Title: Distribution of Largest Root for Single and Double Wishart
Settings
Description: Functions for hypothesis testing in single and double Wishart
settings, based on Roy's largest root. This test statistic is especially
useful in multivariate analysis. The computations are based on results by
Chiani (2014) <DOI:10.1016/j.jmva.2014.04.002> and Chiani (2016)
<DOI:10.1016/j.jmva.2015.10.007>. They use the fact that the CDF is related
to the Pfaffian of a matrix that can be computed in a finite number of
iterations. This package takes advantage of the Boost and Eigen C++ libraries
to perform multi-precision linear algebra.
Author: Maxime Turgeon [aut, cre]
Maintainer: Maxime Turgeon <maxime.turgeon@mail.mcgill.ca>
Diff between rootWishart versions 0.3.0 dated 2016-07-13 and 0.4.0 dated 2017-04-30
DESCRIPTION | 8 ++--- MD5 | 23 ++++++++------- NAMESPACE | 2 - NEWS.md | 9 +++++- R/RcppExports.R | 2 - R/functions.R | 75 ++++++++++++++++++++++++++++++++++++-------------- R/utility.R | 23 ++++++++++++++- README.md | 4 +- man/largestRoot.Rd | 43 ++++++++++++++-------------- src/RcppExports.cpp | 18 ++++++------ src/doubleWishart.cpp | 12 ++++++-- src/init.c |only src/singleWishart.cpp | 10 +++--- 13 files changed, 148 insertions(+), 81 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [aut],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.1.1 dated 2016-11-22 and 3.1.2 dated 2017-04-30
ChangeLog | 13 +++++ DESCRIPTION | 12 ++-- MD5 | 73 +++++++++++++++------------- NAMESPACE | 1 R/buffer.R | 70 +++++++++++++++++---------- R/buffesm.R | 85 +++++++++++++++++++------------- R/carb.R | 77 ++++++++++++++++++----------- R/carbb.R | 132 ++++++++++++++++++++++++++++----------------------- R/derivnum.R | 14 +++-- R/eos.R |only R/errors.R | 106 ++++++++++++++++++++++++++++------------ R/oa.R | 26 ++++++---- R/pCa.R | 29 +++++++++-- R/pHinsi.R | 23 +++++++- R/pTA.R | 12 ++-- R/pgas.R | 6 +- R/pmix.R | 8 +-- R/ppH.R | 12 ++-- R/psi.R | 4 - man/Om.Rd | 7 +- man/buffer.Rd | 11 +++- man/buffesm.Rd | 11 +++- man/carb.Rd | 8 ++- man/carbb.Rd | 12 +++- man/derivnum.Rd | 8 ++- man/eos2teos_chem.Rd |only man/eos2teos_geo.Rd |only man/errors.Rd | 10 +++ man/oa.Rd | 9 ++- man/pCa.Rd | 8 ++- man/pHinsi.Rd | 10 +++ man/pTA.Rd | 10 ++- man/pgas.Rd | 8 ++- man/pmix.Rd | 8 ++- man/ppH.Rd | 7 ++ man/psi.Rd | 9 ++- man/sa2sp_chem.Rd |only man/sa2sp_geo.Rd |only man/sp2sa_chem.Rd |only man/sp2sa_geo.Rd |only man/teos2eos_chem.Rd |only man/teos2eos_geo.Rd |only 42 files changed, 548 insertions(+), 291 deletions(-)
Title: Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock Data
Description: Multiblock data analysis concerns the analysis of several sets of variables (blocks) observed on the same group of individuals. The main aims of the RGCCA package are: (i) to study the relationships between blocks and (ii) to identify subsets of variables of each block which are active in their relationships with the other blocks.
Author: Arthur Tenenhaus and Vincent Guillemot
Maintainer: Arthur Tenenhaus <arthur.tenenhaus@centralesupelec.fr>
Diff between RGCCA versions 2.1 dated 2017-01-22 and 2.1.1 dated 2017-04-30
RGCCA-2.1.1/RGCCA/DESCRIPTION | 22 - RGCCA-2.1.1/RGCCA/MD5 | 61 ++- RGCCA-2.1.1/RGCCA/NAMESPACE | 39 +- RGCCA-2.1.1/RGCCA/R/BinarySearch.R | 52 +-- RGCCA-2.1.1/RGCCA/R/defl.select.R | 54 +-- RGCCA-2.1.1/RGCCA/R/rgcca.R | 78 ++-- RGCCA-2.1.1/RGCCA/R/rgccak.R | 542 ++++++++++++++++---------------- RGCCA-2.1.1/RGCCA/R/sgcca.R | 88 +++-- RGCCA-2.1.1/RGCCA/R/sgccak.R | 228 +++++++------ RGCCA-2.1.1/RGCCA/build |only RGCCA-2.1.1/RGCCA/data/Russett.rda |binary RGCCA-2.1.1/RGCCA/inst |only RGCCA-2.1.1/RGCCA/man/BinarySearch.Rd | 31 - RGCCA-2.1.1/RGCCA/man/Russett.Rd | 79 ++-- RGCCA-2.1.1/RGCCA/man/cov2.Rd | 47 +- RGCCA-2.1.1/RGCCA/man/defl.select.Rd | 57 +-- RGCCA-2.1.1/RGCCA/man/miscrossprod.Rd | 41 +- RGCCA-2.1.1/RGCCA/man/rgcca.Rd | 54 +-- RGCCA-2.1.1/RGCCA/man/rgccak.Rd | 125 +++---- RGCCA-2.1.1/RGCCA/man/scale2.Rd | 47 +- RGCCA-2.1.1/RGCCA/man/sgcca.Rd | 291 ++++++++--------- RGCCA-2.1.1/RGCCA/man/sgccak.Rd | 103 +++--- RGCCA-2.1.1/RGCCA/man/soft.Rd | 35 +- RGCCA-2.1.1/RGCCA/man/soft.threshold.Rd | 49 +- RGCCA-2.1.1/RGCCA/man/tau.estimate.Rd | 1 RGCCA-2.1.1/RGCCA/vignettes |only RGCCA-2.1/RGCCA/R/derivation.R |only RGCCA-2.1/RGCCA/R/select.type.R |only RGCCA-2.1/RGCCA/man/derivation.Rd |only 29 files changed, 1098 insertions(+), 1026 deletions(-)
