +++--- ClustOfVar-0.8/ClustOfVar/man/hclustvar.Rd | 8 ClustOfVar-0.8/ClustOfVar/man/kmeansvar.Rd | 160 ++++---- ClustOfVar-0.8/ClustOfVar/man/plot.hclustvar.Rd | 107 +++-- ClustOfVar-0.8/ClustOfVar/man/predict.clustvar.Rd |only ClustOfVar-0.8/ClustOfVar/man/stability.Rd | 12 ClustOfVar-0.8/ClustOfVar/man/vnf.Rd | 33 - ClustOfVar-0.8/ClustOfVar/man/wine.Rd | 54 +- 24 files changed, 814 insertions(+), 798 deletions(-)
Title: High-speed processing of whole-genome VCF-format variation data,
FASTA-format sequence data and several alignments formats.
Description: WhopGenome's provides very fast access to whole genome, population scale variation data
from VCF files and sequence data from FASTA-formatted files.
It also reads in alignments from FASTA, Phylip, MAF and other file formats.
Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data
from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger
Maintainer: Ulrich Wittelsbuerger
Diff between WhopGenome versions 0.8.1 dated 2013-11-19 and 0.8.2 dated 2013-12-03
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/read_simple.R | 10 +++++----- src/rdnapp_MAF.h | 4 +++- src/t_info.cpp | 2 +- src/tabix/ksort.h | 3 ++- src/w_common.h | 19 +++++++++++++------ src/w_main.cpp | 4 ++-- src/w_snpmat_fnc.cpp | 7 ++++--- src/w_vcf.cpp | 2 +- 10 files changed, 44 insertions(+), 33 deletions(-)
Title: RImpala
Description: A package to connect and run queries on Cloudera Impala (thanks to Mu Sigma)
Author: Austin Chungath Vincent, Sachin Sudarshana, Vikas Raguttahalli
Maintainer: Austin Chungath Vincent
Diff between RImpala versions 0.1.0 dated 2013-11-27 and 0.1.1 dated 2013-12-03
DESCRIPTION | 15 ++++++++------- MD5 | 26 +++++++++++++------------- inst/java/RImpala-1.0.jar |binary man/RImpala.Rd | 19 +++++++++++++++++-- man/RImpala_close.Rd | 5 +++-- man/RImpala_connect.Rd | 5 +++-- man/RImpala_describe.Rd | 5 +++-- man/RImpala_init.Rd | 5 +++-- man/RImpala_invalidate.Rd | 5 +++-- man/RImpala_query.Rd | 5 +++-- man/RImpala_refresh.Rd | 5 +++-- man/RImpala_showdatabases.Rd | 5 +++-- man/RImpala_showtables.Rd | 5 +++-- man/RImpala_usedatabase.Rd | 5 +++-- 14 files changed, 68 insertions(+), 42 deletions(-)
Title: Hourly interpolation of multiple temperature daily series
Description: Hourly interpolation of daily minimum and maximum temperature
series. Carries out interpolation on multiple series ad once. Requires some
hourly series for calibration (alternatively can use default calibration
table).
