Title: Data Management for Hydrology and Beyond Using the Observations
Data Model
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>
Diff between RObsDat versions 15.02 dated 2015-02-27 and 15.08 dated 2015-08-03
RObsDat-15.02/RObsDat/man/restructureDataResult.Rd |only RObsDat-15.08/RObsDat/DESCRIPTION | 10 +++++----- RObsDat-15.08/RObsDat/MD5 | 11 +++++------ RObsDat-15.08/RObsDat/NAMESPACE | 4 ++++ RObsDat-15.08/RObsDat/build/vignette.rds |binary RObsDat-15.08/RObsDat/inst/doc/RObsDat_Einstiegstutorial.pdf |binary RObsDat-15.08/RObsDat/vignettes/RObsDat.bib | 2 +- 7 files changed, 15 insertions(+), 12 deletions(-)
Title: Package Provides Access to Fake User Data
Description: Generates random names with additional information including fake SSNs, gender, location, zip, age, address, and nationality.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>
Diff between randNames versions 0.2 dated 2015-04-28 and 0.2.1 dated 2015-08-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/rand_names.R | 6 +++--- README.md | 6 ++++++ man/rand_names.Rd | 4 ++-- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.3.1 dated 2015-07-07 and 0.4 dated 2015-08-03
ChangeLog | 12 - DESCRIPTION | 12 - MD5 | 75 ++++--- NAMESPACE | 10 - NEWS | 11 - R/0_classesAndMethods.R | 127 ++++++++---- R/1_functions4Fitting.R | 187 ++++++++++--------- R/1_supplementaryPlot.R |only R/2_probabilistic.R | 1 R/5_statisticalTests.R |only R/RcppExports.R | 8 README.md | 3 inst/doc/BayesianInference.pdf |binary inst/doc/CTMC.R | 4 inst/doc/CTMC.Rmd | 6 inst/doc/CTMC.pdf |binary inst/doc/an_introduction_to_markovchain_package.R | 169 ++++++++++------- inst/doc/an_introduction_to_markovchain_package.Rnw | 89 ++++++++- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.Rmd | 6 inst/doc/markovchainCrashIntro.pdf |binary man/ctmcFit.Rd |only man/markovchain-class.Rd | 4 man/markovchain-package.Rd | 4 man/markovchainListFit.Rd | 2 man/multinomialConfidenceIntervals.Rd |only man/verifyMarkovProperty.Rd |only src/1_ctmcFunctions4Fitting.cpp |only src/1_functions4Fitting.cpp | 25 +- src/2_probabilistic.cpp | 4 src/3_multinomCI.cpp | 134 ++++++++++++- src/RcppExports.cpp | 26 ++ tests/testthat/testBasic1.R | 5 tests/testthat/testInference.R |only tests/testthat/testMultinomCI.R | 5 tests/testthat/testPlot.R | 66 ++++-- tests/testthat/testRecurrentClasses.R | 1 tests/testthat/testetm.R |only tests/testthat/testmsm.R |only vignettes/CTMC.Rmd | 6 vignettes/an_introduction_to_markovchain_package.Rnw | 89 ++++++++- vignettes/markovchainBiblio.bib | 27 ++ vignettes/markovchainCrashIntro.Rmd | 6 43 files changed, 799 insertions(+), 325 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between httpuv versions 1.3.2 dated 2014-10-23 and 1.3.3 dated 2015-08-03
DESCRIPTION | 14 +-- MD5 | 36 +++---- NAMESPACE | 3 NEWS | 8 + R/httpuv.R | 8 + man/WebSocket-class.Rd | 3 man/encodeURI.Rd | 3 man/httpuv-package.Rd | 3 man/interrupt.Rd | 3 man/rawToBase64.Rd | 3 man/runServer.Rd | 3 man/service.Rd | 3 man/startDaemonizedServer.Rd | 3 man/startServer.Rd | 3 man/stopDaemonizedServer.Rd | 3 man/stopServer.Rd | 3 src/Makevars | 3 src/RcppExports.cpp | 196 ++++++++++++++++--------------------------- src/http.cpp | 10 +- 19 files changed, 149 insertions(+), 162 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-5 dated 2015-05-22 and 0.1-6 dated 2015-08-03
DESCRIPTION | 11 +++-- MD5 | 14 +++---- NAMESPACE | 33 ++++++++++++++++ R/EvolQG.R | 5 ++ R/ExtendMatrix.R | 2 - R/MatrixStatistics.R | 74 +++++++++++++++++++++++++++++++++---- R/PCAsimilarity.R | 2 - inst/tests/test.MatrixStatistics.r | 28 ++++++++++---- 8 files changed, 139 insertions(+), 30 deletions(-)
Title: Methods for Dimension Reduction for Regression
Description: Functions, methods, and datasets for fitting dimension
reduction regression, using slicing (methods SAVE and SIR), Principal
Hessian Directions (phd, using residuals and the response), and an
iterative IRE. Partial methods, that condition on categorical
predictors are also available. A variety of tests, and stepwise
deletion of predictors, is also included. Also included is
code for computing permutation tests of dimension. Adding additional
methods of estimating dimension is straightforward.