Title: High-Performance Stemmer, Tokenizer, and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for
languages with rich morphology and complex word compounding or character
encoding. The package can check and analyze individual words as well as
search for incorrect words within a text, latex, html or xml document. Use
the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between hunspell versions 2.3 dated 2016-12-07 and 2.4 dated 2017-04-30
DESCRIPTION | 13 - MD5 | 99 +++++----- NEWS | 5 README.md | 2 build/vignette.rds |binary inst/doc/intro.R | 2 inst/doc/intro.Rmd | 2 inst/doc/intro.html | 106 +++++------ man/hunspell.Rd | 1 src/hunspell/affentry.cc | 9 src/hunspell/affentry.hxx | 9 src/hunspell/affixmgr.cc | 35 +-- src/hunspell/affixmgr.hxx | 9 src/hunspell/atypes.hxx | 9 src/hunspell/baseaffix.hxx | 9 src/hunspell/csutil.cc | 66 +++--- src/hunspell/csutil.hxx | 9 src/hunspell/filemgr.cc | 9 src/hunspell/filemgr.hxx | 9 src/hunspell/hashmgr.cc | 25 +- src/hunspell/hashmgr.hxx | 10 - src/hunspell/htypes.hxx | 9 src/hunspell/hunspell.cc | 28 +- src/hunspell/hunspell.hxx | 16 - src/hunspell/hunzip.cc | 9 src/hunspell/hunzip.hxx | 9 src/hunspell/langnum.hxx | 9 src/hunspell/phonet.cc | 3 src/hunspell/replist.cc | 39 +--- src/hunspell/replist.hxx | 9 src/hunspell/suggestmgr.cc | 416 ++++++++++++++++++++++++++++---------------- src/hunspell/suggestmgr.hxx | 13 - src/hunspell/utf_info.cxx | 9 src/hunspell/w_char.hxx | 9 src/parsers/firstparser.cc | 9 src/parsers/firstparser.hxx | 17 - src/parsers/htmlparser.cc | 9 src/parsers/htmlparser.hxx | 17 - src/parsers/latexparser.cc | 9 src/parsers/latexparser.hxx | 17 - src/parsers/manparser.cc | 9 src/parsers/manparser.hxx | 17 - src/parsers/odfparser.cc | 9 src/parsers/odfparser.hxx | 15 - src/parsers/testparser.cc | 17 - src/parsers/textparser.cc | 16 - src/parsers/textparser.hxx | 19 -- src/parsers/xmlparser.cc | 9 src/parsers/xmlparser.hxx | 17 - src/register.c |only vignettes/intro.Rmd | 2 51 files changed, 598 insertions(+), 626 deletions(-)
Title: Codon Usage Bias Fits
Description: Estimating mutation and selection coefficients on synonymous
codon bias usage based on models of ribosome overhead cost (ROC).
Multinomial logistic regression and Markov Chain Monte Carlo are used to
estimate and predict protein production rates with/without the presence
of expressions and measurement errors. Work flows with examples for
simulation, estimation and prediction processes are also provided
with parallelization speedup. The whole framework is tested with
yeast genome and gene expression data of Yassour, et al. (2009)
<doi:10.1073/pnas.0812841106>.
Author: Wei-Chen Chen [aut, cre],
Russell Zaretzki [aut],
William Howell [aut],
Cedric Landerer [aut],
Drew Schmidt [aut],
Michael A. Gilchrist [aut],
Preston Hewgley [ctb],
Students REU13 [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between cubfits versions 0.1-2 dated 2016-01-24 and 0.1-3 dated 2017-04-30
DESCRIPTION | 13 +++++++------ MD5 | 10 ++++++---- inst/doc/cubfits-guide.Rnw | 14 ++++++-------- inst/doc/cubfits-guide.pdf |binary src/zzz.c |only src/zzz.h |only vignettes/cubfits-guide.Rnw | 14 ++++++-------- 7 files changed, 25 insertions(+), 26 deletions(-)
Title: Client for the Amazon Alexa Web Information Services API
Description: Use the Amazon Alexa Web Information Services API to
find information about domains, including the kind of content
that they carry, how popular are they---rank and traffic history,
sites linking to them, among other things. See <https://aws.amazon.com/awis/>
for more information.
