Title: The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Description: The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to
estimate the phylogenetic heritability of continuous traits, to test
hypotheses of neutral evolution versus stabilizing selection, to quantify
the strength of stabilizing selection, to estimate measurement error and to
make predictions about the evolution of a phenotype and phenotypic variation
in a population. The package implements combined maximum likelihood and
Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed
Model, fast parallel likelihood calculation, maximum likelihood
inference of the genotypic values at the tips, functions for summarizing and
plotting traces and posterior samples, functions for simulation of a univariate
continuous trait evolution along a phylogenetic tree. A quick example on
using the POUMM package can be found in the README. More elaborate
examples and use-cases are provided in the vignette
"A User Guide to The POUMM R-package".
Author: Venelin Mitov [aut, cre, cph]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between POUMM versions 1.2.2 dated 2017-03-27 and 1.3.0 dated 2017-06-15
POUMM-1.2.2/POUMM/man/MCMC.Rd |only POUMM-1.2.2/POUMM/man/likPOUMMGivenTreeVTipsC.Rd |only POUMM-1.3.0/POUMM/DESCRIPTION | 17 POUMM-1.3.0/POUMM/MD5 | 64 +-- POUMM-1.3.0/POUMM/NAMESPACE | 16 POUMM-1.3.0/POUMM/R/POUMM.R | 304 ++++++++++++-- POUMM-1.3.0/POUMM/R/fitPOUMM.R | 432 +++++++++++---------- POUMM-1.3.0/POUMM/R/likPOUMM.R | 189 +++++++-- POUMM-1.3.0/POUMM/R/specPOUMM.R | 121 +++-- POUMM-1.3.0/POUMM/R/summaryPOUMM.R | 163 +++++-- POUMM-1.3.0/POUMM/R/utilities.R | 1 POUMM-1.3.0/POUMM/README.md | 12 POUMM-1.3.0/POUMM/inst/CITATION | 8 POUMM-1.3.0/POUMM/inst/REFERENCES.bib | 4 POUMM-1.3.0/POUMM/inst/doc/UserGuide.R | 19 POUMM-1.3.0/POUMM/inst/doc/UserGuide.Rmd | 49 +- POUMM-1.3.0/POUMM/inst/doc/UserGuide.html | 163 ++++--- POUMM-1.3.0/POUMM/man/POUMM.Rd | 38 + POUMM-1.3.0/POUMM/man/analyseMCMCs.Rd |only POUMM-1.3.0/POUMM/man/covFunPOUMM.Rd |only POUMM-1.3.0/POUMM/man/covHPDFunPOUMM.Rd |only POUMM-1.3.0/POUMM/man/dVNodesGivenTreePOUMM.Rd | 13 POUMM-1.3.0/POUMM/man/likPOUMMGivenTreeVTips.Rd | 18 POUMM-1.3.0/POUMM/man/likPOUMM_C.Rd |only POUMM-1.3.0/POUMM/man/loglik_abc_g0_g0Prior.Rd | 6 POUMM-1.3.0/POUMM/man/maxLikPOUMMGivenTreeVTips.Rd | 8 POUMM-1.3.0/POUMM/man/plot.POUMM.Rd | 37 + POUMM-1.3.0/POUMM/man/plot.summary.POUMM.Rd | 37 + POUMM-1.3.0/POUMM/man/pruneTree.Rd | 5 POUMM-1.3.0/POUMM/man/rVNodesGivenTreePOUMM.Rd | 6 POUMM-1.3.0/POUMM/man/specifyPOUMM.Rd | 15 POUMM-1.3.0/POUMM/src/Integrator.cpp | 403 ++++++++++++++++++- POUMM-1.3.0/POUMM/src/Makevars |only POUMM-1.3.0/POUMM/tests/testthat/Rplots.pdf |only POUMM-1.3.0/POUMM/tests/testthat/test-POUMM.R | 91 ++-- POUMM-1.3.0/POUMM/vignettes/UserGuide.Rmd | 49 +- POUMM-1.3.0/POUMM/vignettes/UserGuideCache.RData |binary 37 files changed, 1602 insertions(+), 686 deletions(-)
Title: Dynamic Model Averaging
Description: Dynamic model averaging for binary and continuous
outcomes.
Author: Tyler H. McCormick, Adrian Raftery, David Madigan
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between dma versions 1.2-3 dated 2016-01-06 and 1.3-0 dated 2017-06-15
ChangeLog | 5 DESCRIPTION | 9 - MD5 | 12 +- R/makf4.R | 308 ++++++++++++++++++++++++++-------------------------- man/dma-package.Rd | 5 man/dma.Rd | 8 + man/logistic.dma.Rd | 2 7 files changed, 179 insertions(+), 170 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
Ruben Arslan [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
Eli Grey [ctb, cph] (FileSaver library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 1.5 dated 2017-04-26 and 1.6 dated 2017-06-15
DESCRIPTION | 8 +++---- MD5 | 26 +++++++++++----------- R/base64.R | 14 +++--------- R/github_document.R | 8 +++++++ R/html_notebook.R | 5 ++++ R/html_paged.R | 6 ++++- R/params.R | 12 +++++++--- R/pdf_document.R | 3 ++ R/render.R | 31 +++++++++++++++++++++------ R/shiny_prerendered.R | 6 ++--- R/util.R | 33 ++++++++++++++++------------- inst/NEWS | 22 +++++++++++++++++++ inst/rmd/h/navigation-1.1/codefolding.js | 2 - inst/rmd/h/pagedtable-1.1/js/pagedtable.js | 20 ++++++++--------- 14 files changed, 130 insertions(+), 66 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-06 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-26 0.1
Title: Read, Manipulate and Visualise Magnetic Resonance Images
Description: Functions for working with magnetic resonance images. Analyze,
NIfTI-1, NIfTI-2 and MGH format images can be read and written; DICOM files
can only be read.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between tractor.base versions 3.0.7 dated 2016-11-07 and 3.1.0 dated 2017-06-15