For documentation, see the vignette in the package. With version 3.0.4,
the arguments for dr.step have been modified.
Author: Sanford Weisberg <sandy@umn.edu>,
Maintainer: Sanford Weisberg <sandy@umn.edu>
Diff between dr versions 3.0.9 dated 2014-11-30 and 3.0.10 dated 2015-08-03
DESCRIPTION | 13 +- MD5 | 12 +- NAMESPACE | 9 + NEWS | 4 build/vignette.rds |binary inst/doc/overview.R | 294 +++++++++++++++++++++++++------------------------- inst/doc/overview.pdf |binary 7 files changed, 173 insertions(+), 159 deletions(-)
Title: Split and Recombine Your Data
Description: Sometimes you need to split your data and work on the two chunks independently before bringing them back together. 'Taber' allows you to do that with its two functions.
Author: Seth Wenchel [aut, cre, cph]
Maintainer: Seth Wenchel <seth@wenchel.com>
Diff between taber versions 0.0.1 dated 2015-07-04 and 0.1.0 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++++------ NAMESPACE | 2 ++ NEWS |only R/tabe.R | 50 ++++++++++++++++++++++++++++---------------------- R/zzz.R | 14 +++++++++++++- README.md |only data |only man/clear_stack.Rd |only man/graft.Rd | 20 +++++++++++--------- man/scion.Rd | 13 +++++++------ man/stack_view.Rd |only 12 files changed, 77 insertions(+), 49 deletions(-)
Title: Microsoft Word, Microsoft Powerpoint and HTML Documents
Generation
Description: Create Microsoft Word document (>=2007),
Microsoft Powerpoint document (>=2007) and HTML documents from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document (*.docx and *.pptx). You can use the package as a tool
for fast reporting and as a tool for reporting automation. The package does
not require any installation of Microsoft product to be able to write
Microsoft files (docx and pptx).