Author: Emanuele Eccel & Emanuele Cordano
Maintainer: Emanuele Eccel
Diff between Interpol.T versions 2.1 dated 2012-08-03 and 2.1.1 dated 2013-12-03
Interpol.T-2.1.1/Interpol.T/DESCRIPTION | 21 ++++++++------- Interpol.T-2.1.1/Interpol.T/MD5 | 23 ++++++++--------- Interpol.T-2.1.1/Interpol.T/NAMESPACE | 2 - Interpol.T-2.1.1/Interpol.T/R/F_Th_int_series.R | 6 +++- Interpol.T-2.1.1/Interpol.T/R/F_par_calibration.R | 5 ++- Interpol.T-2.1.1/Interpol.T/R/F_plot_meas_sim.R | 4 ++ Interpol.T-2.1.1/Interpol.T/R/F_shape_calibration.R | 5 ++- Interpol.T-2.1.1/Interpol.T/data/Trentino_hourly_T.rda |binary Interpol.T-2.1.1/Interpol.T/man/Th_int_series.Rd | 6 +++- Interpol.T-2.1.1/Interpol.T/man/par_calibration.Rd | 5 ++- Interpol.T-2.1.1/Interpol.T/man/plot_meas_sim.Rd | 4 ++ Interpol.T-2.1.1/Interpol.T/man/shape_calibration.Rd | 5 ++- Interpol.T-2.1/Interpol.T/data/datalist |only 13 files changed, 55 insertions(+), 31 deletions(-)
Title: Procedures to generate IRT adaptive tests (CAT)
Description: The catR package allows the generation of response
patterns under computerized adaptive testing (CAT)
framework, with the choice of several starting rules,
next item selection routines, stopping rules and
ability estimators. Control methods for item exposure
and content balancing are also included.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM,
Canada)
Maintainer: David Magis
Diff between catR versions 2.5 dated 2013-02-07 and 2.6 dated 2013-12-03
DESCRIPTION | 22 ++++++++++++---------- MD5 | 8 ++++---- NEWS | 19 +++++++++++++++++++ R/nextItem.R | 10 +++++----- inst/doc/catR-manual.pdf |binary 5 files changed, 40 insertions(+), 19 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
Diff between lfe versions 1.5-1118 dated 2013-11-12 and 1.6-1161 dated 2013-12-03
DESCRIPTION | 12 - MD5 | 79 +++--- NAMESPACE | 1 R/kaczmarz.R | 195 ++++++++++------ R/lfe.R | 305 +++++++++++++++++-------- R/utils.R | 53 ++++ configure | 269 +++++++++++++++++----- exec/lfescript | 26 +- inst/CITATION | 55 +++- inst/doc/CHANGELOG |only inst/doc/identification.pdf |binary inst/doc/lfehow.R | 4 inst/doc/lfehow.Rnw | 18 + inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/demeanlist.Rd | 18 + man/efactory.Rd | 8 man/felm.Rd | 43 ++- man/getfe.Rd | 2 man/is.estimable.Rd | 18 + man/lfe-package.Rd | 4 src/Makevars.in | 5 src/build/autoconf/aclocal.m4 | 20 + src/config.h |only src/config.h.in |only src/lfe.c | 500 ++++++++++++++++++++++++++++-------------- tests/comparelm.Rout.save | 7 tests/degenerate.Rout.save | 7 tests/efcheck.R | 2 tests/efcheck.Rout.save | 440 ++++++++++++++++++------------------ tests/fourfac.Rout.save | 12 - tests/interact.R |only tests/interact.Rout.save |only tests/ivtest.R | 5 tests/ivtest.Rout.save | 34 ++ tests/lfetest.R | 4 tests/lfetest.Rout.save | 13 - tests/naomit.Rout.save | 7 tests/nonest.Rout.save | 17 - tests/onefac.R | 11 tests/onefac.Rout.save | 113 +++++++-- tests/verify.Rout.save | 10 vignettes/lfehow.Rnw | 18 + 43 files changed, 1556 insertions(+), 779 deletions(-)
Title: Evaluating the genetic differentiation between populations based
on Gst and D values.
Description: This package allows to calculate the fixation index Gst
(Nei, 1973) and the differentiation index D (Jost, 2008) pairwise
between or averaged over several populations. P-values, stating the
significance of differentiation, and 95 percent confidence intervals
can be estimated using bootstrap resamplings. In the case that more
than two populations are compared pairwise, the p-values are
adjusted by bonferroni correction and in several other ways due to
the multiple comparison from one data set.