DESCRIPTION | 12 ++--- MD5 | 91 ++++++++++++++++++++-------------------- NAMESPACE | 5 ++ R/08_sparse.R | 7 +++ R/10_mri_image.R | 72 ------------------------------- R/12_coerce.R |only R/15_dicom.R | 2 R/deprecated.R | 2 R/dicom_dir.R | 4 - R/files.R | 12 ++++- R/misc.R | 4 - R/nifti.R | 1 R/png.R | 5 -- R/viewer.R | 42 ++++++++++++++++-- R/viz.R | 21 +++++++-- R/zzz.R | 6 +- man/DicomMetadata-class.Rd | 3 - man/MriImage-class.Rd | 3 - man/SerialisableObject-class.Rd | 2 man/SparseArray-class.Rd | 3 - man/allEqual.Rd | 7 +-- man/asMriImage.Rd | 9 +-- man/colourScales.Rd | 8 +-- man/deduplicate.Rd | 7 +-- man/emptyMatrix.Rd | 7 +-- man/equivalent.Rd | 7 +-- man/execute.Rd | 9 +-- man/files.Rd | 13 ++--- man/implode.Rd | 7 +-- man/index.Rd | 13 ++--- man/mergeMriImages.Rd | 7 +-- man/neighbourhoodInfo.Rd | 7 +-- man/newSparseArrayWithData.Rd | 7 +-- man/nilObject.Rd | 9 +-- man/paths.Rd | 15 +++--- man/pluralise.Rd | 7 +-- man/printLabelledValues.Rd | 7 +-- man/promote.Rd | 7 +-- man/readDicomDirectory.Rd | 7 +-- man/readDicomFile.Rd | 7 +-- man/serialisation.Rd | 11 ++-- man/sortDicomDirectories.Rd | 7 +-- man/threadSafeTempFile.Rd | 7 +-- man/tractor.base-deprecated.Rd | 17 +++---- man/vector.Rd | 15 +++--- man/viewer.Rd | 14 ++++-- man/visualisation.Rd | 11 ++-- 47 files changed, 261 insertions(+), 285 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds
to GDAL for reading and writing data, to GEOS for geometrical operations, and to Proj.4 for projection
conversions and datum transformations.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb],
Etienne Racine [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.4-3 dated 2017-05-15 and 0.5-0 dated 2017-06-15
sf-0.4-3/sf/inst/include |only sf-0.4-3/sf/man/geos.Rd |only sf-0.4-3/sf/src/export.cpp |only sf-0.5-0/sf/DESCRIPTION | 14 - sf-0.5-0/sf/MD5 | 150 ++++++++-------- sf-0.5-0/sf/NAMESPACE | 7 sf-0.5-0/sf/NEWS.md | 20 ++ sf-0.5-0/sf/R/RcppExports.R | 8 sf-0.5-0/sf/R/aggregate.R | 2 sf-0.5-0/sf/R/arith.R | 35 ++- sf-0.5-0/sf/R/bbox.R | 2 sf-0.5-0/sf/R/bind.R | 4 sf-0.5-0/sf/R/geom.R | 231 ++++++++++++++++--------- sf-0.5-0/sf/R/graticule.R | 10 - sf-0.5-0/sf/R/grid.R | 54 ++++-- sf-0.5-0/sf/R/init.R | 2 sf-0.5-0/sf/R/join.R | 48 ++--- sf-0.5-0/sf/R/plot.R | 11 - sf-0.5-0/sf/R/read.R | 41 ++-- sf-0.5-0/sf/R/sf.R | 20 +- sf-0.5-0/sf/R/sfc.R | 31 ++- sf-0.5-0/sf/R/sp.R | 16 + sf-0.5-0/sf/R/split.R |only sf-0.5-0/sf/R/tidyverse.R | 84 ++++----- sf-0.5-0/sf/R/valid.R | 12 - sf-0.5-0/sf/R/wkb.R | 2 sf-0.5-0/sf/R/wkt.R | 3 sf-0.5-0/sf/configure | 35 ++- sf-0.5-0/sf/configure.ac | 28 +-- sf-0.5-0/sf/inst/csv |only sf-0.5-0/sf/inst/doc/sf1.html | 25 +- sf-0.5-0/sf/inst/doc/sf2.html | 8 sf-0.5-0/sf/inst/sqlite/b.sqlite |only sf-0.5-0/sf/man/Ops.sfg.Rd | 5 sf-0.5-0/sf/man/dplyr.Rd | 27 ++- sf-0.5-0/sf/man/extension_map.Rd | 2 sf-0.5-0/sf/man/geos_binary_ops.Rd |only sf-0.5-0/sf/man/geos_binary_pred.Rd |only sf-0.5-0/sf/man/geos_combine.Rd |only sf-0.5-0/sf/man/geos_measures.Rd |only sf-0.5-0/sf/man/geos_query.Rd |only sf-0.5-0/sf/man/geos_unary.Rd |only sf-0.5-0/sf/man/plot.Rd | 2 sf-0.5-0/sf/man/sf.Rd | 6 sf-0.5-0/sf/man/sfc.Rd | 2 sf-0.5-0/sf/man/st_as_sf.Rd | 4 sf-0.5-0/sf/man/st_as_sfc.Rd | 2 sf-0.5-0/sf/man/st_interpolate_aw.Rd | 2 sf-0.5-0/sf/man/st_join.Rd | 12 - sf-0.5-0/sf/man/st_line_sample.Rd |only sf-0.5-0/sf/man/st_precision.Rd | 2 sf-0.5-0/sf/man/st_read.Rd | 25 +- sf-0.5-0/sf/man/st_relate.Rd |only sf-0.5-0/sf/man/st_split.Rd |only sf-0.5-0/sf/man/st_write.Rd | 8 sf-0.5-0/sf/man/valid.Rd | 17 - sf-0.5-0/sf/src/RcppExports.cpp | 61 +----- sf-0.5-0/sf/src/gdal.cpp | 32 ++- sf-0.5-0/sf/src/gdal_read.cpp | 59 ++++-- sf-0.5-0/sf/src/gdal_write.cpp | 6 sf-0.5-0/sf/src/geos.cpp | 29 +-- sf-0.5-0/sf/src/init.c | 90 +++++----- sf-0.5-0/sf/src/lwgeom.cpp | 25 ++ sf-0.5-0/sf/src/wkb.cpp | 249 +++++++++++++++------------- sf-0.5-0/sf/tests/% |only sf-0.5-0/sf/tests/dplyr.Rout.save | 8 sf-0.5-0/sf/tests/empty.R | 6 sf-0.5-0/sf/tests/empty.Rout.save | 203 +++++++++++----------- sf-0.5-0/sf/tests/grid.R | 3 sf-0.5-0/sf/tests/grid.Rout.save | 9 - sf-0.5-0/sf/tests/read.R | 36 ++-- sf-0.5-0/sf/tests/read.Rout.save | 73 ++++++-- sf-0.5-0/sf/tests/sfc.R | 5 sf-0.5-0/sf/tests/sfc.Rout.save | 83 ++++----- sf-0.5-0/sf/tests/testthat.Rout.save | 20 +- sf-0.5-0/sf/tests/testthat/test_geos.R | 6 sf-0.5-0/sf/tests/testthat/test_graticule.R |only sf-0.5-0/sf/tests/testthat/test_lwgeom.R | 5 sf-0.5-0/sf/tests/testthat/test_plot.R | 2 sf-0.5-0/sf/tests/testthat/test_read.R | 10 + sf-0.5-0/sf/tests/testthat/test_sfc.R | 5 sf-0.5-0/sf/tests/testthat/test_tidy.R | 26 ++ sf-0.5-0/sf/tests/testthat/test_wkb.R | 13 + sf-0.5-0/sf/tests/testthat/test_wkt.R | 1 84 files changed, 1230 insertions(+), 854 deletions(-)
Title: Interface to the 'Pleiades' 'Archeological' Database
Description: Provides a set of functions for interacting with the
'Pleiades' (<https://pleiades.stoa.org/>) 'API', including
getting status data, places data, and creating a 'GeoJSON'
based map on 'GitHub' 'gists'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pleiades versions 0.1.0 dated 2016-12-19 and 0.2.0 dated 2017-06-15
DESCRIPTION | 20 +-- LICENSE | 2 MD5 | 34 ++--- NEWS.md | 12 ++ R/pl_cache.R | 10 - R/pl_search.R | 24 ++-- R/pl_status.R | 2 R/pleiades-package.r | 4 R/zzz.R | 11 + README.md | 236 ++++++++++++++++++++-------------------- build/vignette.rds |binary man/pl_cache.Rd | 11 - man/pl_gist.Rd | 1 man/pl_places.Rd | 1 man/pl_search.Rd | 4 man/pl_status.Rd | 1 man/pleiades.Rd | 2 tests/testthat/test-pl_search.R | 8 - 18 files changed, 202 insertions(+), 181 deletions(-)
Title: Interactive Analytical Tools for Zooarchaeological Data
Description: The analysis and inference of faunal remains recovered from
archaeological sites concerns the field of zooarchaeology. The zooaRchGUI package
provides a graphical user interface to analytical tools found in the R statistical environment
to make inferences on zooarchaeological data. Functions in this package allow users to interactively
read, manipulate, visualize, and analyze zooarchaeological data.