Author: David Gohel [aut, cre],
Bootstrap [ctb, cph] (Bootstrap development team),
jQuery [ctb, cph] (The jQuery Foundation),
Dmitry Baranovskiy [ctb, cph] (raphael javascript
libraries)
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>
Diff between ReporteRs versions 0.7.8 dated 2015-03-06 and 0.8.2 dated 2015-08-03
ReporteRs-0.7.8/ReporteRs/inst/java/ReporteRs-0.7.jar |only ReporteRs-0.7.8/ReporteRs/java/ReporteRs-0.7-src.jar |only ReporteRs-0.8.2/ReporteRs/DESCRIPTION | 10 ReporteRs-0.8.2/ReporteRs/MD5 | 401 +++++----- ReporteRs-0.8.2/ReporteRs/NAMESPACE | 26 ReporteRs-0.8.2/ReporteRs/NEWS | 97 ++ ReporteRs-0.8.2/ReporteRs/R/00_AllGeneric.R | 21 ReporteRs-0.8.2/ReporteRs/R/01_tools.R | 79 + ReporteRs-0.8.2/ReporteRs/R/CodeBlock.R |only ReporteRs-0.8.2/ReporteRs/R/FlexCell.R | 2 ReporteRs-0.8.2/ReporteRs/R/FlexRow.R | 23 ReporteRs-0.8.2/ReporteRs/R/FlexTable.R | 10 ReporteRs-0.8.2/ReporteRs/R/FlexTablePublicAPI.R | 23 ReporteRs-0.8.2/ReporteRs/R/FlexTable_theme.R | 14 ReporteRs-0.8.2/ReporteRs/R/FontMetric.R | 14 ReporteRs-0.8.2/ReporteRs/R/ReporteRs.R | 4 ReporteRs-0.8.2/ReporteRs/R/add.plot.interactivity.R | 153 ++- ReporteRs-0.8.2/ReporteRs/R/addCodeBlock.bsdoc.R |only ReporteRs-0.8.2/ReporteRs/R/addCodeBlock.docx.R |only ReporteRs-0.8.2/ReporteRs/R/addCodeBlock.pptx.R |only 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1722 insertions(+), 804 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: Schaid Daniel [aut],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 2.1 dated 2014-06-24 and 2.7 dated 2015-08-03
DESCRIPTION | 21 ++++++++++++--------- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ R/pedgene.R | 32 +++++++++++++++++++++++++++----- R/pedgene.stats.R | 13 ++++++++++--- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ man/pedgene.Rd | 14 +++++++++++--- tests/test.pedgene.expanded.R | 10 ++++++++++ tests/test.pedgene.expanded.Rout.save | 26 ++++++++++++++++++++++---- 10 files changed, 111 insertions(+), 33 deletions(-)
Title: Pedigree Functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe
family relationships such as kinship and identity-by-descent, which
can be used to model family data in mixed effects models, such as in the
coxme function. Also includes a tool for pedigree drawing which is
focused on producing compact layouts without intervention. Recent additions
include utilities to trim the pedigree object with various criteria, and
kinship for the X chromosome.
Author: Terry M Therneau [aut],
Schaid Daniel [ctb],
Jason Sinnwell [aut, cre],
Elizabeth Atkinson [ctb]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between kinship2 versions 1.6.0 dated 2014-07-22 and 1.6.4 dated 2015-08-03