Author: Gaurav Sood [aut, cre],
Thomas Leeper [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between aws.alexa versions 0.1.2 dated 2016-06-02 and 0.1.4 dated 2017-04-30
DESCRIPTION | 8 ++-- MD5 | 62 +++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 10 +++++ R/aws.alexa.package.R | 67 +++++++++++++++++----------------- R/browse_categories.R | 64 +++++++++++++++++--------------- R/category_listing.R | 60 +++++++++++++++++------------- R/in_links.R | 28 +++++++------- R/set_secret_key.R | 41 ++++++++++---------- R/traffic_history.R | 35 +++++++++++------ R/url_info.R | 16 +++----- README.md | 7 ++- build/vignette.rds |binary inst/doc/overview.R | 5 ++ inst/doc/overview.Rmd | 5 ++ inst/doc/overview.html | 38 +++++++++++-------- man/alexa_GET.Rd | 1 man/alexa_PROCESS.Rd | 1 man/alexa_check.Rd | 1 man/aws.alexa-package.Rd | 3 - man/browse_categories.Rd | 1 man/category_listing.Rd | 14 ++++--- man/in_links.Rd | 3 - man/set_secret_key.Rd | 1 man/traffic_history.Rd | 5 +- man/url_info.Rd | 5 +- tests/testthat/aws.alexa_key | 2 - tests/testthat/aws.alexa_key.enc | 2 - tests/testthat/test-in-links.R | 4 +- tests/testthat/test-traffic-history.R | 12 +++++- tests/testthat/test-url-info.R | 6 +-- vignettes/overview.Rmd | 5 ++ 32 files changed, 284 insertions(+), 229 deletions(-)
Title: A Collection of Tools for Working with Time Series in R
Description: Coerce between time-based tibbles ('tbl') and 'xts', 'zoo', and 'ts'.
Get the time series index, signature, and summary from time series objects and
time-based tibbles. Create future time series based on properties of
existing time series index.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between timekit versions 0.1.0 dated 2017-04-19 and 0.2.0 dated 2017-04-30
timekit-0.1.0/timekit/man/get_date_variables.Rd |only timekit-0.2.0/timekit/DESCRIPTION | 31 - timekit-0.2.0/timekit/MD5 | 45 +- timekit-0.2.0/timekit/NAMESPACE | 27 + timekit-0.2.0/timekit/NEWS.md | 13 timekit-0.2.0/timekit/R/global_vars.R | 3 timekit-0.2.0/timekit/R/tk_augment_timeseries.R |only timekit-0.2.0/timekit/R/tk_get_timeseries.R |only timekit-0.2.0/timekit/R/tk_index.R | 18 timekit-0.2.0/timekit/R/tk_make_timeseries.R |only timekit-0.2.0/timekit/R/tk_tbl.R | 54 +- timekit-0.2.0/timekit/R/tk_xts.R | 2 timekit-0.2.0/timekit/R/utils-dates.R | 68 ++- timekit-0.2.0/timekit/README.md | 210 ++++++---- timekit-0.2.0/timekit/build/vignette.rds |binary timekit-0.2.0/timekit/inst/doc/TK00_Time_Series_Coercion.html | 82 +-- timekit-0.2.0/timekit/inst/doc/TK01_Working_With_Time_Series_Index.R |only timekit-0.2.0/timekit/inst/doc/TK01_Working_With_Time_Series_Index.Rmd |only timekit-0.2.0/timekit/inst/doc/TK01_Working_With_Time_Series_Index.html |only timekit-0.2.0/timekit/man/tk_augment_timeseries.Rd |only timekit-0.2.0/timekit/man/tk_get_timeseries.Rd |only timekit-0.2.0/timekit/man/tk_get_timeseries_unit_frequency.Rd |only timekit-0.2.0/timekit/man/tk_get_timeseries_variables.Rd |only timekit-0.2.0/timekit/man/tk_make_future_timeseries.Rd |only timekit-0.2.0/timekit/man/tk_tbl.Rd | 6 timekit-0.2.0/timekit/tests/testthat/test_tk_augment_timeseries.R |only timekit-0.2.0/timekit/tests/testthat/test_tk_get_timeseries.R |only timekit-0.2.0/timekit/tests/testthat/test_tk_make_future_timeseries.R |only timekit-0.2.0/timekit/tests/testthat/test_tk_tbl.R | 36 - timekit-0.2.0/timekit/tests/testthat/test_tk_ts.R | 2 timekit-0.2.0/timekit/tools |only timekit-0.2.0/timekit/vignettes/TK01_Working_With_Time_Series_Index.Rmd |only 32 files changed, 374 insertions(+), 223 deletions(-)
Title: Convert Spatial Data Using Tidy Tables
Description: Tools to convert from specific formats to more general forms of
spatial data. Using tables to store the actual entities present in spatial
data provides flexibility, and the functions here deliberately
minimize the level of interpretation applied, leaving that for specific
applications. Includes support for simple features, round-trip for 'Spatial' classes and long-form
tables, analogous to 'ggplot2::fortify'. There is also a more 'normal form' representation
that decomposes simple features and their kin to tables of objects, parts, and unique coordinates.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between spbabel versions 0.4.5 dated 2016-10-06 and 0.4.6 dated 2017-04-30