Author: Erik Otarola-Castillo, Jesse Wolfhagen, John Brian Rapes, and Max D. Price
Maintainer: Erik Otarola-Castillo <eoc@purdue.edu>
Diff between zooaRchGUI versions 1.0.1 dated 2017-05-15 and 1.0.2 dated 2017-06-15
zooaRchGUI-1.0.1/zooaRchGUI/data/LRBkey.rdata |only zooaRchGUI-1.0.2/zooaRchGUI/DESCRIPTION | 24 zooaRchGUI-1.0.2/zooaRchGUI/MD5 | 29 zooaRchGUI-1.0.2/zooaRchGUI/R/Bayesian.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/ConfigureFrame.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Diversity.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Edit.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/File.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/GMM.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Menu.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/MultivariateStatistics.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Plotting.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Sampling.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Spatial.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/Transformations.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/UnivariateStatistics.r |only zooaRchGUI-1.0.2/zooaRchGUI/R/zooarchGUI.r | 8669 -------------- zooaRchGUI-1.0.2/zooaRchGUI/data/LRBkey.RData |only zooaRchGUI-1.0.2/zooaRchGUI/inst/img/zooarchLOGOsmall.gif |binary zooaRchGUI-1.0.2/zooaRchGUI/man/speth83.Rd | 2 zooaRchGUI-1.0.2/zooaRchGUI/man/speth83labels.Rd | 2 zooaRchGUI-1.0.2/zooaRchGUI/man/winslow.fuse.Rd | 4 zooaRchGUI-1.0.2/zooaRchGUI/man/zooaRch_GUI.Rd | 4 23 files changed, 61 insertions(+), 8673 deletions(-)
Title: The Matthews Correlation Coefficient
Description: The Matthews correlation coefficient (MCC) score is calculated (Matthews BW (1975) <DOI:10.1016/0005-2795(75)90109-9>).
Author: Hitoshi Iuchi
Maintainer: Hitoshi Iuchi <hiuchi@sfc.keio.ac.jp>
Diff between mccr versions 0.3.0 dated 2017-06-12 and 0.4.4 dated 2017-06-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mccr.R | 14 +++++--------- man/mccr.Rd | 7 +++---- 4 files changed, 14 insertions(+), 19 deletions(-)
Title: Linear Regression with Non-Constant Variances
Description: Runs a linear regression in which both the expected value and the variance can vary per observation. The expected values mu follows the standard linear model mu = X_mu * beta_mu. The standard deviation sigma follows the model log(sigma) = X_sigma * beta_sigma. The package comes with two vignettes: 'Intro' gives an introduction, 'Math' gives mathematical details.
Author: Posthuma Partners <info@posthuma-partners.nl>
Maintainer: Marco Nijmeijer <nijmeijer@posthuma-partners.nl>
Diff between lmvar versions 1.2.0 dated 2017-06-13 and 1.2.1 dated 2017-06-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/cv.lmvar.R | 6 +++--- build/vignette.rds |binary inst/doc/Intro.html | 4 ++-- inst/doc/Math.pdf |binary 7 files changed, 19 insertions(+), 14 deletions(-)
Title: Nested and Crossed Block Designs for Factorial, Fractional
Factorial and Unstructured Treatment Sets
Description: Constructs randomized nested row-and-column type block designs
with arbitrary depth of nesting for arbitrary factorial or fractional
factorial treatment designs. The treatment model can be defined
by a models.matrix formula which allows any feasible
combination of quantitative or qualitative model terms.
Any feasible design size can be defined and, where necessary,
a D-optimal swapping routine will find the best fraction for the required
design size. Blocks are nested hierarchically and the block model
for any particular level of nesting can comprise either a simple nested blocks
design or a crossed row-and-column blocks design. Block sizes
are either all equal or differ, at most, by one plot within any particular row
or column classification and any particular level of nesting. The design outputs
include a data frame showing the allocation of treatments to blocks, a table
showing block levels, the fractional design efficiency,
the achieved D-efficiency, the achieved A-efficiency
(unstructured treatments only) and A-efficiency upper bounds, where available,
for each stratum in the design. For designs with simple unstructured treatments,
a plan layout showing the allocation of treatments to blocks or to rows and
columns in the bottom stratum of the design is also given.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 2.4 dated 2017-01-08 and 2.5 dated 2017-06-15
DESCRIPTION | 23 MD5 | 12 R/blocks.r | 1535 ++++++++++++++++++++++---------------------- R/blocksdesign-package.r | 1 man/blocks.Rd | 265 +++---- man/blocksdesign-package.Rd | 6 man/upper_bounds.Rd | 1 7 files changed, 948 insertions(+), 895 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides immunoglobulin (Ig) sequence lineage reconstruction,
diversity profiling, and amino acid property analysis.