kinship2-1.6.0/kinship2/noweb/all.pdf |only kinship2-1.6.4/kinship2/DESCRIPTION | 29 kinship2-1.6.4/kinship2/MD5 | 33 kinship2-1.6.4/kinship2/NAMESPACE | 9 kinship2-1.6.4/kinship2/R/kinship.R | 7 kinship2-1.6.4/kinship2/R/pedigree.R | 63 + kinship2-1.6.4/kinship2/build/vignette.rds |binary kinship2-1.6.4/kinship2/inst/NEWS.Rd | 8 kinship2-1.6.4/kinship2/man/pedigree.Rd | 15 kinship2-1.6.4/kinship2/noweb/all.aux | 19 kinship2-1.6.4/kinship2/noweb/all.log | 586 +++++++++++++-- kinship2-1.6.4/kinship2/noweb/all.nw | 86 +- kinship2-1.6.4/kinship2/noweb/all.tex | 1036 +++++++++++++++++---------- kinship2-1.6.4/kinship2/noweb/kinship.R |only kinship2-1.6.4/kinship2/noweb/kinship.Rnw | 7 kinship2-1.6.4/kinship2/noweb/pedigree.R |only kinship2-1.6.4/kinship2/noweb/pedigree.Rnw | 79 +- kinship2-1.6.4/kinship2/tests/kin1.Rout.save | 20 kinship2-1.6.4/kinship2/tests/twin.Rout.save | 8 19 files changed, 1447 insertions(+), 558 deletions(-)
Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>
Diff between D3M versions 0.40 dated 2015-08-02 and 0.41 dated 2015-08-03
DESCRIPTION | 8 +- MD5 | 20 ++--- R/RcppExports.R | 4 - R/d3m_main.R | 12 +-- R/d3m_parallel.R | 5 - R/wasser_test.R | 15 +++- man/D3M.Rd | 5 + man/d3m.parallel.Rd | 5 + man/wasser.test.Rd | 10 ++ src/RcppExports.cpp | 7 + src/funcs.cpp | 184 ++++++++++------------------------------------------ 11 files changed, 96 insertions(+), 179 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.36 dated 2015-07-28 and 1.37 dated 2015-08-03
aSPU-1.36/aSPU/R/aSPUM.R |only aSPU-1.36/aSPU/R/aSPUMpath.r |only aSPU-1.36/aSPU/man/aSPUM.Rd |only aSPU-1.36/aSPU/man/aSPUMpath.Rd |only aSPU-1.37/aSPU/DESCRIPTION | 8 +- aSPU-1.37/aSPU/MD5 | 24 ++++---- aSPU-1.37/aSPU/NAMESPACE | 4 - aSPU-1.37/aSPU/R/aSPUs.R |only aSPU-1.37/aSPU/R/aSPUsPath.r |only aSPU-1.37/aSPU/R/aSPUwpermC.R | 1 aSPU-1.37/aSPU/build/vignette.rds |binary aSPU-1.37/aSPU/inst/doc/aSPUstat.R | 6 +- aSPU-1.37/aSPU/inst/doc/aSPUstat.Rmd | 33 +++++------- aSPU-1.37/aSPU/inst/doc/aSPUstat.html | 93 ++++++++++++++-------------------- aSPU-1.37/aSPU/man/aSPUs.Rd |only aSPU-1.37/aSPU/man/aSPUsPath.Rd |only aSPU-1.37/aSPU/vignettes/aSPUstat.Rmd | 33 +++++------- 17 files changed, 94 insertions(+), 108 deletions(-)
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.0-9 dated 2015-08-02 and 1.0-10 dated 2015-08-03
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/ModisDownload.R | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Enhancements by Thomas P Minka <tpminka@media.mit.edu>
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 2.3-10 dated 2015-07-09 and 2.3-11 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapproj versions 1.2-3 dated 2015-07-09 and 1.2-4 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or
higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapdata versions 2.2-4 dated 2015-07-09 and 2.2-5 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Miscellaneous Functions for Math, Plotting, Printing,
Statistics, Strings, and Tools
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
Author: Christian W. Hoffmann <christian@echoffmann.ch> <http://www.echoffmann.ch>
Maintainer: Christian W. Hoffmann <christian@echoffmann.ch>
Diff between cwhmisc versions 5.0 dated 2014-10-15 and 6.0 dated 2015-08-03