spbabel-0.4.5/spbabel/R/ggplot2.r |only spbabel-0.4.5/spbabel/R/gobbleGeom.r |only spbabel-0.4.5/spbabel/R/mtable.r |only spbabel-0.4.5/spbabel/R/raster_geom.r |only spbabel-0.4.6/spbabel/DESCRIPTION | 21 spbabel-0.4.6/spbabel/MD5 | 95 - spbabel-0.4.6/spbabel/NAMESPACE | 97 - spbabel-0.4.6/spbabel/NEWS.md | 185 +- spbabel-0.4.6/spbabel/R/map_table.r |only spbabel-0.4.6/spbabel/R/release-questions.r | 4 spbabel-0.4.6/spbabel/R/sf.r |only spbabel-0.4.6/spbabel/R/sfFromTable.r |only spbabel-0.4.6/spbabel/R/sp.r |only spbabel-0.4.6/spbabel/R/spFromTable.r | 264 +-- spbabel-0.4.6/spbabel/R/spbabel-package.r | 112 - spbabel-0.4.6/spbabel/R/sptable.r | 224 -- spbabel-0.4.6/spbabel/R/trip.r | 47 spbabel-0.4.6/spbabel/R/unique_ids.r | 52 spbabel-0.4.6/spbabel/R/utils.r | 221 +- spbabel-0.4.6/spbabel/README.md | 243 +-- spbabel-0.4.6/spbabel/build/vignette.rds |binary spbabel-0.4.6/spbabel/inst/devignette/geometry-tables.Rmd | 774 +++++----- spbabel-0.4.6/spbabel/inst/devignette/geometry-tables_demand-read.Rmd | 180 +- spbabel-0.4.6/spbabel/inst/doc/sfbabel.R |only spbabel-0.4.6/spbabel/inst/doc/sfbabel.Rmd |only spbabel-0.4.6/spbabel/inst/doc/sfbabel.html |only spbabel-0.4.6/spbabel/inst/doc/spbabel.R | 151 - spbabel-0.4.6/spbabel/inst/doc/spbabel.Rmd | 323 ++-- spbabel-0.4.6/spbabel/inst/doc/spbabel.html | 495 +++--- spbabel-0.4.6/spbabel/inst/examples/faketrip.r | 84 - spbabel-0.4.6/spbabel/inst/extdata |only spbabel-0.4.6/spbabel/inst/sf_convert.r | 161 +- spbabel-0.4.6/spbabel/inst/sf_convert2.r |only spbabel-0.4.6/spbabel/man/as_tibble.sfg.Rd |only spbabel-0.4.6/spbabel/man/feature_table.Rd |only spbabel-0.4.6/spbabel/man/holey.Rd | 19 spbabel-0.4.6/spbabel/man/map_table.Rd | 85 - spbabel-0.4.6/spbabel/man/mpoint1.Rd | 19 spbabel-0.4.6/spbabel/man/semap.Rd | 35 spbabel-0.4.6/spbabel/man/sf.Rd |only spbabel-0.4.6/spbabel/man/sp-methods.Rd | 57 spbabel-0.4.6/spbabel/man/sp.Rd | 67 spbabel-0.4.6/spbabel/man/spbabel-package.Rd | 33 spbabel-0.4.6/spbabel/man/sptable.Rd | 181 +- spbabel-0.4.6/spbabel/man/track.Rd | 19 spbabel-0.4.6/spbabel/tests/testthat.R | 8 spbabel-0.4.6/spbabel/tests/testthat/test-column-types.R | 46 spbabel-0.4.6/spbabel/tests/testthat/test-map_table.R | 165 +- spbabel-0.4.6/spbabel/tests/testthat/test-misc.R | 19 spbabel-0.4.6/spbabel/tests/testthat/test-replacement.R | 42 spbabel-0.4.6/spbabel/tests/testthat/test-sf.R |only spbabel-0.4.6/spbabel/tests/testthat/test-sfFromTable.R |only spbabel-0.4.6/spbabel/tests/testthat/test-spFromTable.R | 176 +- spbabel-0.4.6/spbabel/tests/testthat/test-sptable.R | 108 - spbabel-0.4.6/spbabel/tests/testthat/test-trip.R | 109 - spbabel-0.4.6/spbabel/tests/testthat/test-utils.R | 38 spbabel-0.4.6/spbabel/vignettes/sfbabel.Rmd |only spbabel-0.4.6/spbabel/vignettes/spbabel.Rmd | 323 ++-- 58 files changed, 2600 insertions(+), 2682 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a
Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.2.4 dated 2017-03-12 and 1.2.5 dated 2017-04-30
DESCRIPTION | 8 MD5 | 18 NEWS | 7 R/rmcfs.R | 1689 +++++++++++++++++++++++++-------------------------- R/rmcfs.plot.R | 12 R/utils.R | 8 man/export.result.Rd | 2 man/fix.data.Rd | 2 man/import.result.Rd | 2 man/mcfs.Rd | 4 10 files changed, 880 insertions(+), 872 deletions(-)
Title: Analyze Two Choice Reaction Time Data with the D*M Method
Description: A collection of functions to estimate parameters of a diffusion model via a D*M analysis. Build in models are: the Ratcliff diffusion model, the RWiener diffusion model, and Linear Ballistic Accumulator models. Custom models functions can be specified as long as they have a density function.
Author: Don van den Bergh, Stijn Verdonck, Francis Tuerlinckx
Maintainer: Don van den Bergh <donvdbergh@hotmail.com>
Diff between DstarM versions 0.2.1 dated 2017-02-04 and 0.2.2 dated 2017-04-30
DstarM-0.2.1/DstarM/README.md |only DstarM-0.2.2/DstarM/DESCRIPTION | 8 DstarM-0.2.2/DstarM/MD5 | 45 - DstarM-0.2.2/DstarM/R/estDstarM.R | 1032 +++++++++++++++--------------- DstarM-0.2.2/DstarM/R/estND.R | 460 ++++++------- DstarM-0.2.2/DstarM/man/Voss.density.Rd | 3 DstarM-0.2.2/DstarM/man/byParticipant.Rd | 1 DstarM-0.2.2/DstarM/man/calcIC.Rd | 1 DstarM-0.2.2/DstarM/man/chisq.Rd | 3 DstarM-0.2.2/DstarM/man/chisqFit.Rd | 1 DstarM-0.2.2/DstarM/man/estCdf.Rd | 1 DstarM-0.2.2/DstarM/man/estDstarM.Rd | 1 DstarM-0.2.2/DstarM/man/estND.Rd | 1 DstarM-0.2.2/DstarM/man/estObserved.Rd | 1 DstarM-0.2.2/DstarM/man/estQdf.Rd | 1 DstarM-0.2.2/DstarM/man/getPdfs.Rd | 1 DstarM-0.2.2/DstarM/man/getSter.Rd | 1 DstarM-0.2.2/DstarM/man/getTer.Rd | 1 DstarM-0.2.2/DstarM/man/obsQuantiles.Rd | 1 DstarM-0.2.2/DstarM/man/plotObserved.Rd | 1 DstarM-0.2.2/DstarM/man/rtDescriptives.Rd | 1 DstarM-0.2.2/DstarM/man/rtHist.Rd | 1 DstarM-0.2.2/DstarM/man/simData.Rd | 1 DstarM-0.2.2/DstarM/man/testFun.Rd | 1 24 files changed, 774 insertions(+), 794 deletions(-)
Title: Learning Principal Graphs with DDRTree
Description: Provides an implementation of the framework of reversed graph embedding (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of the single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as bifurcation structure of any datatype.