Author: Jason Vander Heiden [aut, cre],
Namita Gupta [aut],
Susanna Marquez [ctb],
Daniel Gadala-Maria [ctb],
Roy Jiang [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between alakazam versions 0.2.6 dated 2017-03-23 and 0.2.7 dated 2017-06-15
alakazam-0.2.6/alakazam/src/Init.c |only alakazam-0.2.7/alakazam/DESCRIPTION | 12 - alakazam-0.2.7/alakazam/MD5 | 53 +++---- alakazam-0.2.7/alakazam/NAMESPACE | 1 alakazam-0.2.7/alakazam/NEWS.md | 16 ++ alakazam-0.2.7/alakazam/R/Alakazam.R | 1 alakazam-0.2.7/alakazam/R/Core.R | 16 +- alakazam-0.2.7/alakazam/R/Diversity.R | 20 -- alakazam-0.2.7/alakazam/R/Gene.R | 107 ++++++++------- alakazam-0.2.7/alakazam/R/Lineage.R | 9 - alakazam-0.2.7/alakazam/R/RcppExports.R | 8 - alakazam-0.2.7/alakazam/R/Topology.R | 10 - alakazam-0.2.7/alakazam/build/vignette.rds |binary alakazam-0.2.7/alakazam/data/ExampleDb.rda |binary alakazam-0.2.7/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-0.2.7/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-0.2.7/alakazam/inst/doc/GeneUsage-Vignette.R |only alakazam-0.2.7/alakazam/inst/doc/GeneUsage-Vignette.Rmd |only alakazam-0.2.7/alakazam/inst/doc/GeneUsage-Vignette.pdf |only alakazam-0.2.7/alakazam/inst/doc/Lineage-Vignette.Rmd | 4 alakazam-0.2.7/alakazam/inst/doc/Lineage-Vignette.pdf |binary alakazam-0.2.7/alakazam/inst/doc/Topology-Vignette.Rmd | 2 alakazam-0.2.7/alakazam/inst/doc/Topology-Vignette.pdf |binary alakazam-0.2.7/alakazam/man/countGenes.Rd | 35 ++-- alakazam-0.2.7/alakazam/man/makeChangeoClone.Rd | 8 - alakazam-0.2.7/alakazam/src/RcppDistance.cpp | 4 alakazam-0.2.7/alakazam/src/RcppExports.cpp | 13 + alakazam-0.2.7/alakazam/vignettes/GeneUsage-Vignette.Rmd |only alakazam-0.2.7/alakazam/vignettes/Lineage-Vignette.Rmd | 4 alakazam-0.2.7/alakazam/vignettes/Topology-Vignette.Rmd | 2 30 files changed, 194 insertions(+), 131 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
Author: Minghui Wang, Yongzhong Zhao and Bin Zhang
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 0.99.3 dated 2017-05-06 and 0.99.4 dated 2017-06-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/intersect.R | 2 +- build/vignette.rds |binary inst/doc/set_html.html | 12 ++++++------ 5 files changed, 16 insertions(+), 16 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from
international assessment studies (TIMSS, PIRLS, PISA. ICILS, and PIAAC).
Author: Daniel Caro <daniel.caro@education.ox.ac.uk>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <daniel.caro@education.ox.ac.uk>
Diff between intsvy versions 1.9 dated 2016-04-27 and 2.0 dated 2017-06-15
intsvy-1.9/intsvy/inst |only intsvy-1.9/intsvy/vignettes |only intsvy-2.0/intsvy/DESCRIPTION | 8 intsvy-2.0/intsvy/MD5 | 283 ++++++-------- intsvy-2.0/intsvy/NAMESPACE | 186 ++++----- intsvy-2.0/intsvy/R/adj.input.R | 22 - intsvy-2.0/intsvy/R/adj.measlev.R | 12 intsvy-2.0/intsvy/R/intsvy.ben.pv.R | 354 ++++++++--------- intsvy-2.0/intsvy/R/intsvy.config.R | 120 ++--- intsvy-2.0/intsvy/R/intsvy.log.R | 230 +++++------ intsvy-2.0/intsvy/R/intsvy.log.pv.R | 300 +++++++------- intsvy-2.0/intsvy/R/intsvy.mean.R | 174 ++++---- intsvy-2.0/intsvy/R/intsvy.mean.pv.R | 232 +++++------ intsvy-2.0/intsvy/R/intsvy.per.pv.R | 208 +++++----- intsvy-2.0/intsvy/R/intsvy.reg.R | 246 ++++++------ intsvy-2.0/intsvy/R/intsvy.reg.pv.R | 375 +++++++++--------- intsvy-2.0/intsvy/R/intsvy.rho.R | 138 +++--- intsvy-2.0/intsvy/R/intsvy.rho.pv.R | 172 ++++---- intsvy-2.0/intsvy/R/intsvy.select.merge.R | 523 +++++++++++++------------- intsvy-2.0/intsvy/R/intsvy.table.R | 152 +++---- intsvy-2.0/intsvy/R/intsvy.var.label.R | 114 ++--- intsvy-2.0/intsvy/R/is.vlabeled.R | 24 - intsvy-2.0/intsvy/R/my.methods.R | 40 - intsvy-2.0/intsvy/R/piaac.ben.pv.R | 12 intsvy-2.0/intsvy/R/piaac.mean.R | 16 intsvy-2.0/intsvy/R/piaac.mean.pv.R | 18 intsvy-2.0/intsvy/R/piaac.reg.R | 14 intsvy-2.0/intsvy/R/piaac.reg.pv.R | 14 intsvy-2.0/intsvy/R/piaac.table.R | 20 intsvy-2.0/intsvy/R/pirls.ben.pv.R | 14 intsvy-2.0/intsvy/R/pirls.log.R | 10 intsvy-2.0/intsvy/R/pirls.log.pv.R | 14 intsvy-2.0/intsvy/R/pirls.mean.R | 12 intsvy-2.0/intsvy/R/pirls.mean.pv.R | 16 intsvy-2.0/intsvy/R/pirls.per.pv.R | 14 intsvy-2.0/intsvy/R/pirls.reg.R | 12 intsvy-2.0/intsvy/R/pirls.reg.pv.R | 14 intsvy-2.0/intsvy/R/pirls.rho.R | 12 intsvy-2.0/intsvy/R/pirls.rho.pv.R | 14 intsvy-2.0/intsvy/R/pirls.select.merge.R | 12 intsvy-2.0/intsvy/R/pirls.table.R | 20 intsvy-2.0/intsvy/R/pirls.var.label.R | 14 intsvy-2.0/intsvy/R/pisa.ben.pv.R | 22 - intsvy-2.0/intsvy/R/pisa.log.R | 19 intsvy-2.0/intsvy/R/pisa.log.pv.R | 26 - intsvy-2.0/intsvy/R/pisa.mean.R | 24 - intsvy-2.0/intsvy/R/pisa.mean.pv.R | 25 - intsvy-2.0/intsvy/R/pisa.per.pv.R | 19 intsvy-2.0/intsvy/R/pisa.reg.R | 18 intsvy-2.0/intsvy/R/pisa.reg.pv.R | 19 intsvy-2.0/intsvy/R/pisa.rho.R | 20 