cwhmisc-5.0/cwhmisc/R/SetPPT.R |only cwhmisc-5.0/cwhmisc/R/dim.R |only cwhmisc-5.0/cwhmisc/R/heading.R |only cwhmisc-5.0/cwhmisc/R/paste.infix.R |only cwhmisc-5.0/cwhmisc/R/rotL.R |only cwhmisc-5.0/cwhmisc/R/vector.R |only cwhmisc-5.0/cwhmisc/inst/doc/cwhmisc.R |only cwhmisc-5.0/cwhmisc/man/SetPPT.Rd |only cwhmisc-5.0/cwhmisc/man/dim.Rd |only cwhmisc-5.0/cwhmisc/man/figures |only cwhmisc-5.0/cwhmisc/man/heading.Rd |only cwhmisc-5.0/cwhmisc/man/numeric.Rd |only cwhmisc-5.0/cwhmisc/man/paste.infix.Rd |only cwhmisc-5.0/cwhmisc/man/plotSymbol.Rd |only cwhmisc-5.0/cwhmisc/man/rotL.Rd |only cwhmisc-5.0/cwhmisc/man/vector.Rd |only cwhmisc-6.0/cwhmisc/ChangeLog |only cwhmisc-6.0/cwhmisc/DESCRIPTION | 15 - cwhmisc-6.0/cwhmisc/MD5 | 110 ++++++------ cwhmisc-6.0/cwhmisc/NAMESPACE | 4 cwhmisc-6.0/cwhmisc/R/Ddim.R |only cwhmisc-6.0/cwhmisc/R/RCA.R | 63 +++---- cwhmisc-6.0/cwhmisc/R/clocksense.R | 9 - cwhmisc-6.0/cwhmisc/R/const.R | 7 cwhmisc-6.0/cwhmisc/R/coords.R | 98 +++++++++-- cwhmisc-6.0/cwhmisc/R/date.R |only cwhmisc-6.0/cwhmisc/R/dcmpf.R | 2 cwhmisc-6.0/cwhmisc/R/ellipse.R | 15 + cwhmisc-6.0/cwhmisc/R/factor.R | 2 cwhmisc-6.0/cwhmisc/R/frac.R | 8 cwhmisc-6.0/cwhmisc/R/functions.R | 18 +- cwhmisc-6.0/cwhmisc/R/lpr.R | 7 cwhmisc-6.0/cwhmisc/R/n2c.R | 8 cwhmisc-6.0/cwhmisc/R/operators.R |only cwhmisc-6.0/cwhmisc/R/plt.R | 4 cwhmisc-6.0/cwhmisc/README | 3 cwhmisc-6.0/cwhmisc/build/vignette.rds |binary cwhmisc-6.0/cwhmisc/inst/doc/SplomT.pdf |only cwhmisc-6.0/cwhmisc/inst/doc/cwhmisc-Scw.pdf |only cwhmisc-6.0/cwhmisc/inst/doc/cwhmisc.Rnw | 228 ++++++++++++-------------- cwhmisc-6.0/cwhmisc/inst/doc/cwhmisc.pdf |binary cwhmisc-6.0/cwhmisc/man/Ddim.Rd |only cwhmisc-6.0/cwhmisc/man/FinneyCorr.Rd | 2 cwhmisc-6.0/cwhmisc/man/RCA.Rd | 27 +-- cwhmisc-6.0/cwhmisc/man/astroC.Rd | 4 cwhmisc-6.0/cwhmisc/man/astroGeo.Rd | 2 cwhmisc-6.0/cwhmisc/man/const.Rd | 18 +- cwhmisc-6.0/cwhmisc/man/coords.Rd | 102 +++++++++-- cwhmisc-6.0/cwhmisc/man/cwhmisc-internal.Rd |only cwhmisc-6.0/cwhmisc/man/cwhmisc-package.Rd | 27 ++- cwhmisc-6.0/cwhmisc/man/date.Rd |only cwhmisc-6.0/cwhmisc/man/dcmpf.Rd | 4 cwhmisc-6.0/cwhmisc/man/delayt.Rd | 2 cwhmisc-6.0/cwhmisc/man/digits.Rd | 5 cwhmisc-6.0/cwhmisc/man/ellipse.Rd | 22 +- cwhmisc-6.0/cwhmisc/man/f.log.Rd | 6 cwhmisc-6.0/cwhmisc/man/factor.Rd | 3 cwhmisc-6.0/cwhmisc/man/format.fix.Rd | 1 cwhmisc-6.0/cwhmisc/man/functions.Rd | 23 ++ cwhmisc-6.0/cwhmisc/man/grepnot.Rd | 19 -- cwhmisc-6.0/cwhmisc/man/int2.Rd | 5 cwhmisc-6.0/cwhmisc/man/lpr.Rd | 11 - cwhmisc-6.0/cwhmisc/man/n2c.Rd | 3 cwhmisc-6.0/cwhmisc/man/numer.Rd |only cwhmisc-6.0/cwhmisc/man/operators.Rd |only cwhmisc-6.0/cwhmisc/man/plotSymbols.Rd |only cwhmisc-6.0/cwhmisc/man/plt.Rd | 7 cwhmisc-6.0/cwhmisc/man/replacechar.Rd | 3 cwhmisc-6.0/cwhmisc/vignettes/SplomT.pdf |only cwhmisc-6.0/cwhmisc/vignettes/cwhmisc-Scw.pdf |only cwhmisc-6.0/cwhmisc/vignettes/cwhmisc.Rnw | 228 ++++++++++++-------------- 71 files changed, 633 insertions(+), 492 deletions(-)
Title: Multivariate Curve Resolution Alternating Least Squares
(MCR-ALS)
Description: Alternating least squares is often used to resolve
components contributing to data with a bilinear structure; the
basic technique may be extended to alternating constrained
least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components.