Author: Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann
Maintainer: Alexander Jueterbock
Diff between DEMEtics versions 0.8-5 dated 2012-02-26 and 0.8-7 dated 2013-12-03
DESCRIPTION | 29 +++++++++++++-------------- MD5 | 39 +++++++++++++++++++------------------ NAMESPACE | 2 - R/Bootstrapping.CI.r | 12 +++++------ R/Bootstrapping.p.r | 10 ++++----- R/D.Jost.r | 4 +-- R/DEMEtics.env.r |only R/Gst.Nei.r | 6 ++--- R/H.out.r | 21 ++++++++++---------- R/Hardy.Weinberg.r | 2 - R/allelefreq.r | 6 ++--- R/calc.r | 2 - R/calculate.anzahlk.r | 2 - R/inputformat.r | 1 R/locus.means.calc.r | 6 ++--- R/over.all.pops.r | 38 ++++++++++++++++++------------------ R/p.val.r | 2 - R/p.value.correcture.r | 2 - R/pair.pops.r | 50 ++++++++++++++++++++++++------------------------ man/D.JostaGst.Nei.Rd | 1 man/DEMEtics-package.Rd | 6 ++--- 21 files changed, 122 insertions(+), 119 deletions(-)
Title: Gene-level statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Dan Schaid and Jason Sinnwell
Maintainer: Jason Sinnwell
Diff between pedgene versions 1.2 dated 2013-11-18 and 1.3 dated 2013-12-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/pedgene.R | 15 ++++++++------- inst/NEWS.Rd | 9 +++++++-- tests/test.pedgene.expanded.R | 11 +++++++++++ tests/test.pedgene.expanded.Rout.save | 18 ++++++++++++++++-- 6 files changed, 52 insertions(+), 21 deletions(-)
Title: Sample from the posterior of the negative binomial mixed-effect
regression model. The random effect is modeled with DP mixture
of beta distributions.
Description: This package contains a gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. For the distribution of subject-specific random intercept, user can choose a beta distribution or an infinite mixture of beta distributions. For the safety monitoring, subject-specific conditional probability indices can be computed. For details, see Kondo,Y. and Zhao, Y. A Flexible Mixed Effect Negative Binomial Regression for Detecting Abrupt Increase in MRI Lesion Counts in Multiple Sclerosis Patients.
Author: Yumi Kondo
Maintainer: Yumi Kondo
Diff between lmeNBBayes versions 1.0 dated 2013-04-16 and 1.1 dated 2013-12-03
lmeNBBayes-1.0/lmeNBBayes/man/metaMultGibb.Rd |only lmeNBBayes-1.1/lmeNBBayes/DESCRIPTION | 19 lmeNBBayes-1.1/lmeNBBayes/MD5 | 19 lmeNBBayes-1.1/lmeNBBayes/NAMESPACE | 11 lmeNBBayes-1.1/lmeNBBayes/R/nbinDPmix_C.R | 4991 ++++++++++++++------------ lmeNBBayes-1.1/lmeNBBayes/man/dqmix.Rd | 2 lmeNBBayes-1.1/lmeNBBayes/man/getDIC.Rd | 17 lmeNBBayes-1.1/lmeNBBayes/man/lmeNBBayes.Rd | 36 lmeNBBayes-1.1/lmeNBBayes/src/clencurt.h |only lmeNBBayes-1.1/lmeNBBayes/src/converged.h |only lmeNBBayes-1.1/lmeNBBayes/src/cubature.h |only lmeNBBayes-1.1/lmeNBBayes/src/nbinDPmix.c | 1402 ++++++- lmeNBBayes-1.1/lmeNBBayes/src/vwrapper.h |only 13 files changed, 4098 insertions(+), 2399 deletions(-)
Title: Fit negative binomial mixed-effect regression model.
Description: Fit negative binomial mixed-effect regression model. For the distribution of subject-specific random intercept, a gamma or log-normal distributions or semi-parametric procedure are allowed. For the safety monitoring, subject-specific conditional probability index can be computed. For details, see Zhao, Y., Li, D.K.B., Petkau, J.A., Riddehough, A. & Traboulsee, A. Detection of unusual increases in MRI lesion counts in multiple sclerosis patients.