Author: Xiaojie Qiu, Cole Trapnell, Qi Mao, Li Wang
Maintainer: Xiaojie Qiu <xqiu@uw.edu>
Diff between DDRTree versions 0.1.4 dated 2016-07-25 and 0.1.5 dated 2017-04-30
DESCRIPTION | 13 +++++++------ MD5 | 22 ++++++++++++---------- NAMESPACE | 3 ++- NEWS |only R/DDRTree.R | 32 ++++++++++++++++++++++++++------ R/RcppExports.R | 2 +- man/DDRTree.Rd | 15 ++++++++++++--- man/get_major_eigenvalue.Rd | 1 - man/pca_projection_R.Rd | 1 - man/sqdist_R.Rd | 1 - src/DDRTree.cpp | 18 ++++++++++++------ src/DDRTree_init.c |only src/RcppExports.cpp | 27 +++++++++++++-------------- 13 files changed, 85 insertions(+), 50 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.2.1 dated 2017-04-01 and 0.2.2 dated 2017-04-30
ChangeLog | 10 ++++++++++ DESCRIPTION | 6 +++--- MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 1 + R/configr.R | 4 ++-- R/merge.R | 30 +++++++++++++++--------------- R/parse.R | 4 ++-- R/read.R | 31 +++++++++++++++++++++++++++++-- R/utils.R | 1 + README.md | 16 ++++++++-------- inst/extdata/config.json | 3 ++- inst/extdata/config.other.yaml | 2 ++ man/configr.Rd | 4 ++-- man/eval.config.Rd | 2 +- man/eval.config.groups.Rd | 4 ++-- man/eval.config.merge.Rd | 16 ++++++++-------- man/eval.config.sections.Rd |only tests/testthat/test_b_read.R | 9 +++++++++ tests/testthat/test_f_toml.R | 4 ++-- 19 files changed, 117 insertions(+), 65 deletions(-)
Title: Brazilian Economic Time Series
Description: It provides access to and information about the most important
Brazilian economic time series - from the Getulio Vargas Foundation, the Central
Bank of Brazil and the Brazilian Institute of Geography and Statistics. It also
presents tools for managing, analysing (e.g. generating dynamic reports with a
complete analysis of a series) and exporting these time series.
Author: Pedro Costa Ferreira [aut, cre],
Talitha Speranza [aut],
Jonatha Azevedo [aut]
Maintainer: Pedro Costa Ferreira <pedro.guilherme@fgv.br>
Diff between BETS versions 0.2.0 dated 2017-04-12 and 0.2.1 dated 2017-04-30
DESCRIPTION | 19 ++++------ MD5 | 82 ++++++++++++++++++++++----------------------- R/BETS.R | 9 +++- R/BETS.get.R | 2 - man/BETS.Rd | 8 +++- man/BETS.addin_en.Rd | 1 man/BETS.addin_pt.Rd | 1 man/BETS.chart.Rd | 1 man/BETS.corrgram.Rd | 1 man/BETS.dashboard.Rd | 1 man/BETS.deflate.Rd | 1 man/BETS.dummy.Rd | 1 man/BETS.get.Rd | 1 man/BETS.grnn.test.Rd | 1 man/BETS.grnn.train.Rd | 1 man/BETS.normalize.Rd | 1 man/BETS.predict.Rd | 1 man/BETS.report.Rd | 1 man/BETS.save.Rd | 1 man/BETS.save.sas.Rd | 1 man/BETS.save.spss.Rd | 1 man/BETS.save.stata.Rd | 1 man/BETS.search.Rd | 1 man/BETS.std_resid.Rd | 1 man/BETS.t_test.Rd | 1 man/BETS.ur_test.Rd | 1 man/check.series.Rd | 1 man/draw.animal_spirits.Rd | 1 man/draw.cap_utl.Rd | 1 man/draw.conf_lvl.Rd | 1 man/draw.ei_comps.Rd | 1 man/draw.ei_vars.Rd | 1 man/draw.gdp_comps.Rd | 1 man/draw.gdp_unemp.Rd | 1 man/draw.gdp_vars.Rd | 1 man/draw.iie_br.Rd | 1 man/draw.lab_mrkt.Rd | 1 man/draw.misery_index.Rd | 1 man/draw.survey.Rd | 1 man/get.data.frame.Rd | 1 man/get.series.bacen.Rd | 1 man/msg.Rd | 1 42 files changed, 101 insertions(+), 56 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch <robert.e.mcculloch@gmail.com> and Rodney Sparapani <rsparapa@mcw.edu>
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 1.1 dated 2017-04-13 and 1.2 dated 2017-04-30
DESCRIPTION | 8 +++--- MD5 | 37 +++++++++++++++------------- R/crisk.pre.bart.R | 4 +-- R/recur.pre.bart.R | 2 - R/surv.pre.bart.R | 2 - data/ACTG175.rda |only data/bladder.rda |binary data/datalist | 1 data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary man/ACTG175.Rd |only man/pbart.Rd | 13 +++------ src/BROWSE |only src/TAGS |only src/common.h | 67 +++++---------------------------------------------- src/cpbart.cpp | 63 +++++++++++++++++++++++++++++------------------ src/cwbart.cpp | 46 ++++++++++++++++++++++++++++------- src/rn.h |only 22 files changed, 119 insertions(+), 124 deletions(-)
Title: Read Text Documents into R
Description: A small collection of convenience tools for reading text documents
into R.