Several data matrices may be decomposed simultaneously by
assuming that one of the two matrices in the bilinear
decomposition is shared between datasets.
Author: Katharine M. Mullen
Maintainer: Katharine Mullen <mullenkate@gmail.com>
Diff between ALS versions 0.0.5 dated 2012-07-02 and 0.0.6 dated 2015-08-03
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NAMESPACE | 8 ++++++++ NEWS | 4 ++++ R/getC.R | 4 ++-- R/getCList.R | 4 ++-- R/getS.R | 4 ++-- inst |only man/als.Rd | 4 ++-- 9 files changed, 33 insertions(+), 19 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 1.0.5.0 dated 2015-04-15 and 1.0.6.0 dated 2015-08-03
ggtern-1.0.5.0/ggtern/R/geom-density2d.R |only ggtern-1.0.5.0/ggtern/R/stat-density-2d.R |only ggtern-1.0.5.0/ggtern/man/geom_density2d.Rd |only ggtern-1.0.5.0/ggtern/man/geom_smooth.Rd |only ggtern-1.0.5.0/ggtern/man/stat_density2d.Rd |only ggtern-1.0.5.0/ggtern/man/stat_smooth.Rd |only ggtern-1.0.6.0/ggtern/DESCRIPTION | 29 +- ggtern-1.0.6.0/ggtern/MD5 | 180 +++++++++-------- ggtern-1.0.6.0/ggtern/NAMESPACE | 18 + ggtern-1.0.6.0/ggtern/NEWS | 11 + ggtern-1.0.6.0/ggtern/R/clip-polygons.R |only ggtern-1.0.6.0/ggtern/R/coord-tern.R | 110 +++++----- ggtern-1.0.6.0/ggtern/R/geom-confidence.R | 52 +--- ggtern-1.0.6.0/ggtern/R/geom-density-tern.R |only ggtern-1.0.6.0/ggtern/R/geom-errorbarT.R | 6 ggtern-1.0.6.0/ggtern/R/geom-interpolate-tern.R |only ggtern-1.0.6.0/ggtern/R/geom-polygon-tern.R |only ggtern-1.0.6.0/ggtern/R/geom-smooth.R | 10 ggtern-1.0.6.0/ggtern/R/gg-internal.R | 4 ggtern-1.0.6.0/ggtern/R/ggtern-build.R | 26 +- ggtern-1.0.6.0/ggtern/R/onLoad.R | 6 ggtern-1.0.6.0/ggtern/R/panel.R | 1 ggtern-1.0.6.0/ggtern/R/plot-construction.R | 36 +-- ggtern-1.0.6.0/ggtern/R/scales.R | 15 + ggtern-1.0.6.0/ggtern/R/stat-density-tern.R |only ggtern-1.0.6.0/ggtern/R/stat-interpolate-tern.R |only ggtern-1.0.6.0/ggtern/R/stat-smooth.R | 10 ggtern-1.0.6.0/ggtern/R/statnew.R | 12 - ggtern-1.0.6.0/ggtern/R/strip-unapproved.R | 26 +- ggtern-1.0.6.0/ggtern/R/tern-render.R | 114 ++++++---- ggtern-1.0.6.0/ggtern/R/theme-defaults.R | 117 +++++------ ggtern-1.0.6.0/ggtern/R/theme-novar-tern.R |only ggtern-1.0.6.0/ggtern/R/theme.R | 1 ggtern-1.0.6.0/ggtern/R/utilities-help.R | 8 ggtern-1.0.6.0/ggtern/R/utilities.R | 123 ++++++++++- ggtern-1.0.6.0/ggtern/build/partial.rdb |binary ggtern-1.0.6.0/ggtern/man/aes.Rd | 17 - ggtern-1.0.6.0/ggtern/man/approved_geometries.Rd | 10 ggtern-1.0.6.0/ggtern/man/clipPolygons.Rd |only ggtern-1.0.6.0/ggtern/man/convenience_functions.Rd | 52 ++-- ggtern-1.0.6.0/ggtern/man/coord.Rd | 32 +-- ggtern-1.0.6.0/ggtern/man/coord_tern.Rd | 74 +++--- ggtern-1.0.6.0/ggtern/man/data.Rd | 9 ggtern-1.0.6.0/ggtern/man/data_Feldspar.Rd | 5 ggtern-1.0.6.0/ggtern/man/data_USDA.Rd | 12 - ggtern-1.0.6.0/ggtern/man/element_ternary.Rd | 61 ++--- ggtern-1.0.6.0/ggtern/man/enforceTernaryCoordinates.Rd |only ggtern-1.0.6.0/ggtern/man/expandRange.Rd |only ggtern-1.0.6.0/ggtern/man/expandTern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_TLRline.Rd | 85 +++----- ggtern-1.0.6.0/ggtern/man/geom_density_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_errorbarTLR.Rd | 63 ++--- ggtern-1.0.6.0/ggtern/man/geom_interpolate_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_polygon_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_segment.Rd | 48 ++-- ggtern-1.0.6.0/ggtern/man/geom_smooth_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geomconfidence.Rd | 57 ++--- ggtern-1.0.6.0/ggtern/man/ggplot_build.Rd | 17 - ggtern-1.0.6.0/ggtern/man/ggplot_gtable.Rd | 22 +- ggtern-1.0.6.0/ggtern/man/ggsave.Rd | 51 ++-- ggtern-1.0.6.0/ggtern/man/ggtern-labels.Rd | 65 ++---- ggtern-1.0.6.0/ggtern/man/ggtern-package.Rd | 133 +++++------- ggtern-1.0.6.0/ggtern/man/ggtern.Rd | 21 - ggtern-1.0.6.0/ggtern/man/ggtern.multi.Rd | 39 +-- ggtern-1.0.6.0/ggtern/man/iflasttern.Rd | 10 ggtern-1.0.6.0/ggtern/man/kde2d.weighted.Rd | 36 ++- ggtern-1.0.6.0/ggtern/man/logratio.Rd | 28 +- ggtern-1.0.6.0/ggtern/man/mahalanobis.Rd | 15 - ggtern-1.0.6.0/ggtern/man/notransform.Rd | 11 - ggtern-1.0.6.0/ggtern/man/overloaded.Rd | 157 ++++++-------- ggtern-1.0.6.0/ggtern/man/point.in.sequence.Rd | 42 +-- ggtern-1.0.6.0/ggtern/man/print.Rd | 16 - ggtern-1.0.6.0/ggtern/man/scale_TLR_continuous.Rd | 39 +-- ggtern-1.0.6.0/ggtern/man/showhidegrid.Rd | 41 +-- ggtern-1.0.6.0/ggtern/man/stat_density_tern.Rd |only ggtern-1.0.6.0/ggtern/man/stat_interpolate_tern.Rd |only ggtern-1.0.6.0/ggtern/man/stat_smooth_tern.Rd |only ggtern-1.0.6.0/ggtern/man/strip_unapproved.Rd | 15 - ggtern-1.0.6.0/ggtern/man/suffix_arrow.Rd | 31 +- ggtern-1.0.6.0/ggtern/man/suppressColours.Rd |only ggtern-1.0.6.0/ggtern/man/ternLimitsForCoord.Rd |only ggtern-1.0.6.0/ggtern/man/tern_dep.Rd | 43 +--- ggtern-1.0.6.0/ggtern/man/tern_limits.Rd | 26 -- ggtern-1.0.6.0/ggtern/man/tern_stop.Rd | 9 ggtern-1.0.6.0/ggtern/man/ternary_transformations.Rd | 106 +++------- ggtern-1.0.6.0/ggtern/man/theme_arrowbaseline.Rd | 16 - ggtern-1.0.6.0/ggtern/man/theme_bw.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_classic.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_clockwise.Rd | 10 ggtern-1.0.6.0/ggtern/man/theme_complete.Rd | 22 -- ggtern-1.0.6.0/ggtern/man/theme_custom.Rd | 20 - ggtern-1.0.6.0/ggtern/man/theme_elements.Rd | 49 +--- ggtern-1.0.6.0/ggtern/man/theme_gray.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_minimal.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_novar_tern.Rd |only ggtern-1.0.6.0/ggtern/man/theme_rgbg.