Author: Zhao, Y. and Kondo, Y.
Maintainer: Yumi Kondo
Diff between lmeNB versions 1.0 dated 2013-04-16 and 1.1 dated 2013-12-03
lmeNB-1.0/lmeNB/R/max.ln.R |only lmeNB-1.1/lmeNB/DESCRIPTION | 17 -- lmeNB-1.1/lmeNB/MD5 | 31 +-- lmeNB-1.1/lmeNB/R/cum1.gn.R | 11 - lmeNB-1.1/lmeNB/R/index.batch.R | 298 +++++++++++++++++++++--------------- lmeNB-1.1/lmeNB/R/mle.a3.fun.R | 8 lmeNB-1.1/lmeNB/R/mle.fun.R | 106 +++++++----- lmeNB-1.1/lmeNB/R/nb-mix-ar1.R | 258 ++++++------------------------- lmeNB-1.1/lmeNB/man/CP_se.Rd | 12 - lmeNB-1.1/lmeNB/man/index_batch.Rd | 6 lmeNB-1.1/lmeNB/man/jCP_ar1.Rd | 9 - lmeNB-1.1/lmeNB/man/lmeNB.Rd | 30 ++- lmeNB-1.1/lmeNB/man/mle_a3_fun.Rd | 55 ++++-- lmeNB-1.1/lmeNB/man/mle_ar1_fun.Rd | 102 ++++-------- lmeNB-1.1/lmeNB/man/mle_ar1_non3.Rd | 42 +++-- lmeNB-1.1/lmeNB/man/mle_fun.Rd | 24 +- lmeNB-1.1/lmeNB/man/rNBME_R.Rd | 180 ++++----------------- 17 files changed, 500 insertions(+), 689 deletions(-)
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su
Diff between GLDEX versions 1.0.4.4 dated 2012-10-24 and 1.0.4.5 dated 2013-12-03
GLDEX-1.0.4.4/GLDEX/CONTENTS |only GLDEX-1.0.4.4/GLDEX/R/cutdefault.R |only GLDEX-1.0.4.4/GLDEX/man/cutdefault.Rd |only GLDEX-1.0.4.5/GLDEX/DESCRIPTION | 28 GLDEX-1.0.4.5/GLDEX/MD5 | 27 GLDEX-1.0.4.5/GLDEX/R/hiddenfunctions.R | 11 GLDEX-1.0.4.5/GLDEX/R/histsu.R | 26 GLDEX-1.0.4.5/GLDEX/R/ks.gof.R | 90 -- GLDEX-1.0.4.5/GLDEX/man/GLDEX.package.Rd | 227 +++-- GLDEX-1.0.4.5/GLDEX/man/GLDfunctions.Rd | 21 GLDEX-1.0.4.5/GLDEX/man/histsu.Rd | 2 GLDEX-1.0.4.5/GLDEX/man/starship.Rd | 6 GLDEX-1.0.4.5/GLDEX/man/starship.adaptivegrid.Rd | 6 GLDEX-1.0.4.5/GLDEX/man/starship.obj.Rd | 4 GLDEX-1.0.4.5/GLDEX/man/which.na.Rd | 10 GLDEX-1.0.4.5/GLDEX/src/085A-LowDiscrepancy.f | 988 +++++++++++------------ 16 files changed, 676 insertions(+), 770 deletions(-)
Title: GeMTC network meta-analysis
Description: An R package for performing network meta-analyses (mixed treatment comparisons).