Author: Tyler Rinker [aut, cre],
Bryan Goodrich [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between textreadr versions 0.3.1 dated 2017-02-19 and 0.5.1 dated 2017-04-30
textreadr-0.3.1/textreadr/R/antiword_loc.R |only textreadr-0.3.1/textreadr/R/check_antiword_installed.R |only textreadr-0.3.1/textreadr/man/check_antiword_installed.Rd |only textreadr-0.5.1/textreadr/DESCRIPTION | 20 - textreadr-0.5.1/textreadr/MD5 | 44 +-- textreadr-0.5.1/textreadr/NAMESPACE | 4 textreadr-0.5.1/textreadr/NEWS | 36 ++ textreadr-0.5.1/textreadr/R/read_doc.R | 35 +- textreadr-0.5.1/textreadr/R/read_document.R | 43 ++- textreadr-0.5.1/textreadr/R/read_docx.R | 42 ++- textreadr-0.5.1/textreadr/R/read_html.R |only textreadr-0.5.1/textreadr/R/read_pdf.R | 28 +- textreadr-0.5.1/textreadr/R/read_transcript.R | 46 ++- textreadr-0.5.1/textreadr/R/utils.R | 14 - textreadr-0.5.1/textreadr/README.md | 149 +++++++---- textreadr-0.5.1/textreadr/data/presidential_debates_2012.rda |binary textreadr-0.5.1/textreadr/inst/CITATION | 4 textreadr-0.5.1/textreadr/inst/docs/pres.deb1.docx |only textreadr-0.5.1/textreadr/inst/docs/textreadr_creed.html |only textreadr-0.5.1/textreadr/inst/docs/textreadr_creed.txt | 8 textreadr-0.5.1/textreadr/man/read_doc.Rd | 18 + textreadr-0.5.1/textreadr/man/read_document.Rd | 30 +- textreadr-0.5.1/textreadr/man/read_docx.Rd | 16 - textreadr-0.5.1/textreadr/man/read_html.Rd |only textreadr-0.5.1/textreadr/man/read_pdf.Rd | 17 + textreadr-0.5.1/textreadr/man/read_transcript.Rd | 3 textreadr-0.5.1/textreadr/tools |only 27 files changed, 371 insertions(+), 186 deletions(-)
Title: Annotation of Metabolites from Liquid Chromatography-Mass
Spectrometry Data
Description: Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS) data from .mzXML files, providing an inclusion list of metabolites/fragments (Only the ion mass). The function returns the identification and quantification of the peaks presented in the sample, as well as the non-identified metabolites/fragments.
Author: Manuel David Peris Diaz
Maintainer: Manuel David Peris Diaz <madape@alumni.uv.es>
Diff between MetaboList versions 1.1 dated 2017-04-09 and 1.2 dated 2017-04-30
DESCRIPTION | 6 +- MD5 | 6 +- R/annotation.R | 148 +++++++++++++++++++++++++++--------------------------- man/annotation.rd | 4 - 4 files changed, 84 insertions(+), 80 deletions(-)
Title: Stock Assessment Graphs Database Web Services
Description: R interface to access the web services of the ICES Stock Assessment
Graphs database <http://sg.ices.dk>.