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_rgbw.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_showlabels.Rd | 12 - ggtern-1.0.6.0/ggtern/man/theme_showprimary.Rd | 56 +---- ggtern-1.0.6.0/ggtern/man/theme_showtitles.Rd | 10 ggtern-1.0.6.0/ggtern/man/themearrowlength.Rd | 79 ++----- ggtern-1.0.6.0/ggtern/man/themeshowhidearrows.Rd | 11 - ggtern-1.0.6.0/ggtern/man/themeticksoutside.Rd | 9 ggtern-1.0.6.0/ggtern/man/undoCartesian.Rd |only ggtern-1.0.6.0/ggtern/man/undocumented.Rd | 128 ++++-------- 105 files changed, 1392 insertions(+), 1497 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, and algorithms for z-identifiability, transportability, z-transportability and meta-transportability of causal effects by Elias Bareinboim and Judea Pearl. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.1.3 dated 2015-06-30 and 1.2.0 dated 2015-08-03
causaleffect-1.1.3/causaleffect/R/getNonIgnorableNodes.probability.R |only causaleffect-1.1.3/causaleffect/R/organizeTerms.probability.R |only causaleffect-1.2.0/causaleffect/DESCRIPTION | 14 +- causaleffect-1.2.0/causaleffect/MD5 | 48 ++++++--- causaleffect-1.2.0/causaleffect/NAMESPACE | 2 causaleffect-1.2.0/causaleffect/NEWS | 5 - causaleffect-1.2.0/causaleffect/R/activate.interventions.R |only causaleffect-1.2.0/causaleffect/R/causal.effect.R | 17 ++- causaleffect-1.2.0/causaleffect/R/get.expression.R | 29 +++-- causaleffect-1.2.0/causaleffect/R/getNonIgnorableNodes.R | 8 + causaleffect-1.2.0/causaleffect/R/id.R | 7 - causaleffect-1.2.0/causaleffect/R/idc.R | 4 causaleffect-1.2.0/causaleffect/R/meta.transport.R |only causaleffect-1.2.0/causaleffect/R/observed.graph.R | 2 causaleffect-1.2.0/causaleffect/R/organizeTerms.R | 17 +++ causaleffect-1.2.0/causaleffect/R/probability.R | 4 causaleffect-1.2.0/causaleffect/R/sc.components.R |only causaleffect-1.2.0/causaleffect/R/sid.R |only causaleffect-1.2.0/causaleffect/R/simplify.expression.R |only causaleffect-1.2.0/causaleffect/R/simplify.meta.expression.R |only causaleffect-1.2.0/causaleffect/R/transport.R |only causaleffect-1.2.0/causaleffect/R/trz.R |only causaleffect-1.2.0/causaleffect/R/unobserved.graph.R | 4 causaleffect-1.2.0/causaleffect/R/usid.R |only causaleffect-1.2.0/causaleffect/R/zid.R |only causaleffect-1.2.0/causaleffect/R/zzaux.effect.R |only causaleffect-1.2.0/causaleffect/man/causal.effect.Rd | 9 + causaleffect-1.2.0/causaleffect/man/causaleffect-package.Rd | 50 +++++++--- causaleffect-1.2.0/causaleffect/man/get.expression.Rd | 7 - causaleffect-1.2.0/causaleffect/man/meta.transport.Rd |only causaleffect-1.2.0/causaleffect/man/parse.graphml.Rd | 8 - causaleffect-1.2.0/causaleffect/man/transport.Rd |only causaleffect-1.2.0/causaleffect/man/zzaux.effect.Rd |only 33 files changed, 151 insertions(+), 84 deletions(-)