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef
Diff between gemtc versions 0.5-1 dated 2013-10-30 and 0.5-2 dated 2013-12-03
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS | 11 ++++++++++- R/mtc.model.ume.R | 2 +- src/rank.c | 4 ++-- 5 files changed, 23 insertions(+), 14 deletions(-)
Title: Analysis and visualisation of ecological communities
Description: Cheddar provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. It also allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson
Diff between cheddar versions 0.1-622 dated 2013-03-21 and 0.1-624 dated 2013-12-03
cheddar-0.1-622/cheddar/inst/doc/Grassland1994 |only cheddar-0.1-622/cheddar/inst/doc/Stream12 |only cheddar-0.1-622/cheddar/inst/doc/cheddar.bib |only cheddar-0.1-622/cheddar/man/cheddar-package.Rd |only cheddar-0.1-622/cheddar/release_history.md |only cheddar-0.1-624/cheddar/DESCRIPTION | 22 cheddar-0.1-624/cheddar/MD5 | 103 +-- cheddar-0.1-624/cheddar/R/community.R | 77 +- cheddar-0.1-624/cheddar/R/community_MN.R | 5 cheddar-0.1-624/cheddar/R/community_collection.R | 89 ++ cheddar-0.1-624/cheddar/R/community_trophic_links.R | 377 ++++++++++- cheddar-0.1-624/cheddar/R/graph_nodes.R | 8 cheddar-0.1-624/cheddar/R/graph_trophic_links.R | 9 cheddar-0.1-624/cheddar/R/util.R | 33 cheddar-0.1-624/cheddar/build |only cheddar-0.1-624/cheddar/data/ChesapeakeBay.RData |only cheddar-0.1-624/cheddar/inst/doc/CheddarQuickstart.R |only cheddar-0.1-624/cheddar/inst/doc/CheddarQuickstart.pdf |binary cheddar-0.1-624/cheddar/inst/doc/Collections.R |only cheddar-0.1-624/cheddar/inst/doc/Collections.pdf |binary cheddar-0.1-624/cheddar/inst/doc/Community.R |only cheddar-0.1-624/cheddar/inst/doc/Community.Rnw | 35 - cheddar-0.1-624/cheddar/inst/doc/Community.pdf |binary cheddar-0.1-624/cheddar/inst/doc/ImportExport.R |only cheddar-0.1-624/cheddar/inst/doc/ImportExport.Rnw | 2 cheddar-0.1-624/cheddar/inst/doc/ImportExport.pdf |binary cheddar-0.1-624/cheddar/inst/doc/PlotsAndStats.R |only cheddar-0.1-624/cheddar/inst/doc/PlotsAndStats.Rnw | 96 +- cheddar-0.1-624/cheddar/inst/doc/PlotsAndStats.pdf |binary cheddar-0.1-624/cheddar/man/ChesapeakeBay.Rd |only cheddar-0.1-624/cheddar/man/IsCannibal.Rd | 7 cheddar-0.1-624/cheddar/man/NvMTriTrophicStatistics.Rd | 7 cheddar-0.1-624/cheddar/man/NvMTriTrophicTable.Rd |only cheddar-0.1-624/cheddar/man/Omnivory.Rd |only cheddar-0.1-624/cheddar/man/PredationMatrixToLinks.Rd | 29 cheddar-0.1-624/cheddar/man/QuantitativeDescriptors.Rd |only cheddar-0.1-624/cheddar/man/RemoveNodes.Rd | 38 - cheddar-0.1-624/cheddar/man/ResourcesByNode.Rd | 9 cheddar-0.1-624/cheddar/man/SiteBySpeciesMatrix.Rd |only cheddar-0.1-624/cheddar/man/TrophicSimilarity.Rd |only cheddar-0.1-624/cheddar/man/cheddar.Rd |only cheddar-0.1-624/cheddar/src/anneal.cpp | 3 cheddar-0.1-624/cheddar/tests/community_MN_test.R | 90 -- cheddar-0.1-624/cheddar/tests/community_collection_test.R | 30 cheddar-0.1-624/cheddar/tests/community_test.R | 42 + cheddar-0.1-624/cheddar/tests/community_trophic_links_test.R | 223 +++++- cheddar-0.1-624/cheddar/tests/run.R | 27 cheddar-0.1-624/cheddar/tests/util_test.R | 81 +- cheddar-0.1-624/cheddar/vignettes |only 49 files changed, 1119 insertions(+), 323 deletions(-)
Title: An Interpretation of the ADM method - automated detection
algorithm.