intsvy-2.0/intsvy/R/pisa.select.merge.R | 343 ++++++++--------- intsvy-2.0/intsvy/R/pisa.table.R | 33 + intsvy-2.0/intsvy/R/pisa.var.label.R | 94 ++-- intsvy-2.0/intsvy/R/plot.intsvy.mean.R | 72 +-- intsvy-2.0/intsvy/R/plot.intsvy.reg.R | 82 ++-- intsvy-2.0/intsvy/R/plot.intsvy.table.R | 110 ++--- intsvy-2.0/intsvy/R/surv_conf.R | 297 +++++++------- intsvy-2.0/intsvy/R/timss.ben.pv.R | 12 intsvy-2.0/intsvy/R/timss.log.R | 10 intsvy-2.0/intsvy/R/timss.log.pv.R | 14 intsvy-2.0/intsvy/R/timss.mean.R | 14 intsvy-2.0/intsvy/R/timss.mean.pv.R | 16 intsvy-2.0/intsvy/R/timss.per.pv.R | 14 intsvy-2.0/intsvy/R/timss.reg.R | 14 intsvy-2.0/intsvy/R/timss.reg.pv.R | 14 intsvy-2.0/intsvy/R/timss.rho.R | 12 intsvy-2.0/intsvy/R/timss.rho.pv.R | 14 intsvy-2.0/intsvy/R/timss.table.R | 20 intsvy-2.0/intsvy/R/timssg4.select.merge.R | 12 intsvy-2.0/intsvy/R/timssg4.var.label.R | 12 intsvy-2.0/intsvy/R/timssg8.select.merge.R | 30 - intsvy-2.0/intsvy/R/timssg8.var.label.R | 8 intsvy-2.0/intsvy/README.md | 34 - intsvy-2.0/intsvy/man/adj.input.Rd | 72 +-- intsvy-2.0/intsvy/man/adj.measlev.Rd | 76 +-- intsvy-2.0/intsvy/man/confs.Rd | 34 - intsvy-2.0/intsvy/man/intsvy-package.Rd | 40 - intsvy-2.0/intsvy/man/intsvy.ben.pv.Rd | 110 ++--- intsvy-2.0/intsvy/man/intsvy.config.Rd | 164 ++++---- intsvy-2.0/intsvy/man/intsvy.log.Rd | 138 +++--- intsvy-2.0/intsvy/man/intsvy.log.pv.Rd | 110 ++--- intsvy-2.0/intsvy/man/intsvy.mean.Rd | 104 ++--- intsvy-2.0/intsvy/man/intsvy.mean.pv.Rd | 108 ++--- intsvy-2.0/intsvy/man/intsvy.per.pv.Rd | 110 ++--- intsvy-2.0/intsvy/man/intsvy.reg.Rd | 104 ++--- intsvy-2.0/intsvy/man/intsvy.reg.pv.Rd | 118 ++--- intsvy-2.0/intsvy/man/intsvy.rho.Rd | 98 ++-- intsvy-2.0/intsvy/man/intsvy.rho.pv.Rd | 102 ++--- intsvy-2.0/intsvy/man/intsvy.select.merge.Rd | 164 ++++---- intsvy-2.0/intsvy/man/intsvy.table.Rd | 82 ++-- intsvy-2.0/intsvy/man/intsvy.var.label.Rd | 82 ++-- intsvy-2.0/intsvy/man/is.vlabeled.Rd | 72 +-- intsvy-2.0/intsvy/man/piaac.ben.pv.Rd | 104 ++--- intsvy-2.0/intsvy/man/piaac.mean.Rd | 94 ++-- intsvy-2.0/intsvy/man/piaac.mean.pv.Rd | 96 ++-- intsvy-2.0/intsvy/man/piaac.reg.Rd | 96 ++-- intsvy-2.0/intsvy/man/piaac.reg.pv.Rd | 106 ++--- intsvy-2.0/intsvy/man/piaac.table.Rd | 94 ++-- intsvy-2.0/intsvy/man/pirls.ben.pv.Rd | 104 ++--- intsvy-2.0/intsvy/man/pirls.log.Rd | 132 +++--- intsvy-2.0/intsvy/man/pirls.log.pv.Rd | 102 ++--- intsvy-2.0/intsvy/man/pirls.mean.Rd | 94 ++-- intsvy-2.0/intsvy/man/pirls.mean.pv.Rd | 98 ++-- intsvy-2.0/intsvy/man/pirls.per.pv.Rd | 90 ++-- intsvy-2.0/intsvy/man/pirls.reg.Rd | 112 ++--- intsvy-2.0/intsvy/man/pirls.reg.pv.Rd | 106 ++--- intsvy-2.0/intsvy/man/pirls.rho.Rd | 92 ++-- intsvy-2.0/intsvy/man/pirls.rho.pv.Rd | 96 ++-- intsvy-2.0/intsvy/man/pirls.select.merge.Rd | 110 ++--- intsvy-2.0/intsvy/man/pirls.table.Rd | 92 ++-- intsvy-2.0/intsvy/man/pirls.var.label.Rd | 74 +-- intsvy-2.0/intsvy/man/pisa.ben.pv.Rd | 97 ++-- intsvy-2.0/intsvy/man/pisa.log.Rd | 131 +++--- intsvy-2.0/intsvy/man/pisa.log.pv.Rd | 104 ++--- intsvy-2.0/intsvy/man/pisa.mean.Rd | 111 ++--- intsvy-2.0/intsvy/man/pisa.mean.pv.Rd | 118 +++-- intsvy-2.0/intsvy/man/pisa.per.pv.Rd | 102 ++--- intsvy-2.0/intsvy/man/pisa.reg.Rd | 109 ++--- intsvy-2.0/intsvy/man/pisa.reg.pv.Rd | 104 ++--- intsvy-2.0/intsvy/man/pisa.rho.Rd | 98 ++-- intsvy-2.0/intsvy/man/pisa.select.merge.Rd | 121 +++--- intsvy-2.0/intsvy/man/pisa.table.Rd | 101 ++--- intsvy-2.0/intsvy/man/pisa.var.label.Rd | 96 ++-- intsvy-2.0/intsvy/man/plot.intsvy.mean.Rd | 134 +++--- intsvy-2.0/intsvy/man/plot.intsvy.reg.Rd | 102 ++--- intsvy-2.0/intsvy/man/plot.intsvy.table.Rd | 114 ++--- intsvy-2.0/intsvy/man/timss.ben.pv.Rd | 112 ++--- intsvy-2.0/intsvy/man/timss.log.Rd | 124 +++--- intsvy-2.0/intsvy/man/timss.log.pv.Rd | 102 ++--- intsvy-2.0/intsvy/man/timss.mean.Rd | 100 ++-- intsvy-2.0/intsvy/man/timss.mean.pv.Rd | 100 ++-- intsvy-2.0/intsvy/man/timss.per.pv.Rd | 90 ++-- intsvy-2.0/intsvy/man/timss.reg.Rd | 94 ++-- intsvy-2.0/intsvy/man/timss.reg.pv.Rd | 106 ++--- intsvy-2.0/intsvy/man/timss.rho.Rd | 92 ++-- intsvy-2.0/intsvy/man/timss.rho.pv.Rd | 96 ++-- intsvy-2.0/intsvy/man/timss.table.Rd | 112 ++--- intsvy-2.0/intsvy/man/timssg4.select.merge.Rd | 114 ++--- intsvy-2.0/intsvy/man/timssg4.var.label.Rd | 70 +-- intsvy-2.0/intsvy/man/timssg8.select.merge.Rd | 102 ++--- intsvy-2.0/intsvy/man/timssg8.var.label.Rd | 72 +-- 142 files changed, 6362 insertions(+), 6204 deletions(-)
Title: Efficient Initials for Computing the Maximal Eigenpair
Description: An implementation for using efficient initials to compute the
maximal eigenpair in R. It provides two algorithms to find the efficient
initials under two cases: the tridiagonal matrix case and the general matrix
case. Besides, it also provides algorithms for the next to the maximal eigenpair under
these two cases.