Author: Colin Millar [aut, cre],
Scott Large [aut],
Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesSAG versions 1.2-1 dated 2017-03-24 and 1.3-0 dated 2017-04-30
icesSAG-1.2-1/icesSAG/R/findKey.R |only icesSAG-1.2-1/icesSAG/man/findKey.Rd |only icesSAG-1.3-0/icesSAG/DESCRIPTION | 10 icesSAG-1.3-0/icesSAG/MD5 | 60 +- icesSAG-1.3-0/icesSAG/NAMESPACE | 18 icesSAG-1.3-0/icesSAG/NEWS | 10 icesSAG-1.3-0/icesSAG/R/SAGtokens.R |only icesSAG-1.3-0/icesSAG/R/SAGxml.R |only icesSAG-1.3-0/icesSAG/R/WSDL_parser.R |only icesSAG-1.3-0/icesSAG/R/checkKeyArg.R |only icesSAG-1.3-0/icesSAG/R/findAssessmentKey.R |only icesSAG-1.3-0/icesSAG/R/getFishStockReferencePoints.R | 32 - icesSAG-1.3-0/icesSAG/R/getGraph.R | 43 -- icesSAG-1.3-0/icesSAG/R/getListStocks.R | 15 icesSAG-1.3-0/icesSAG/R/getSAG.R | 38 - icesSAG-1.3-0/icesSAG/R/getSAGGraphs.R | 41 - icesSAG-1.3-0/icesSAG/R/getSAGTypeGraphsSettings.R |only icesSAG-1.3-0/icesSAG/R/getStockDownloadData.R |only icesSAG-1.3-0/icesSAG/R/getStockStatusValues.R |only icesSAG-1.3-0/icesSAG/R/getSummaryTable.R | 28 - icesSAG-1.3-0/icesSAG/R/getYSBRSummaryTable.R |only icesSAG-1.3-0/icesSAG/R/getsetSettingsForAStock.R |only icesSAG-1.3-0/icesSAG/R/icesSAG-package.R | 2 icesSAG-1.3-0/icesSAG/R/onLoad.R |only icesSAG-1.3-0/icesSAG/R/uploadStock.R |only icesSAG-1.3-0/icesSAG/R/uploadXMLFile.R |only icesSAG-1.3-0/icesSAG/R/utilities.R | 318 +++++++-------- icesSAG-1.3-0/icesSAG/man/findAssessmentKeydocs.Rd |only icesSAG-1.3-0/icesSAG/man/getFishStockReferencePoints.Rd | 13 icesSAG-1.3-0/icesSAG/man/getGraphs.Rd | 37 - icesSAG-1.3-0/icesSAG/man/getSAG.Rd | 9 icesSAG-1.3-0/icesSAG/man/getSAGGraphs.Rd | 10 icesSAG-1.3-0/icesSAG/man/getSAGSettings.Rd |only icesSAG-1.3-0/icesSAG/man/getStockStatusValues.Rd |only icesSAG-1.3-0/icesSAG/man/getSummaryTable.Rd | 13 icesSAG-1.3-0/icesSAG/man/getYSBRSummaryTable.Rd |only icesSAG-1.3-0/icesSAG/man/getsetStockSettings.Rd |only icesSAG-1.3-0/icesSAG/man/icesSAG-package.Rd | 2 icesSAG-1.3-0/icesSAG/man/readCreateSAGxml.Rd |only icesSAG-1.3-0/icesSAG/man/stockFishdata.Rd |only icesSAG-1.3-0/icesSAG/man/stockInfo.Rd |only icesSAG-1.3-0/icesSAG/man/uploadStock.Rd |only icesSAG-1.3-0/icesSAG/tests/testthat/test-test.R | 51 ++ 43 files changed, 399 insertions(+), 351 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <arXiv:1103.3817> and
Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework
allows for elastic analysis of functional data through phase and
amplitude separation.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.8.0 dated 2017-04-17 and 1.8.1 dated 2017-04-30
DESCRIPTION | 14 ++--- MD5 | 24 ++++----- NEWS | 7 ++ R/AmplitudeBoxplot.R | 116 ++++++++++++++++++++++++++++++++++++------------ R/PhaseBoxplot.R | 116 +++++++++++++++++++++++++++++++++++++----------- R/time_warping.R | 6 +- R/utility_functions.R | 8 --- R/vertFPCA.R | 3 - README.md | 2 man/AmplitudeBoxplot.Rd | 18 ++++--- man/PhaseBoxplot.Rd | 15 +++--- man/time_warping.Rd | 8 +-- man/vertFPCA.Rd | 4 - 13 files changed, 233 insertions(+), 108 deletions(-)
Title: Partition-Assisted Clustering and Multiple Alignments of
Networks
Description: Implements Partition-Assisted Clustering and Multiple Alignments of Networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set.
Author: Ye Henry Li, Dangna Li
Maintainer: Ye Henry Li <ywli@stanford.edu>
Diff between PAC versions 1.0.7 dated 2017-03-12 and 1.0.8 dated 2017-04-30
PAC-1.0.7/PAC/cleanup.win |only PAC-1.0.7/PAC/configure.win |only PAC-1.0.7/PAC/vignettes/bioexample.Rmd |only PAC-1.0.7/PAC/vignettes/bioexample.html |only PAC-1.0.7/PAC/vignettes/bioexample.md |only PAC-1.0.8/PAC/DESCRIPTION | 9 - PAC-1.0.8/PAC/MD5 | 41 ++--- PAC-1.0.8/PAC/R/PAC.R | 5 PAC-1.0.8/PAC/R/fmeasure.R | 2 PAC-1.0.8/PAC/R/getRepresentativeNetworks.R | 10 + PAC-1.0.8/PAC/R/refineSubpopulationLabels.R | 12 + PAC-1.0.8/PAC/R/samplePass.R | 33 ++++ PAC-1.0.8/PAC/inst/doc/intro.R | 56 ++++--- PAC-1.0.8/PAC/inst/doc/intro.Rmd | 96 ++++++++----- PAC-1.0.8/PAC/inst/doc/intro.html | 166 +++++++++++++++-------- PAC-1.0.8/PAC/inst/doc/intro.md | 176 +++++++++++++++++-------- PAC-1.0.8/PAC/man/BSPLeaveCenter.Rd | 2 PAC-1.0.8/PAC/man/PAC.Rd | 6 PAC-1.0.8/PAC/man/fmeasure.Rd | 2 PAC-1.0.8/PAC/man/getRepresentativeNetworks.Rd | 7 PAC-1.0.8/PAC/man/refineSubpopulationLabels.Rd | 5 PAC-1.0.8/PAC/man/samplePass.Rd | 9 - PAC-1.0.8/PAC/vignettes/intro.Rmd | 96 ++++++++----- PAC-1.0.8/PAC/vignettes/intro.md | 176 +++++++++++++++++-------- 24 files changed, 609 insertions(+), 300 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 2.0-5 dated 2016-03-17 and 2.0-8 dated 2017-04-30
ChangeLog | 27 DESCRIPTION | 10 MD5 | 37 NAMESPACE | 2 R/auc.R | 40 - R/cv.glmnet.R | 49 - R/elnet.R | 1 R/glmnet.R | 14 R/lambda.interp.R | 4 R/lognet.R | 8 R/response.coxnet.R | 6 build/vignette.rds |binary inst/doc/Coxnet.pdf |binary inst/doc/glmnet_beta.R | 10 inst/doc/glmnet_beta.Rmd | 185 +++- inst/doc/glmnet_beta.html | 1713 +++++++++++++++------------------------------- man/cv.glmnet.Rd | 8 src/glmnet5.f90 | 574 +++++++-------- src/glmnet_init.c |only vignettes/glmnet_beta.Rmd | 185 +++- 20 files changed, 1200 insertions(+), 1673 deletions(-)
Title: Financial Market Building Blocks
Description: Implements basic financial market objects like currencies, currency
pairs, interest rates and interest rate indices. You will be able to use
Benchmark instances of these objects which have been defined using their most
common conventions or those defined by International Swap Dealer Association
(ISDA, <http://www2.isda.org>) legal documentation.