Description: Robust change point detection using ADM3 algorithm.
Author: Tomas William Fitzgerald
Maintainer: Tom Fitzgerald
Diff between ADM3 versions 1.2 dated 2013-07-15 and 1.3 dated 2013-12-03
ADM3-1.2/ADM3/R/zzz.R |only ADM3-1.3/ADM3/DESCRIPTION | 7 ++++--- ADM3-1.3/ADM3/MD5 | 5 ++--- ADM3-1.3/ADM3/NAMESPACE | 1 + 4 files changed, 7 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-19 1.0-2
2011-05-21 1.0-1
2008-01-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-08-23 0.9-1
2010-04-02 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-08-12 1.0
Title: An R package for meta-analyzing region-based tests of rare DNA
variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arend Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Arend Voorman
Diff between seqMeta versions 1.2 dated 2013-09-09 and 1.3 dated 2013-12-03
DESCRIPTION | 8 MD5 | 24 +- NAMESPACE | 2 R/burdenMeta.R | 191 +++++++++--------- R/c.seqMeta.R | 10 R/check_format_skat.R | 6 R/prepCox.R | 25 ++ R/prepScores.R | 395 ++++++++++++++++++++++++++++---------- R/singlesnpMeta.R | 165 ++++++++-------- R/skatMeta.R | 74 +++---- R/skatOMeta.R | 515 +++++++++++++++++++++++++------------------------- inst/doc/seqMeta.pdf |binary man/prepScores.Rd | 9 13 files changed, 825 insertions(+), 599 deletions(-)
Title: Rcmdr Plug-In for Business and Customer Analytics
Description: This package provides an Rcmdr "plug-in" to accompany the
book Customer and Business Analytics: Applied Data Mining for
Business Decision Making Using R by Daniel S. Putler and Robert
E. Krider.
Author: Dan Putler
Maintainer: Dan Putler
Diff between RcmdrPlugin.BCA versions 0.9-6 dated 2013-07-15 and 0.9-7 dated 2013-12-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 +- R/RcmdrPlugin.BCA.R | 17 +++++++++-------- 4 files changed, 17 insertions(+), 16 deletions(-)
More information about RcmdrPlugin.BCA at CRAN
Permanent link
Title: Create cryptographic hash digests of R objects
Description: The digest package provides a function 'digest()' for the
creation of hash digests of arbitrary R objects (using the md5, sha-1,
sha-256 and crc32 algorithms) permitting easy comparison of R language
objects, as well as a function 'hmac()' to create hash-based message
authentication code.
The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1
and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2,
and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine. For crc32, code
from the zlib library is used. For sha-512, an implementation by Aaron
D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely
tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Diff between digest versions 0.6.3 dated 2013-02-16 and 0.6.4 dated 2013-12-03
ChangeLog | 7 +++++++ DESCRIPTION | 48 ++++++++++++++++++++++++------------------------ MD5 | 10 +++++----- man/digest.Rd | 11 +++++++---- man/hmac.Rd | 6 ++++-- src/sha2.h | 13 +++++++++++++ 6 files changed, 60 insertions(+), 35 deletions(-)
Title: Aspects of Multivariables
Description: This package consists of two main functions: The first function is corAspect() performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. The second function is lineals() performs optimal scaling by minimization a non-correlational aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as SEM. A platform including related PsychoR packages is provided on R-Forge.