Author: Mu-Fa Chen <mfchen@bnu.edu.cn>
Maintainer: Xiao-Jun Mao <maoxj.ki@gmail.com>
Diff between EfficientMaxEigenpair versions 0.1.0 dated 2016-12-07 and 0.1.1 dated 2017-06-15
EfficientMaxEigenpair-0.1.0/EfficientMaxEigenpair/vignettes/EfficientMaxEigenpair.pdf |only EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/DESCRIPTION | 8 ++--- EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/MD5 | 15 +++++----- EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/R/eff.ini.maxeig.tri.R | 2 - EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/build/vignette.rds |binary EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/inst/doc/EfficientMaxEigenpair.R |only EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/inst/doc/EfficientMaxEigenpair.Rmd | 2 - EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/inst/doc/EfficientMaxEigenpair.pdf |binary EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/vignettes/EfficientMaxEigenpair.Rmd | 2 - EfficientMaxEigenpair-0.1.1/EfficientMaxEigenpair/vignettes/EfficientMaxEigenpair.html |only 10 files changed, 15 insertions(+), 14 deletions(-)
More information about EfficientMaxEigenpair at CRAN
Permanent link
Title: Population Assignment using Genetic, Non-Genetic or Integrated
Data in a Machine Learning Framework
Description: Use Monte-Carlo and K-fold cross-validation coupled with machine-learning classification algorithms to perform population assignment, with functionalities of evaluating discriminatory power of independent training samples, identifying informative loci, reducing data dimensionality for genomic data, integrating genetic and non-genetic data, and visualizing results.
Author: Kuan-Yu (Alex) Chen [aut, cre], Elizabeth A. Marschall [aut], Michael G. Sovic [aut], Anthony C. Fries [aut], H. Lisle Gibbs [aut], Stuart A. Ludsin [aut]
Maintainer: Kuan-Yu (Alex) Chen <alexkychen@gmail.com>
Diff between assignPOP versions 1.1.2 dated 2017-05-16 and 1.1.3 dated 2017-06-15
DESCRIPTION | 8 MD5 | 64 +- R/assign.MC.R | 885 ++++++++++++++++++++++++++++---- R/assign.X.R | 15 R/assign.kfold.R | 1316 +++++++++++++++++++++++++++++++++++-------------- R/check.loci.R | 211 ++++--- R/compile.data.R | 236 ++++---- R/membership.plot.R | 39 - README.md | 95 +-- man/assign.MC.Rd | 6 man/assign.X.Rd | 4 man/assign.kfold.Rd | 8 man/compile.data.Rd | 4 man/membership.plot.Rd | 4 tests |only 15 files changed, 2105 insertions(+), 790 deletions(-)
Title: Tools for Preprocessing Visual World Data
Description: Gaze data from the Visual World Paradigm requires significant
preprocessing prior to plotting and analyzing the data. This package
provides functions for preparing visual world eye-tracking data for
statistical analysis and plotting. It can prepare data for linear
analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as
well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM).
Additionally, it contains various plotting functions for creating grand average and
conditional average plots. See the vignette for samples of the functionality.
Currently, the functions in this package are designed for handling data
collected with SR Research Eyelink eye trackers using Sample Reports created
in SR Research Data Viewer. While we would like to add functionality
for data collected with other systems in the future, the current package is
considered to be feature-complete and will shortly enter maintenance mode.
Author: Vincent Porretta [aut, cre],
Aki-Juhani Kyröläinen [aut],
Jacolien van Rij [ctb],
Juhani Järvikivi [ctb]
Maintainer: Vincent Porretta <vincentporretta@gmail.com>
Diff between VWPre versions 0.9.5 dated 2016-11-25 and 0.9.6 dated 2017-06-15
DESCRIPTION | 13 MD5 | 78 +- R/calculations.R | 876 +++++++++++----------- R/diagnostics.R | 32 R/plotting.R | 1339 +++++++++++++++++------------------ build/vignette.rds |binary inst/NEWS | 32 inst/doc/SR_Basic_Preprocessing.html | 50 - inst/doc/SR_Interest_Areas.html | 30 inst/doc/SR_Message_Alignment.html | 68 - inst/doc/SR_Plotting.Rmd | 2 inst/doc/SR_Plotting.html | 36 man/VWPre.Rd | 2 man/VWdat.Rd | 1 man/align_msg.Rd | 1 man/bin_prop.Rd | 1 man/check_eye_recording.Rd | 1 man/check_ia.Rd | 1 man/check_msg_time.Rd | 1 man/check_samples_per_bin.Rd | 1 man/check_samplingrate.Rd | 1 man/check_time_series.Rd | 1 man/create_binomial.Rd | 1 man/create_time_series.Rd | 1 man/custom_ia.Rd | 1 man/ds_options.Rd | 1 man/fasttrack.Rd | 1 man/plot_avg.Rd | 7 man/plot_avg_contour.Rd | 1 man/plot_avg_diff.Rd | 1 man/plot_indiv_app.Rd | 1 man/plot_transformation_app.Rd | 1 man/plot_var_app.Rd | 1 man/prep_data.Rd | 1 man/recode_ia.Rd | 1 man/relabel_na.Rd | 1 man/rename_columns.Rd | 1 man/select_recorded_eye.Rd | 1 man/transform_to_elogit.Rd | 1 vignettes/SR_Plotting.Rmd | 2 40 files changed, 1301 insertions(+), 1291 deletions(-)
Title: Genome Interval Arithmetic in R
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R,
enabling interactive analysis and visualization of genome-scale data.
Author: Jay Hesselberth [aut, cre],
Kent Riemondy [aut],
Ryan Sheridan [ctb]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between valr versions 0.2.0 dated 2017-05-05 and 0.3.0 dated 2017-06-15