Author: Imanuel Costigan <i.costigan@me.com>
Maintainer: Imanuel Costigan <i.costigan@me.com>
Diff between fmbasics versions 0.1.0 dated 2017-02-12 and 0.2.0 dated 2017-04-30
DESCRIPTION | 9 ++++---- MD5 | 41 +++++++++++++++++++++++++------------- NAMESPACE | 20 ++++++++++++++++++ NEWS | 13 ++++++++++++ R/indices-class.R | 2 - R/utils.R |only R/zero-curve.R |only README.md | 26 ++++++++++++++++++++++-- build/vignette.rds |binary inst/README-unnamed-chunk-7-1.png |only inst/doc/basics.Rmd | 2 - inst/doc/basics.html | 10 ++++----- inst/doc/rates.R | 12 +++++++++++ inst/doc/rates.Rmd | 22 ++++++++++++++++++++ inst/doc/rates.html | 29 ++++++++++++++++++++++---- inst/extdata |only man/Interpolation.Rd |only man/ZeroCurve.Rd |only man/as_tibble.ZeroCurve.Rd |only man/build_zero_curve.Rd |only man/fmdata_example.Rd |only man/iborindices.Rd | 2 - man/interpolate.Rd |only man/interpolate.ZeroCurve.Rd |only man/is.Interpolation.Rd |only tests/testthat/test-interpolate.R |only vignettes/basics.Rmd | 2 - vignettes/rates.Rmd | 22 ++++++++++++++++++++ 28 files changed, 178 insertions(+), 34 deletions(-)
Title: Cluster Evaluation
Description: CLUster Evaluation (CLUE) is a computational method for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms and subsequently identify key kinases or pathways from each cluster. Its implementation in R is called ClueR. See Readme on <https://github.com/PengyiYang/ClueR> for more details.
Author: Pengyi Yang
Maintainer: Pengyi Yang <pengyi.yang@sydney.edu.au>
Diff between ClueR versions 1.1 dated 2015-10-27 and 1.2 dated 2017-04-30
DESCRIPTION | 20 ++++---- MD5 | 38 +++++++++------- NAMESPACE | 5 -- R/clustEnrichment.R | 34 +++++++-------- R/clustOptimal.R | 59 +++++++++++--------------- R/fuzzPlot.R | 16 +++---- R/runClue.R | 106 +++++++++++++++++++++++++++++++++-------------- R/temporalSimu.R | 6 +- README.md | 70 +++++++++++++++++++++---------- data/Pathways.rda |binary data/PhosphoELM.rda |only data/datalist |only man/ClueR-package.Rd | 22 ++++++--- man/Pathways.DAVID.Rd |only man/Pathways.biocarta.Rd |only man/PhosphoELM.human.Rd |only man/PhosphoELM.mouse.Rd |only man/clustEnrichment.Rd | 42 +++++++++--------- man/clustOptimal.Rd | 65 ++++++++++++---------------- man/enrichmentTest.Rd | 5 -- man/fuzzPlot.Rd | 20 ++++---- man/runClue.Rd | 97 +++++++++++++++++++++++++++++++------------ man/temporalSimu.Rd | 10 ++-- 23 files changed, 367 insertions(+), 248 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Abdolreza Mohammadi
Maintainer: Abdolreza Mohammadi <a.mohammadi@uvt.nl>
Diff between bmixture versions 0.3 dated 2017-02-08 and 0.4 dated 2017-04-30
DESCRIPTION | 10 +++++----- MD5 | 44 +++++++++++++++++++++++--------------------- NAMESPACE | 11 ++++++++--- R/bmixgamma.R | 2 +- R/bmixnorm.R | 6 +++--- R/bmixt.R | 8 ++++---- inst |only man/bmixgamma.Rd | 8 +++++--- man/bmixt.Rd | 8 +++++--- man/bmixture-package.Rd | 10 +++++++++- man/mixgamma.Rd | 2 ++ man/mixnorm.Rd | 2 ++ man/mixt.Rd | 2 ++ man/plot.bmixgamma.Rd | 2 ++ man/plot.bmixt.Rd | 2 ++ man/print.bmixgamma.Rd | 2 ++ man/print.bmixt.Rd | 2 ++ man/summary.bmixgamma.Rd | 2 ++ man/summary.bmixt.Rd | 2 ++ src/bmix_gamma.cpp | 19 +++++++++---------- src/bmix_norm.cpp | 32 +++++++++++++------------------- src/bmix_t.cpp | 28 ++++++++++++++-------------- src/funs_in_mcmc.cpp | 4 ++-- src/init.c |only 24 files changed, 119 insertions(+), 89 deletions(-)