Author: Jan de Leeuw, Kurt Hornik, Patrick Mair
Maintainer: Jan de Leeuw
Diff between aspect versions 1.0-0 dated 2010-01-02 and 1.0-2 dated 2013-12-03
aspect-1.0-0/aspect/COPYRIGHTS |only aspect-1.0-0/aspect/inst/CITATION |only aspect-1.0-0/aspect/inst/doc |only aspect-1.0-2/aspect/DESCRIPTION | 30 +++++++++++++----------------- aspect-1.0-2/aspect/MD5 |only aspect-1.0-2/aspect/R/corAspect.R | 1 + aspect-1.0-2/aspect/R/lineals.R | 4 +++- aspect-1.0-2/aspect/data/duncan.rda |binary aspect-1.0-2/aspect/data/galo.rda |binary aspect-1.0-2/aspect/data/wurzer.rda |binary aspect-1.0-2/aspect/inst/COPYRIGHTS |only aspect-1.0-2/aspect/man/aspect-package.Rd | 6 +++--- aspect-1.0-2/aspect/man/corAspect.Rd | 2 +- aspect-1.0-2/aspect/man/lineals.Rd | 2 +- 14 files changed, 22 insertions(+), 23 deletions(-)
Title: Simple and Canonical Correspondence Analysis.
Description: This package performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.
Author: Jan de Leeuw, Patrick Mair
Maintainer: Jan de Leeuw
Diff between anacor versions 1.0-2 dated 2013-04-05 and 1.0-4 dated 2013-12-03
anacor-1.0-2/anacor/COPYRIGHTS |only anacor-1.0-2/anacor/inst/doc/anacor.Rnw |only anacor-1.0-2/anacor/inst/doc/anacor.bib |only anacor-1.0-2/anacor/inst/doc/anacor.pdf |only anacor-1.0-2/anacor/inst/doc/bit2dcols.pdf |only anacor-1.0-2/anacor/inst/doc/bit2drows.pdf |only anacor-1.0-2/anacor/inst/doc/bit5dcols.pdf |only anacor-1.0-2/anacor/inst/doc/bit5drows.pdf |only anacor-1.0-2/anacor/inst/doc/glassreg1.pdf |only anacor-1.0-2/anacor/inst/doc/glassreg2.pdf |only anacor-1.0-2/anacor/inst/doc/maxord.pdf |only anacor-1.0-2/anacor/inst/doc/maxtrans.pdf |only anacor-1.0-2/anacor/inst/doc/tochergraph.pdf |only anacor-1.0-2/anacor/inst/doc/tocherjoint.pdf |only anacor-1.0-4/anacor/DESCRIPTION | 19 +++---- anacor-1.0-4/anacor/MD5 | 69 ++++++++++++++------------- anacor-1.0-4/anacor/NAMESPACE | 4 + anacor-1.0-4/anacor/R/anacor.R | 1 anacor-1.0-4/anacor/R/burtTable.R | 38 +++++++++----- anacor-1.0-4/anacor/R/expandFrame.R | 11 ++++ anacor-1.0-4/anacor/R/mkIndiList.R | 23 ++++++--- anacor-1.0-4/anacor/data/bitterling.rda |binary anacor-1.0-4/anacor/data/galton.rda |binary anacor-1.0-4/anacor/data/glass.rda |binary anacor-1.0-4/anacor/data/maxwell.rda |binary anacor-1.0-4/anacor/data/sleeping.rda |only anacor-1.0-4/anacor/data/spider.rda |binary anacor-1.0-4/anacor/data/srole.rda |binary anacor-1.0-4/anacor/data/tocher.rda |binary anacor-1.0-4/anacor/inst/COPYRIGHTS |only anacor-1.0-4/anacor/inst/doc/vignettes |only anacor-1.0-4/anacor/man/anacor-package.Rd | 4 - anacor-1.0-4/anacor/man/anacor.Rd | 6 +- anacor-1.0-4/anacor/man/burtTable.Rd | 22 +++++--- anacor-1.0-4/anacor/man/expandFrame.Rd | 17 +++++- anacor-1.0-4/anacor/man/mkIndiList.Rd | 35 ++++++++++--- anacor-1.0-4/anacor/man/plot.anacor.Rd | 11 ++-- anacor-1.0-4/anacor/man/sleeping.Rd |only 38 files changed, 166 insertions(+), 94 deletions(-)