valr-0.2.0/valr/R/valr.r |only valr-0.2.0/valr/inst/extdata/mm9.bed12.gz |only valr-0.3.0/valr/DESCRIPTION | 12 - valr-0.3.0/valr/MD5 | 136 ++++++++++--------- valr-0.3.0/valr/NAMESPACE | 9 - valr-0.3.0/valr/NEWS.md | 12 + valr-0.3.0/valr/R/RcppExports.R | 34 +++- valr-0.3.0/valr/R/bed12_to_exons.r | 23 --- valr-0.3.0/valr/R/bed_absdist.r | 5 valr-0.3.0/valr/R/bed_closest.r | 4 valr-0.3.0/valr/R/bed_cluster.r | 4 valr-0.3.0/valr/R/bed_complement.r | 8 - valr-0.3.0/valr/R/bed_fisher.r | 1 valr-0.3.0/valr/R/bed_flank.r | 78 ---------- valr-0.3.0/valr/R/bed_glyph.r | 3 valr-0.3.0/valr/R/bed_intersect.r | 6 valr-0.3.0/valr/R/bed_makewindows.r | 33 ---- valr-0.3.0/valr/R/bed_map.r | 8 - valr-0.3.0/valr/R/bed_merge.r | 24 +-- valr-0.3.0/valr/R/bed_projection.r | 2 valr-0.3.0/valr/R/bed_random.r | 6 valr-0.3.0/valr/R/db.r | 28 +-- valr-0.3.0/valr/R/features.r |only valr-0.3.0/valr/R/globals.r | 3 valr-0.3.0/valr/R/read_bed.r | 2 valr-0.3.0/valr/R/read_genome.r | 4 valr-0.3.0/valr/R/spacing.r | 2 valr-0.3.0/valr/R/strands.r | 2 valr-0.3.0/valr/R/valr-package.r |only valr-0.3.0/valr/README.md | 48 +++++- valr-0.3.0/valr/inst/doc/interval-stats.R | 17 -- valr-0.3.0/valr/inst/doc/interval-stats.Rmd | 17 -- valr-0.3.0/valr/inst/doc/interval-stats.html | 86 +++++------- valr-0.3.0/valr/inst/doc/valr.R | 41 ++++- valr-0.3.0/valr/inst/doc/valr.Rmd | 39 +++++ valr-0.3.0/valr/inst/doc/valr.html | 101 ++++++++++---- valr-0.3.0/valr/inst/extdata/mm9.refGene.bed.gz |only valr-0.3.0/valr/inst/include/group_apply.h | 2 valr-0.3.0/valr/inst/include/random.h | 2 valr-0.3.0/valr/inst/include/valr.h | 4 valr-0.3.0/valr/man/bed12_to_exons.Rd | 3 valr-0.3.0/valr/man/bed_complement.Rd | 4 valr-0.3.0/valr/man/bed_map.Rd | 2 valr-0.3.0/valr/man/create_introns.Rd |only valr-0.3.0/valr/man/create_utrs3.Rd |only valr-0.3.0/valr/man/create_utrs5.Rd |only valr-0.3.0/valr/man/db.Rd | 4 valr-0.3.0/valr/man/read_bed.Rd | 2 valr-0.3.0/valr/man/valr.Rd | 2 valr-0.3.0/valr/src/RcppExports.cpp | 51 ++++++- valr-0.3.0/valr/src/bed12toexons.cpp |only valr-0.3.0/valr/src/closest.cpp | 12 + valr-0.3.0/valr/src/complement.cpp | 4 valr-0.3.0/valr/src/flank.cpp |only valr-0.3.0/valr/src/init.c | 40 ++--- valr-0.3.0/valr/src/makewindows.cpp |only valr-0.3.0/valr/src/merge.cpp | 104 +++++++++++--- valr-0.3.0/valr/src/random.cpp | 2 valr-0.3.0/valr/src/subtract.cpp | 5 valr-0.3.0/valr/tests/testthat/test_absdist.r | 34 ++-- valr-0.3.0/valr/tests/testthat/test_bed12_to_exons.r | 4 valr-0.3.0/valr/tests/testthat/test_complement.r | 72 +++++----- valr-0.3.0/valr/tests/testthat/test_coverage.r | 16 +- valr-0.3.0/valr/tests/testthat/test_features.r |only valr-0.3.0/valr/tests/testthat/test_flank.r | 6 valr-0.3.0/valr/tests/testthat/test_makewindows.r | 26 +-- valr-0.3.0/valr/tests/testthat/test_map.r | 34 ++-- valr-0.3.0/valr/tests/testthat/test_projection.r | 30 ++-- valr-0.3.0/valr/tests/testthat/test_random.r | 24 +-- valr-0.3.0/valr/tests/testthat/test_read_bed.r | 2 valr-0.3.0/valr/tests/testthat/test_reldist.R | 14 - valr-0.3.0/valr/tests/testthat/test_sort.r | 2 valr-0.3.0/valr/tests/testthat/test_strands.r | 2 valr-0.3.0/valr/vignettes/interval-stats.Rmd | 17 -- valr-0.3.0/valr/vignettes/valr.Rmd | 39 +++++ 75 files changed, 787 insertions(+), 576 deletions(-)
Title: A Two-Stage Approach to Maximize Interpretability of Drug
Response Models Based on Multiple Molecular Data Types
Description: A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016, <doi:10.1093/bioinformatics/btw449>), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
Author: Nanne Aben
Maintainer: Nanne Aben <nanne.aben@gmail.com>
Diff between TANDEM versions 1.0.1 dated 2017-04-07 and 1.0.2 dated 2017-06-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/functions.R | 2 +- inst/doc/my-vignette.html | 6 +++--- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Methods for Dimension Reduction
Description: Functions for dimension reduction, using MAVE (Minimum Average Variance Estimation), OPG (Outer Product of Gradient) and KSIR (sliced inverse regression of kernel version). Methods for selecting the best dimension are also included.
Author: Hang Weiqiang<E0010758@u.nus.edu>, Xia Yingcun<staxyc@nus.edu.sg>
Maintainer: Hang Weiqiang<E0010758@u.nus.edu>
Diff between MAVE versions 1.1.5 dated 2017-05-15 and 1.2.8 dated 2017-06-15
DESCRIPTION | 10 ++-- MD5 | 27 +++++++----- NAMESPACE | 5 +- R/Concrete.R |only R/MAVE.R | 3 - R/MAVE_DATA.R |only R/predict_mave.R | 53 ++++++++++++++++-------- R/predict_mave_dim.R | 23 +++------- data/Concrete.rda |only inst/doc/Short_introduction_to_package_MAVE.pdf |binary man/Concrete.Rd |only man/kc_house_data.Rd | 10 ++++ man/mave.data.Rd |only man/predict.mave.Rd | 8 +-- man/predict.mave.dim.Rd | 6 +- man/spam.Rd | 10 ++++ src/RcppExports.cpp | 12 +++++ 17 files changed, 109 insertions(+), 58 deletions(-)
Title: A Lending Club API Wrapper
Description: Functions to access Lending Club's API and assist the investor manage
their account. Lending Club is a peer-to-peer lending service where loans are
broken up into $25 notes that investors buy with the expectation of earning a
return on the interest. You can learn more about the API here:
<http://www.lendingclub.com/developers/lc-api.action>.
Author: Ryan Kuhn [aut, cre]
Maintainer: Ryan Kuhn <kuhnrl30@gmail.com>
Diff between LendingClub versions 1.0.2 dated 2017-02-20 and 1.0.3 dated 2017-06-15
LendingClub-1.0.2/LendingClub/R/ResponseHandler.R |only LendingClub-1.0.3/LendingClub/DESCRIPTION | 17 +- LendingClub-1.0.3/LendingClub/LICENSE | 2 LendingClub-1.0.3/LendingClub/MD5 | 75 ++++++------- LendingClub-1.0.3/LendingClub/R/AccountSummary.R | 11 + LendingClub-1.0.3/LendingClub/R/AddFunds.R | 9 + LendingClub-1.0.3/LendingClub/R/CreatePortfolio.R | 13 +- LendingClub-1.0.3/LendingClub/R/FolioBuy.R | 9 + LendingClub-1.0.3/LendingClub/R/FolioSell.R | 9 + LendingClub-1.0.3/LendingClub/R/LC_POST.R | 7 - LendingClub-1.0.3/LendingClub/R/ListedLoans.R | 4 LendingClub-1.0.3/LendingClub/R/PendingTransfers.R | 2 LendingClub-1.0.3/LendingClub/R/PortfoliosOwned.R | 2 LendingClub-1.0.3/LendingClub/R/ResponserHandler.R |only LendingClub-1.0.3/LendingClub/R/SubmitOrder.R | 42 ++++++- LendingClub-1.0.3/LendingClub/R/WithdrawFunds.R | 1 LendingClub-1.0.3/LendingClub/README.md | 31 ----- LendingClub-1.0.3/LendingClub/build/vignette.rds |binary LendingClub-1.0.3/LendingClub/inst/CITATION |only LendingClub-1.0.3/LendingClub/man/AccountSummary.Rd | 10 + LendingClub-1.0.3/LendingClub/man/AddFunds.Rd | 5 LendingClub-1.0.3/LendingClub/man/AvailableCash.Rd | 1 LendingClub-1.0.3/LendingClub/man/CancelTransfer.Rd | 1 LendingClub-1.0.3/LendingClub/man/CleanData.Rd | 1 LendingClub-1.0.3/LendingClub/man/CreatePortfolio.Rd | 5 LendingClub-1.0.3/LendingClub/man/FolioListing.Rd | 1 LendingClub-1.0.3/LendingClub/man/FolioSell.Rd | 14 +- LendingClub-1.0.3/LendingClub/man/LC_GET.Rd | 1 LendingClub-1.0.3/LendingClub/man/LC_POST.Rd | 3 LendingClub-1.0.3/LendingClub/man/LendingClub.Rd | 1 LendingClub-1.0.3/LendingClub/man/ListedLoans.Rd | 14 +- LendingClub-1.0.3/LendingClub/man/MakeCredential.Rd | 1 LendingClub-1.0.3/LendingClub/man/MakeURL.Rd | 1 LendingClub-1.0.3/LendingClub/man/NotesOwned.Rd | 1 LendingClub-1.0.3/LendingClub/man/PendingTransfers.Rd | 3 LendingClub-1.0.3/LendingClub/man/PortfoliosOwned.Rd | 3 LendingClub-1.0.3/LendingClub/man/SubmitOrder.Rd | 13 +- LendingClub-1.0.3/LendingClub/man/WithdrawFunds.Rd | 1 LendingClub-1.0.3/LendingClub/man/print.LendingClub_api.Rd | 1 LendingClub-1.0.3/LendingClub/vignettes/LendingClub.Rmd | 58 ++++++---- 40 files changed, 218 insertions(+), 155 deletions(-)
Title: Intrinsic Dimension for Data Mining
Description: Contains techniques for mining large high-dimensional data sets
by using the concept of Intrinsic Dimension (ID). Here the ID is
not necessarily integer. It is extended to fractal dimensions. And
the Morisita estimator is used for the ID estimation, but other
tools are included as well.
Author: Jean Golay and Mohamed Laib
Maintainer: Jean Golay <Jean.Golay@unil.ch>
Diff between IDmining versions 1.0.0 dated 2016-11-25 and 1.0.1 dated 2017-06-15
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 +- R/Butterfly.R | 16 ++++++++-------- R/IDmining.R | 6 +++--- R/MINDEX_SP.R | 38 +++++++++++++++++++------------------- R/MINDID.R | 47 ++++++++++++++++++++++------------------------- R/RenDim.R | 43 ++++++++++++++++++++----------------------- R/SwissRoll.R | 15 +++++++-------- R/logMINDEX.R | 36 ++++++++++++++++++------------------ man/Butterfly.Rd | 18 +++++++++--------- man/IDmining-package.Rd | 26 ++++++++++++++++---------- man/MINDEX_SP.Rd | 17 ++++++++--------- man/MINDID.Rd | 25 ++++++++++++------------- man/RenDim.Rd | 23 +++++++++++------------ man/SwissRoll.Rd | 7 +++---- man/logMINDEX.Rd | 17 ++++++++--------- 17 files changed, 188 insertions(+), 194 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.3 dated 2017-01-01 and 1.0.4 dated 2017-06-15
glinternet-1.0.3/glinternet/README.md |only glinternet-1.0.4/glinternet/DESCRIPTION | 8 ++++---- glinternet-1.0.4/glinternet/MD5 | 10 +++++----- glinternet-1.0.4/glinternet/NAMESPACE | 2 +- glinternet-1.0.4/glinternet/src/c_routines.c | 3 +-- glinternet-1.0.4/glinternet/src/fista.c | 3 +-- glinternet-1.0.4/glinternet/src/glinternet_init.c |only 7 files changed, 12 insertions(+), 14 deletions(-)
Title: Cytobank API Wrapper for R
Description: Tools to interface with Cytobank's API via R, organized by various
endpoints that represent various areas of Cytobank functionality. Learn more
about Cytobank at <https://www.cytobank.org>.
Author: Preston Ng
Maintainer: Preston Ng <preston@cytobank.org>
Diff between CytobankAPI versions 1.0.1 dated 2017-04-13 and 1.0.1.1 dated 2017-06-15
DESCRIPTION | 8 +-- MD5 | 31 ++++++------ NAMESPACE | 4 - R/CITRUS-class.R | 2 R/SPADE-class.R | 16 ++++-- R/UserSession-class.R | 2 R/helper_functions.R | 76 +++++++++++++++++-------------- R/spade.R | 29 +++++++++-- R/startup.R |only R/viSNE-class.R | 1 inst/NEWS |only inst/doc/cytobank-advanced-analyses.html | 15 +++--- man/CITRUS-class.Rd | 2 man/SPADE-class.Rd | 7 ++ man/helper_functions.Rd | 27 +++-------- man/news.Rd |only man/spade.Rd | 3 - man/viSNE-class.Rd | 2 18 files changed, 132 insertions(+), 93 deletions(-)
Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with p-value adjustment for multiple comparisons introduced in Oleson et al (2015) <DOI:10.1177/0962280215607411>.
Author: Michael Seedorff, Jacob Oleson, Grant Brown, Joseph Cavanaugh, and Bob McMurray
Maintainer: Michael Seedorff <michael-seedorff@uiowa.edu>
Diff between bdots versions 0.1.9 dated 2016-08-16 and 0.1.13 dated 2017-06-15
DESCRIPTION | 8 MD5 | 39 ++-- NAMESPACE | 2 R/doubleGaussBoot.r | 144 +++++++++++++---- R/doubleGaussFit.r | 46 +++-- R/doubleGaussRefit.r | 61 +++++-- R/logisticBoot.r | 132 +++++++++++----- R/logisticFit.r | 46 +++-- R/logisticRefit.r | 66 +++++--- R/subsDelete.r | 16 + R/subsPlot.r | 253 ++++++++++++++++--------------- build/vignette.rds |binary inst/doc/bdots.R | 396 ++++++++++++++++++++++++------------------------- inst/doc/bdots.Rnw | 14 - inst/doc/bdots.pdf |binary man/fit.Rd | 5 man/refit.Rd | 7 man/subsDelete.Rd | 6 man/subsPlot.Rd | 10 - vignettes/bdots.Rnw | 14 - vignettes/fancyvrb.sty |only 21 files changed, 747 insertions(+), 518 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more empirical distributions.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 1.4.0 dated 2017-01-19 and 1.5.0 dated 2017-06-15
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 5 +++++ R/final.plot.R | 2 +- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.7 dated 2017-05-03 and 3.98-1.8 dated 2017-06-15
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- man/getNodeSet.Rd | 2 ++ src/DocParse.c | 10 +++++++--- src/EventParse.c | 17 +++++++++-------- src/NodeGC.c | 4 +++- src/RSDTD.c | 8 ++++++-- src/Utils.c | 2 +- src/XMLHashTree.c | 7 ++++--- 9 files changed, 43 insertions(+), 29 deletions(-)